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Onoja BA, Oguzie JU, George UE, Asoh KE, Ajayi P, Omofaye TF, Igeleke IO, Eromon P, Harouna S, Parker E, Adeniji AJ, Happi CT. Whole genome sequencing unravels cryptic circulation of divergent dengue virus lineages in the rainforest region of Nigeria. Emerg Microbes Infect 2024; 13:2307511. [PMID: 38240324 PMCID: PMC10829817 DOI: 10.1080/22221751.2024.2307511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Dengue is often misclassified and underreported in Africa due to inaccurate differential diagnoses of nonspecific febrile illnesses such as malaria, sparsity of diagnostic testing and poor clinical and genomic surveillance. There are limited reports on the seroprevalence and genetic diversity of dengue virus (DENV) in humans and vectors in Nigeria. In this study, we investigated the epidemiology and genetic diversity of dengue in the rainforest region of Nigeria. We screened 515 febrile patients who tested negative for malaria and typhoid fever in three hospitals in Oyo and Ekiti States in southern Nigeria with a combination of anti-dengue IgG/IgM/NS1 rapid test kits and metagenomic sequencing. We found that approximately 28% of screened patients had previous DENV exposure, with the highest prevalence in persons over sixty. Approximately 8% of the patients showed evidence of recent or current infection, and 2.7% had acute infection. Following sequencing of sixty samples, we assembled twenty DENV-1 genomes (3 complete and 17 partial). We found that all assembled genomes belonged to DENV-1 genotype III. Our phylogenetic analyses showed evidence of prolonged cryptic circulation of divergent DENV lineages in Oyo state. We were unable to resolve the source of DENV in Nigeria owing to limited sequencing data from the region. However, our sequences clustered closely with sequences in Tanzania and sequences reported in Chinese with travel history to Tanzania in 2019. This may reflect the wider unsampled bidirectional transmission of DENV-1 in Africa, which strongly emphasizes the importance of genomic surveillance in monitoring ongoing DENV transmission in Africa.
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Affiliation(s)
- Bernard Anyebe Onoja
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Judith Uche Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Uwem Etop George
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Kaego Emmanuel Asoh
- Department of Medical Laboratory Science, College of Medicine, University of Ibadan, Ibadan, State Nigeria
| | - Philip Ajayi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | | | - Philomena Eromon
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Soumare Harouna
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Edyth Parker
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Christian T. Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA
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2
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Pathak AK, Simonian H, Ibrahim IAA, Hrechdakian P, Behar DM, Ayub Q, Arsanov P, Metspalu E, Yepiskoposyan L, Rootsi S, Endicott P, Villems R, Sahakyan H. Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection. iScience 2024; 27:110016. [PMID: 38883810 PMCID: PMC11177204 DOI: 10.1016/j.isci.2024.110016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/06/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.
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Affiliation(s)
- Ajai Kumar Pathak
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Hovann Simonian
- Armenian DNA Project at Family Tree DNA, Houston, TX 77008, USA
| | - Ibrahim Abdel Aziz Ibrahim
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | | | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Qasim Ayub
- Monash University Malaysia Genomics Platform, School of Science, Monash University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
| | - Pakhrudin Arsanov
- Chechen-Noahcho DNA Project at Family Tree DNA, Kostanay 110008, Kazakhstan
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Levon Yepiskoposyan
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Phillip Endicott
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Department of Archaeology and Anthropology, Bournemouth University, Fern Barrow, Poole, Dorset BH12 5BB, UK
- Department of Linguistics, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
- DFG Center for Advanced Studies, University of Tübingen, 72074 Tübingen, Germany
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia
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3
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Zhao L, Guo X, Li L, Jing Q, Ma J, Xie T, Lin D, Li L, Yin Q, Wang Y, Zhang X, Li Z, Liu X, Hu T, Hu M, Ren W, Li J, Peng J, Yu L, Peng Z, Hong W, Leng X, Luo L, Ngobeh JJK, Tang X, Wu R, Zhao W, Shi B, Liu J, Yang Z, Chen XG, Zhou X, Zhang F. Phylodynamics unveils invading and diffusing patterns of dengue virus serotype-1 in Guangdong, China from 1990 to 2019 under a global genotyping framework. Infect Dis Poverty 2024; 13:43. [PMID: 38863070 PMCID: PMC11165891 DOI: 10.1186/s40249-024-01211-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND The strong invasiveness and rapid expansion of dengue virus (DENV) pose a great challenge to global public health. However, dengue epidemic patterns and mechanisms at a genetic scale, particularly in term of cross-border transmissions, remain poorly understood. Importation is considered as the primary driver of dengue outbreaks in China, and since 1990 a frequent occurrence of large outbreaks has been triggered by the imported cases and subsequently spread to the western and northern parts of China. Therefore, this study aims to systematically reveal the invasion and diffusion patterns of DENV-1 in Guangdong, China from 1990 to 2019. METHODS These analyses were performed on 179 newly assembled genomes from indigenous dengue cases in Guangdong, China and 5152 E gene complete sequences recorded in Chinese mainland. The genetic population structure and epidemic patterns of DENV-1 circulating in Chinese mainland were characterized by phylogenetics, phylogeography, phylodynamics based on DENV-1 E-gene-based globally unified genotyping framework. RESULTS Multiple serotypes of DENV were co-circulating in Chinese mainland, particularly in Guangdong and Yunnan provinces. A total of 189 transmission clusters in 38 clades belonging to 22 subgenotypes of genotype I, IV and V of DENV-1 were identified, with 7 Clades of Concern (COCs) responsible for the large outbreaks since 1990. The epidemic periodicity was inferred from the data to be approximately 3 years. Dengue transmission events mainly occurred from Great Mekong Subregion-China (GMS-China), Southeast Asia (SEA), South Asia Subcontinent (SASC), and Oceania (OCE) to coastal and land border cities respectively in southeastern and southwestern China. Specially, Guangzhou was found to be the most dominant receipting hub, where DENV-1 diffused to other cities within the province and even other parts of the country. Genome phylogeny combined with epidemiological investigation demonstrated a clear local consecutive transmission process of a 5C1 transmission cluster (5C1-CN4) of DENV-1 in Guangzhou from 2013 to 2015, while the two provinces of Guangdong and Yunnan played key roles in ongoing transition of dengue epidemic patterns. In contextualizing within Invasion Biology theories, we have proposed a derived three-stage model encompassing the stages of invasion, colonization, and dissemination, which is supposed to enhance our understanding of dengue spreading patterns. CONCLUSIONS This study demonstrates the invasion and diffusion process of DENV-1 in Chinese mainland within a global genotyping framework, characterizing the genetic diversities of viral populations, multiple sources of importation, and periodic dynamics of the epidemic. These findings highlight the potential ongoing transition trends from epidemic to endemic status offering a valuable insight into early warning, prevention and control of rapid spreading of dengue both in China and worldwide.
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Affiliation(s)
- Lingzhai Zhao
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, Guangdong, China
| | - Xiang Guo
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | - Liqiang Li
- Department of Clinical Laboratory, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Infectious Diseases (Tuberculosis), Shenzhen Clinical Research Center for Tuberculosis, Shenzhen, China
| | - Qinlong Jing
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Jinmin Ma
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Tian Xie
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | | | - Li Li
- Department of Biostatistics, School of Public Health, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, 510515, China
| | - Qingqing Yin
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | - Yuji Wang
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | - Xiaoqing Zhang
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | - Ziyao Li
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | - Xiaohua Liu
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | - Tian Hu
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | - Minling Hu
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | - Wenwen Ren
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | - Jun Li
- Guangdong Provincial Key Laboratory of Research On Emergency in TCM, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, 510120, China
| | - Jie Peng
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Lei Yu
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, Guangdong, China
| | - Zhiqiang Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Wenxin Hong
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, Guangdong, China
| | - Xingyu Leng
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, Guangdong, China
| | - Lei Luo
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Jone Jama Kpanda Ngobeh
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China
| | - Xiaoping Tang
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, Guangdong, China
| | - Rangke Wu
- The School of Foreign Studies, Southern Medical University, Guangzhou, 510515, China
| | - Wei Zhao
- BSL-3 Laboratory(Guangdong), School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Benyun Shi
- College of Computer and Information Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Jiming Liu
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Zhicong Yang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China.
| | - Xiao-Guang Chen
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China.
| | - Xiaohong Zhou
- Department of Pathogen Biology, School of Public Health, Institute of Tropical Medicine, Southern Medical University; Guangdong Provincial Key Laboratory of Tropical Disease Research; Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes; Key Laboratory of Infectious Diseases Research in South China of Ministry of Education, Guangzhou, 510515, China.
| | - Fuchun Zhang
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, Guangdong, China.
- Guangzhou Medical Research Institute of Infectious Diseases, Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China.
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4
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Machado LC, Dezordi FZ, de Lima GB, de Lima RE, Silva LCA, Pereira LDM, da Silva AF, Silva Neto AMD, Oliveira ALSD, Armstrong ADC, Pessoa-E-Silva R, Loyo RM, Silva BDO, de Almeida AR, da Rocha Pitta MG, Santos FDADS, Mendonça Siqueira M, Resende PC, Delatorre E, Naveca FG, Miyajima F, Gräf T, do Carmo RF, Pereira MC, Campos TDL, Bezerra MF, Paiva MHS, Wallau GDL. Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco-Brazil. Microbiol Spectr 2024; 12:e0421823. [PMID: 38651879 DOI: 10.1128/spectrum.04218-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
SARS-CoV-2 virus emerged as a new threat to humans and spread around the world, leaving a large death toll. As of January 2023, Brazil is among the countries with the highest number of registered deaths. Nonpharmacological and pharmacological interventions have been heterogeneously implemented in the country, which, associated with large socioeconomic differences between the country regions, has led to distinct virus spread dynamics. Here, we investigate the spatiotemporal dispersion of SARS-CoV-2 lineages in the Pernambuco state (Northeast Brazil) throughout the distinct epidemiological scenarios that unfolded in the first 2 years of the pandemic. We generated a total of 1,389 new SARS-CoV-2 genomes from June 2020 to August 2021. This sampling captured the arrival, communitary transmission, and the circulation of the B1.1, B.1.1.28, and B.1.1.33 lineages; the emergence of the former variant of interest P.2; and the emergence and fast replacement of all previous variants by the more transmissible variant of concern P.1 (Gamma). Based on the incidence and lineage spread pattern, we observed an East-to-West to inner state pattern of transmission, which is in agreement with the transmission of more populous metropolitan areas to medium- and small-size country-side cities in the state. Such transmission patterns may be partially explained by the main routes of traffic across municipalities in the state. Our results highlight that the fine-grained intrastate analysis of lineages and incidence spread can provide actionable insights for planning future nonpharmacological intervention for air-borne transmissible human pathogens.IMPORTANCEDuring the COVID-19 pandemic, Brazil was one of the most affected countries, mainly due its continental-size, socioeconomic differences among regions, and heterogeneous implementation of intervention methods. In order to investigate SARS-CoV-2 dynamics in the state of Pernambuco, we conducted a spatiotemporal dispersion study, covering the period from June 2020 to August 2021, to comprehend the dynamics of viral transmission during the first 2 years of the pandemic. Throughout this study, we were able to track three significant epidemiological waves of transmission caused by B1.1, B.1.1.28, B.1.1.33, P.2, and P.1 lineages. These analyses provided valuable insights into the evolution of the epidemiological landscape, contributing to a deeper understanding of the dynamics of virus transmission during the early years of the pandemic in the state of Pernambuco.
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Affiliation(s)
- Lais Ceschini Machado
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
| | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Gustavo Barbosa de Lima
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Raul Emídio de Lima
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Lilian Caroliny Amorim Silva
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Leandro de Mattos Pereira
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Alexandre Freitas da Silva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | | | - André Luiz Sá de Oliveira
- Núcleo de Estatística e Geoprocessamento, Instituto Aggeu Magalhães (IAM)- Fundação Oswaldo Cruz Pernambuco- FIOCRUZ-PE, Recife, Brazil
| | | | - Rômulo Pessoa-E-Silva
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Rodrigo Moraes Loyo
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Barbara de Oliveira Silva
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Anderson Rodrigues de Almeida
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Maira Galdino da Rocha Pitta
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Manaus, Amazonas, Brazil
| | - Fabio Miyajima
- Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceará, Fortaleza, Ceará, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | | | - Michelly Cristiny Pereira
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Tulio de Lima Campos
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Matheus Filgueira Bezerra
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Marcelo Henrique Santos Paiva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste, Caruaru, Brazil
| | - Gabriel da Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
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5
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Plessy C, Mansfield MJ, Bliznina A, Masunaga A, West C, Tan Y, Liu AW, Grašič J, Del Río Pisula MS, Sánchez-Serna G, Fabrega-Torrus M, Ferrández-Roldán A, Roncalli V, Navratilova P, Thompson EM, Onuma T, Nishida H, Cañestro C, Luscombe NM. Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. Genome Res 2024; 34:426-440. [PMID: 38621828 PMCID: PMC11067885 DOI: 10.1101/gr.278295.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
Abstract
Genome structural variations within species are rare. How selective constraints preserve gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several genomes of the appendicularian tunicate Oikopleura dioica around the globe reveals extreme genome scrambling caused by thousands of chromosomal rearrangements, although showing no obvious morphological differences between these animals. The breakpoint accumulation rate is an order of magnitude higher than in ascidian tunicates, nematodes, Drosophila, or mammals. Chromosome arms and sex-specific regions appear to be the primary unit of macrosynteny conservation. At the microsyntenic level, scrambling did not preserve operon structures, suggesting an absence of selective pressure to maintain them. The uncoupling of the genome scrambling with morphological conservation in O. dioica suggests the presence of previously unnoticed cryptic species and provides a new biological system that challenges our previous vision of speciation in which similar animals always share similar genome structures.
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Affiliation(s)
- Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan;
| | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Aleksandra Bliznina
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Aki Masunaga
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Charlotte West
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Yongkai Tan
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Andrew W Liu
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Jan Grašič
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - María Sara Del Río Pisula
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
| | - Gaspar Sánchez-Serna
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Marc Fabrega-Torrus
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Alfonso Ferrández-Roldán
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Vittoria Roncalli
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Pavla Navratilova
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, 779 00 Olomouc, Czech Republic
- Sars International Centre, University of Bergen, Bergen N-5008, Norway
| | - Eric M Thompson
- Sars International Centre, University of Bergen, Bergen N-5008, Norway
- Department of Biological Sciences, University of Bergen, Bergen N-5020, Norway
| | - Takeshi Onuma
- Faculty of Science, Kagoshima University, Kagoshima 890-0065, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Spain
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa 904-0495, Japan
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de Souza WM, Fumagalli MJ, de Lima STS, Parise PL, Carvalho DCM, Hernandez C, de Jesus R, Delafiori J, Candido DS, Carregari VC, Muraro SP, Souza GF, Simões Mello LM, Claro IM, Díaz Y, Kato RB, Trentin LN, Costa CHS, Maximo ACBM, Cavalcante KF, Fiuza TS, Viana VAF, Melo MEL, Ferraz CPM, Silva DB, Duarte LMF, Barbosa PP, Amorim MR, Judice CC, Toledo-Teixeira DA, Ramundo MS, Aguilar PV, Araújo ELL, Costa FTM, Cerqueira-Silva T, Khouri R, Boaventura VS, Figueiredo LTM, Fang R, Moreno B, López-Vergès S, Mello LP, Skaf MS, Catharino RR, Granja F, Martins-de-Souza D, Plante JA, Plante KS, Sabino EC, Diamond MS, Eugenin E, Proença-Módena JL, Faria NR, Weaver SC. Pathophysiology of chikungunya virus infection associated with fatal outcomes. Cell Host Microbe 2024; 32:606-622.e8. [PMID: 38479396 PMCID: PMC11018361 DOI: 10.1016/j.chom.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/08/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes acute, subacute, and chronic human arthritogenic diseases and, in rare instances, can lead to neurological complications and death. Here, we combined epidemiological, virological, histopathological, cytokine, molecular dynamics, metabolomic, proteomic, and genomic analyses to investigate viral and host factors that contribute to chikungunya-associated (CHIK) death. Our results indicate that CHIK deaths are associated with multi-organ infection, central nervous system damage, and elevated serum levels of pro-inflammatory cytokines and chemokines compared with survivors. The histopathologic, metabolite, and proteomic signatures of CHIK deaths reveal hemodynamic disorders and dysregulated immune responses. The CHIKV East-Central-South-African lineage infecting our study population causes both fatal and survival cases. Additionally, CHIKV infection impairs the integrity of the blood-brain barrier, as evidenced by an increase in permeability and altered tight junction protein expression. Overall, our findings improve the understanding of CHIK pathophysiology and the causes of fatal infections.
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Affiliation(s)
- William M de Souza
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, College of Medicine, Lexington, KY, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Global Virus Network, Baltimore, MD, USA.
| | - Marcilio J Fumagalli
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Shirlene T S de Lima
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil; Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Pierina L Parise
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Deyse C M Carvalho
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Laboratory of Immunobiotechnology, Biotechnology Center, Federal University of Paraíba, João Pessoa, Paraíba, Brazil
| | - Cristian Hernandez
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jeany Delafiori
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Darlan S Candido
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Victor C Carregari
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Stefanie P Muraro
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Gabriela F Souza
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Ingra M Claro
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Yamilka Díaz
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama
| | - Rodrigo B Kato
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lucas N Trentin
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Clauber H S Costa
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Tayna S Fiuza
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil; Programa de Pós Graduação em Bioinformática, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Vânia A F Viana
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
| | | | | | - Débora B Silva
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
| | | | - Priscilla P Barbosa
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mariene R Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carla C Judice
- Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mariana S Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Patricia V Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Emerson L L Araújo
- Coordenação Geral de Atenção às Doenças Transmissíveis na Atenção Primária, Departamento de Gestão ao cuidado Integral, Secretaria de Atenção Primária à Saúde, Ministério da Saúde, Brasília, Brazil
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Thiago Cerqueira-Silva
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil
| | - Ricardo Khouri
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil
| | - Viviane S Boaventura
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil; Hospital Santa Izabel, Santa Casa de Misericórdia da Bahia, Serviço de Otorrinolaringologia, Salvador, Bahia, Brazil
| | - Luiz Tadeu M Figueiredo
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rong Fang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Brechla Moreno
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama
| | - Sandra López-Vergès
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama; Sistema Nacional de Investigación from SENACYT, Panama, Panama
| | | | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Rodrigo R Catharino
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Biodiversity Research Centre, Federal University of Roraima, Boa Vista, Roraima, Brazil
| | - Daniel Martins-de-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; D'Or Institute for Research and Education, São Paulo, São Paulo, Brazil; Experimental Medicine Research Cluster, University of Campinas, Campinas, São Paulo, Brazil
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Eliseo Eugenin
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX, USA
| | - José Luiz Proença-Módena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Global Virus Network, Baltimore, MD, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
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7
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Despabiladeras JB, Bautista MAM. Complete Mitochondrial Genome of the Eggplant Fruit and Shoot Borer, Leucinodes orbonalis Guenée (Lepidoptera: Crambidae), and Comparison with Other Pyraloid Moths. INSECTS 2024; 15:220. [PMID: 38667350 PMCID: PMC11050083 DOI: 10.3390/insects15040220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024]
Abstract
The eggplant fruit and shoot borer (EFSB) (Leucinodes orbonalis Guenée) is a devastating lepidopteran pest of eggplant (Solanum melongena L.) in the Philippines. Management of an insect pest like the EFSB requires an understanding of its biology, evolution, and adaptations. Genomic resources provide a starting point for understanding EFSB biology, as the resources can be used for phylogenetics and population structure studies. To date, genomic resources are scarce for EFSB; thus, this study generated its complete mitochondrial genome (mitogenome). The circular mitogenome is 15,244 bp-long. It contains 37 genes, namely 13 protein-coding, 22 tRNA, and 2 rRNA genes, and has conserved noncoding regions, motifs, and gene syntenies characteristic of lepidopteran mitogenomes. Some protein-coding genes start and end with non-canonical codons. The tRNA genes exhibit a conserved cloverleaf structure, with the exception in trnS1. Partitioned phylogenetic analysis using 72 pyraloids generated highly supported maximum likelihood and Bayesian inference trees revealing expected basal splits between Crambidae and Pyralidae, and Spilomelinae and Pyraustinae. Spilomelinae was recovered to be paraphyletic, with the EFSB robustly placed before the split of Spilomelinae and Pyraustinae. Overall, the EFSB mitogenome resource will be useful for delineations within Spilomelinae and population structure analysis.
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Affiliation(s)
| | - Ma. Anita M. Bautista
- Functional Genomics Laboratory, National Institute of Molecular Biology and Biotechnology, College of Science, University of the Philippines-Diliman, Quezon City 1101, Philippines;
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8
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Lv JX, Liu X, Pei YY, Song ZG, Chen X, Hu SJ, She JL, Liu Y, Chen YM, Zhang YZ. Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak. Virus Evol 2024; 10:veae020. [PMID: 38562953 PMCID: PMC10984623 DOI: 10.1093/ve/veae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/24/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Despite extensive scientific efforts directed toward the evolutionary trajectory of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans at the beginning of the COVID-19 epidemic, it remains unclear how the virus jumped into and evolved in humans so far. Herein, we recruited almost all adult coronavirus disease 2019 (COVID-19) cases appeared locally or imported from abroad during the first 8 months of the outbreak in Shanghai. From these patients, SARS-CoV-2 genomes occupying the important phylogenetic positions in the virus phylogeny were recovered. Phylogenetic and mutational landscape analyses of viral genomes recovered here and those collected in and outside of China revealed that all known SARS-CoV-2 variants exhibited the evolutionary continuity despite the co-circulation of multiple lineages during the early period of the epidemic. Various mutations have driven the rapid SARS-CoV-2 diversification, and some of them favor its better adaptation and circulation in humans, which may have determined the waxing and waning of various lineages.
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Affiliation(s)
- Jia-Xin Lv
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Xiang Liu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yuan-Yuan Pei
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Zhi-Gang Song
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, Guangdong 510642, China
| | - Shu-Jian Hu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Jia-Lei She
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Yi Liu
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Yan-Mei Chen
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yong-Zhen Zhang
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
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9
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Yang Q, Wang B, Lemey P, Dong L, Mu T, Wiebe RA, Guo F, Trovão NS, Park SW, Lewis N, Tsui JLH, Bajaj S, Cheng Y, Yang L, Haba Y, Li B, Zhang G, Pybus OG, Tian H, Grenfell B. Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders. Nat Commun 2024; 15:1126. [PMID: 38321046 PMCID: PMC10847442 DOI: 10.1038/s41467-024-45462-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecological process contributing to the global dispersal of HPAIV H5. However, this mechanism has not been quantified using bird movement data from different species, and the timing and location of exposure of different species is unclear. We sought to explore these questions through phylodynamic analyses based on empirical data of bird movement tracking and virus genome sequences of clade 2.3.4.4 and 2.3.2.1. First, we demonstrate that seasonal bird migration can explain salient features of the global dispersal of clade 2.3.4.4. Second, we detect synchrony between the seasonality of bird annual cycle phases and virus lineage movements. We reveal the differing exposed bird orders at geographical origins and destinations of HPAIV H5 clade 2.3.4.4 lineage movements, including relatively under-discussed orders. Our study provides a phylodynamic framework that links the bird movement ecology and genomic epidemiology of avian influenza; it highlights the importance of integrating bird behavior and life history in avian influenza studies.
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Affiliation(s)
- Qiqi Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Ben Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Phillipe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Lu Dong
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tong Mu
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - R Alex Wiebe
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Fengyi Guo
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Nicola Lewis
- Animal and Plant Health Agency-Weybridge, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Department of Virology, Addlestone, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | | | - Sumali Bajaj
- Department of Biology, University of Oxford, Oxford, UK
| | - Yachang Cheng
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Luojun Yang
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Yuki Haba
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Guogang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Oliver G Pybus
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
- Department of Biology, University of Oxford, Oxford, UK
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China.
| | - Bryan Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA.
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10
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Peng W, Fu C, Shu S, Wang G, Wang H, Yue B, Zhang M, Liu X, Liu Y, Zhang J, Zhong J, Wang J. Whole-genome resequencing of major populations revealed domestication-related genes in yaks. BMC Genomics 2024; 25:69. [PMID: 38233755 PMCID: PMC10795378 DOI: 10.1186/s12864-024-09993-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND The yak is a symbol of the Qinghai-Tibet Plateau and provides important basic resources for human life on the plateau. Domestic yaks have been subjected to strong artificial selection and environmental pressures over the long-term. Understanding the molecular mechanisms of phenotypic differences in yak populations can reveal key functional genes involved in the domestication process and improve genetic breeding. MATERIAL AND METHOD Here, we re-sequenced 80 yaks (Maiwa, Yushu, and Huanhu populations) to identify single-nucleotide polymorphisms (SNPs) as genetic variants. After filtering and quality control, remaining SNPs were kept to identify the genome-wide regions of selective sweeps associated with domestic traits. The four methods (π, XPEHH, iHS, and XP-nSL) were used to detect the population genetic separation. RESULTS By comparing the differences in the population stratification, linkage disequilibrium decay rate, and characteristic selective sweep signals, we identified 203 putative selective regions of domestic traits, 45 of which were mapped to 27 known genes. They were clustered into 4 major GO biological process terms. All known genes were associated with seven major domestication traits, such as dwarfism (ANKRD28), milk (HECW1, HECW2, and OSBPL2), meat (SPATA5 and GRHL2), fertility (BTBD11 and ARFIP1), adaptation (NCKAP5, ANTXR1, LAMA5, OSBPL2, AOC2, and RYR2), growth (GRHL2, GRID2, SMARCAL1, and EPHB2), and the immune system (INPP5D and ADCYAP1R1). CONCLUSIONS We provided there is an obvious genetic different among domestic progress in these three yak populations. Our findings improve the understanding of the major genetic switches and domestic processes among yak populations.
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Affiliation(s)
- Wei Peng
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Changqi Fu
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Shi Shu
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Guowen Wang
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China
| | - Binglin Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China
| | - Ming Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China
| | - Xinrui Liu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China
| | - Yaxin Liu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China
| | - Jun Zhang
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China.
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China.
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China.
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11
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Withnell CB, Scarpetta SG. A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade. PeerJ 2024; 12:e16693. [PMID: 38223757 PMCID: PMC10785794 DOI: 10.7717/peerj.16693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 11/28/2023] [Indexed: 01/16/2024] Open
Abstract
Background Arvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group. Methods Here we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data. Results Our results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (Lemmus and Myopus) and bog lemmings (Synaptomys), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ∼6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary.
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Affiliation(s)
- Charles B. Withnell
- Department of Medical Education/ Anne Burnett Marion School of Medicine, Texas Christian University, Fort Worth, TX, United States of America
- Department of Earth and Planetary Sciences/ Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Simon G. Scarpetta
- Department of Earth and Planetary Sciences/ Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Environmental Science, University of San Francisco, San Francisco, CA, United States of America
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12
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Puenpa J, Chansaenroj J, Suwannakarn K, Poovorawan Y. Genomic epidemiology and evolutionary analysis during XBB.1.16-predominant periods of SARS-CoV-2 omicron variant in Bangkok, Thailand: December 2022-August 2023. Sci Rep 2024; 14:645. [PMID: 38182705 PMCID: PMC10770311 DOI: 10.1038/s41598-023-50856-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024] Open
Abstract
The growing occurrence of novel recombinants, such as XBB.1.16, has emerged and become predominant, raising concerns about the impact of genomic recombination on the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study investigated the molecular epidemiological trends and evolution of the Omicron XBB.1.16 epidemic in Bangkok between December 2022 and August 2023. Partial spike and complete genome sequencing of SARS-CoV-2 samples collected from collaborating hospitals were performed. The analysis of 491 partial spike sequences identified 15 distinct lineages, with XBB.1.16 dominating the lineages beginning in March 2023. Phylogenetic analysis revealed at least four distinct XBB.1.16 lineages, suggesting multiple independent introductions into Bangkok. The estimated emergence of XBB.1.16 occurred approximately in January 2022, with an evolutionary rate of 0.79 × 10-3 substitutions per site per year. Monitoring the genomic epidemiology and evolution of XBB.1.16 is vital for the early detection of new strains or emerging variants, which may guide vaccine design and the inclusion of new vaccine strains.
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Affiliation(s)
- Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jira Chansaenroj
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kamol Suwannakarn
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- FRS(T), The Royal Society of Thailand, Sanam Sueapa, Dusit, Bangkok, Thailand.
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13
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Gutiérrez-Ortega JS, Pérez-Farrera MA, Matsuo A, Sato MP, Suyama Y, Calonje M, Vovides AP, Kajita T, Watano Y. The phylogenetic reconstruction of the Neotropical cycad genus Ceratozamia (Zamiaceae) reveals disparate patterns of niche evolution. Mol Phylogenet Evol 2024; 190:107960. [PMID: 37918683 DOI: 10.1016/j.ympev.2023.107960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
The cycad genus Ceratozamia comprises 40 species from Mexico, Guatemala, Belize, and Honduras, where cycads occur throughout climatically varied montane habitats. Ceratozamia has the potential to reveal the history and processes of species diversification across diverse Neotropical habitats in this region. However, the species relationships within Ceratozamia and the ecological trends during its evolution remain unclear. Here, we aimed to clarify the phylogenetic relationships, the timing of clade and species divergences, and the niche evolution throughout the phylogenetic history of Ceratozamia. Genome-wide DNA sequences were obtained with MIG-seq, and multiple data-filtering steps were used to optimize the dataset used to construct an ultrametric species tree. Divergence times among branches and ancestral niches were estimated. The niche variation among species was evaluated, summarized into two principal components, and their ancestral states were reconstructed to test whether niche shifts among branches can be explained by random processes, under a Brownian Motion model. Ceratozamia comprises three main clades, and most species relationships within the clades were resolved. Ceratozamia has diversified since the Oligocene, with major branching events occurring during the Miocene. This timing is consistent with fossil evidence, the timing estimated for other Neotropical plant groups, and the major geological events that shaped the topographic and climatic variation in Mexico. Patterns of niche evolution in the genus do not accord with the Brownian Motion model. Rather, non-random evolution with shifts towards more seasonal environments at high latitudes, or shifts towards humid or dry environments at low latitudes explain the diversification of Ceratozamia. We present a comprehensive phylogenetic reconstruction for Ceratozamia and identify for the first time the environmental factors involved in clade and species diversification within the genus. This study alleviates the controversies regarding the species relationships in the genus and provides the first evidence that latitude-associated environmental factors may influence processes of niche evolution in cycads.
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Affiliation(s)
| | - Miguel Angel Pérez-Farrera
- Herbario Eizi Matuda, Laboratorio de Ecología Evolutiva, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez 29039, Mexico.
| | - Ayumi Matsuo
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Mitsuhiko P Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | | | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., 91070 Xalapa, Mexico
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa 907-1541, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
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14
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Heeren S, Maes I, Sanders M, Lye LF, Adaui V, Arevalo J, Llanos-Cuentas A, Garcia L, Lemey P, Beverley SM, Cotton JA, Dujardin JC, Van den Broeck F. Diversity and dissemination of viruses in pathogenic protozoa. Nat Commun 2023; 14:8343. [PMID: 38102141 PMCID: PMC10724245 DOI: 10.1038/s41467-023-44085-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses are the most abundant biological entities on Earth and play a significant role in the evolution of many organisms and ecosystems. In pathogenic protozoa, the presence of viruses has been linked to an increased risk of treatment failure and severe clinical outcome. Here, we studied the molecular epidemiology of the zoonotic disease cutaneous leishmaniasis in Peru and Bolivia through a joint evolutionary analysis of Leishmania braziliensis and their dsRNA Leishmania virus 1. We show that parasite populations circulate in tropical rainforests and are associated with single viral lineages that appear in low prevalence. In contrast, groups of hybrid parasites are geographically and ecologically more dispersed and associated with an increased prevalence, diversity and spread of viruses. Our results suggest that parasite gene flow and hybridization increased the frequency of parasite-virus symbioses, a process that may change the epidemiology of leishmaniasis in the region.
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Affiliation(s)
- Senne Heeren
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Lon-Fye Lye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vanessa Adaui
- Laboratory of Biomolecules, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Jorge Arevalo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Lineth Garcia
- Instituto de Investigación Biomédicas e Investigación Social, Universidad Mayor de San Simon, Cochabamba, Bolivia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - James A Cotton
- Welcome Sanger Institute, Hinxton, UK
- School of Biodiversity, One Health and Comparative Medicine, Wellcome Centre for Integrative Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Frederik Van den Broeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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15
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Shi L, Hu M, Lai W, Yi W, Liu Z, Sun H, Li F, Yan S. Detection of genomic variations and selection signatures in Wagyu using whole-genome sequencing data. Anim Genet 2023; 54:808-812. [PMID: 37792466 DOI: 10.1111/age.13364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/28/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023]
Abstract
Wagyu is recognized for producing marbled beef with high nutritional value and flavor. Reportedly, Wagyu has been widely used to improve the meat quality of local breeds around the world. However, studies on the genetic mechanism of meat quality in Wagyu at the whole-genome level are rarely reported. Here, whole-genome sequencing data of 11 Wagyu and 115 other individuals were used to explore the genomic variations and genes under selection pressure in Wagyu. A total of 31 349 non-synonymous variants and 53 102 synonymous variants were identified in Wagyu. The population structure analysis showed that Wagyu had the closest genetic relationship with Mishima-Ushi cattle and was apparently separated from other cattle breeds. Then, composite likelihood ratio (CLR), integrated haplotype score, fixation index and cross-population composite likelihood ratio (XP-CLR) tests were performed to identify the candidate genes under positive selection in Wagyu. In total, 770 regions containing 312 genes were identified by at least three methods. Among them, 97 regions containing 27 genes were detected by all four methods. We specifically illustrate a list of interesting genes, including LRP2BP, GAA, CACNG6, CXADR, GPCPD1, KLF2, KLF13, SOX5, MYBPC1, SLC25A10, ATP8A1 and MYH15, which are associated with lipid metabolism, fat deposition, muscle development, bone development, feed intake and growth traits in Wagyu. This is the first study to explore the genomic variations and selection signatures of Wagyu at the whole-genome level. These results will provide significant help to beef cattle improvement and breeding.
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Affiliation(s)
- Lulu Shi
- College of Animal Science, Jilin University, Changchun, China
| | - Mingyue Hu
- College of Animal Science, Jilin University, Changchun, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun, China
| | - Wenfeng Yi
- College of Animal Science, Jilin University, Changchun, China
| | - Zhengxi Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Hao Sun
- College of Animal Science, Jilin University, Changchun, China
| | - Feng Li
- Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun, China
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16
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Penn MJ, Scheidwasser N, Penn J, Donnelly CA, Duchêne DA, Bhatt S. Leaping through Tree Space: Continuous Phylogenetic Inference for Rooted and Unrooted Trees. Genome Biol Evol 2023; 15:evad213. [PMID: 38085949 PMCID: PMC10745275 DOI: 10.1093/gbe/evad213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains challenging. To address this problem, for the first time, we perform both tree exploration and inference in a continuous space where the computation of gradients is possible. This continuous relaxation allows for major leaps across tree space in both rooted and unrooted trees, and is less susceptible to convergence to local minima. Our approach outperforms the current best methods for inference on unrooted trees and, in simulation, accurately infers the tree and root in ultrametric cases. The approach is effective in cases of empirical data with negligible amounts of data, which we demonstrate on the phylogeny of jawed vertebrates. Indeed, only a few genes with an ultrametric signal were generally sufficient for resolving the major lineages of vertebrates. Optimization is possible via automatic differentiation and our method presents an effective way forward for exploring the most difficult, data-deficient phylogenetic questions.
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Affiliation(s)
- Matthew J Penn
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Neil Scheidwasser
- Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Penn
- Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Christl A Donnelly
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, School of Public Health, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - David A Duchêne
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Samir Bhatt
- Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, School of Public Health, Faculty of Medicine, Imperial College London, London, United Kingdom
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17
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Li T, Yang H, Zhang X, Zhu L, Zhang J, Wei N, Li R, Dong Y, Feng Z, Zhang X, Xue J, Xu S. Genetic architecture of ear traits based on association mapping and co-expression networks in maize inbred lines and hybrids. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:78. [PMID: 37928364 PMCID: PMC10624778 DOI: 10.1007/s11032-023-01426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
Ear traits are key contributors to grain yield in maize; therefore, exploring their genetic basis facilitates the improvement of grain yield. However, the underlying molecular mechanisms of ear traits remain obscure in both inbred lines and hybrids. Here, two association panels, respectively, comprising 203 inbred lines (IP) and 246 F1 hybrids (HP) were employed to identify candidate genes for six ear traits. The IP showed higher phenotypic variation and lower phenotypic mean than the HP for all traits, except ear tip-barrenness length. By conducting a genome-wide association study (GWAS) across multiple environments, 101 and 228 significant single-nucleotide polymorphisms (SNPs) associated with six ear traits were identified in the IP and HP, respectively. Of these significant SNPs identified in the HP, most showed complete-incomplete dominance and over-dominance effects for each ear trait. Combining a gene co-expression network with GWAS results, 186 and 440 candidate genes were predicted in the IP and HP, respectively, including known ear development genes ids1 and sid1. Of these, nine candidate genes were detected in both populations and expressed in maize ear and spikelet tissues. Furthermore, two key shared genes (GRMZM2G143330 and GRMZM2G171139) in both populations were found to be significantly associated with ear traits in the maize Goodman diversity panel with high-density variations. These findings advance our knowledge of the genetic architecture of ear traits between inbred lines and hybrids and provide a valuable resource for the genetic improvement of ear traits in maize. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01426-9.
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Affiliation(s)
- Ting Li
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Haoxiang Yang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Xiaojun Zhang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Liangjia Zhu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Jun Zhang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Ningning Wei
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Ranran Li
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Yuan Dong
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Zhiqian Feng
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Xinghua Zhang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Jiquan Xue
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Shutu Xu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
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18
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Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
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Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
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19
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Xie R, Edwards KM, Wille M, Wei X, Wong SS, Zanin M, El-Shesheny R, Ducatez M, Poon LLM, Kayali G, Webby RJ, Dhanasekaran V. The episodic resurgence of highly pathogenic avian influenza H5 virus. Nature 2023; 622:810-817. [PMID: 37853121 DOI: 10.1038/s41586-023-06631-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023]
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 activity has intensified globally since 2021, increasingly causing mass mortality in wild birds and poultry and incidental infections in mammals1-3. However, the ecological and virological properties that underscore future mitigation strategies still remain unclear. Using epidemiological, spatial and genomic approaches, we demonstrate changes in the origins of resurgent HPAI H5 and reveal significant shifts in virus ecology and evolution. Outbreak data show key resurgent events in 2016-2017 and 2020-2021, contributing to the emergence and panzootic spread of H5N1 in 2021-2022. Genomic analysis reveals that the 2016-2017 epizootics originated in Asia, where HPAI H5 reservoirs are endemic. In 2020-2021, 2.3.4.4b H5N8 viruses emerged in African poultry, featuring mutations altering HA structure and receptor binding. In 2021-2022, a new H5N1 virus evolved through reassortment in wild birds in Europe, undergoing further reassortment with low-pathogenic avian influenza in wild and domestic birds during global dissemination. These results highlight a shift in the HPAI H5 epicentre beyond Asia and indicate that increasing persistence of HPAI H5 in wild birds is facilitating geographic and host range expansion, accelerating dispersion velocity and increasing reassortment potential. As earlier outbreaks of H5N1 and H5N8 were caused by more stable genomic constellations, these recent changes reflect adaptation across the domestic-bird-wild-bird interface. Elimination strategies in domestic birds therefore remain a high priority to limit future epizootics.
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Affiliation(s)
- Ruopeng Xie
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kimberly M Edwards
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Michelle Wille
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Xiaoman Wei
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sook-San Wong
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mark Zanin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Mariette Ducatez
- IHAP, Université de Toulouse, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | | | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Vijaykrishna Dhanasekaran
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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20
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Gao P, Zhao H, Luo Z, Lin Y, Feng W, Li Y, Kong F, Li X, Fang C, Wang X. SoyDNGP: a web-accessible deep learning framework for genomic prediction in soybean breeding. Brief Bioinform 2023; 24:bbad349. [PMID: 37824739 DOI: 10.1093/bib/bbad349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
Soybean is a globally significant crop, playing a vital role in human nutrition and agriculture. Its complex genetic structure and wide trait variation, however, pose challenges for breeders and researchers aiming to optimize its yield and quality. Addressing this biological complexity requires innovative and accurate tools for trait prediction. In response to this challenge, we have developed SoyDNGP, a deep learning-based model that offers significant advancements in the field of soybean trait prediction. Compared to existing methods, such as DeepGS and DNNGP, SoyDNGP boasts a distinct advantage due to its minimal increase in parameter volume and superior predictive accuracy. Through rigorous performance comparison, including prediction accuracy and model complexity, SoyDNGP represents improved performance to its counterparts. Furthermore, it effectively predicted complex traits with remarkable precision, demonstrating robust performance across different sample sizes and trait complexities. We also tested the versatility of SoyDNGP across multiple crop species, including cotton, maize, rice and tomato. Our results showed its consistent and comparable performance, emphasizing SoyDNGP's potential as a versatile tool for genomic prediction across a broad range of crops. To enhance its accessibility to users without extensive programming experience, we designed a user-friendly web server, available at http://xtlab.hzau.edu.cn/SoyDNGP. The server provides two features: 'Trait Lookup', offering users the ability to access pre-existing trait predictions for over 500 soybean accessions, and 'Trait Prediction', allowing for the upload of VCF files for trait estimation. By providing a high-performing, accessible tool for trait prediction, SoyDNGP opens up new possibilities in the quest for optimized soybean breeding.
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Affiliation(s)
- Pengfei Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Haonan Zhao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Zheng Luo
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Yifan Lin
- Hubei Hongshan Laboratory, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Wanjie Feng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Yaling Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Fanjiang Kong
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Chao Fang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xutong Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
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21
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Li G, Zhang Y, He HL, Chen CY, Li X, Xiao Y, Yan ZB, Chu Y, Luo J, Guo XF. Evolution and distribution of rabies viruses from a panorama view. Microbiol Spectr 2023; 11:e0525722. [PMID: 37668395 PMCID: PMC10581214 DOI: 10.1128/spectrum.05257-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/10/2023] [Indexed: 09/06/2023] Open
Abstract
Rabies kills more than 59,000 people annually, mainly in developing countries. Previous studies on the evolution and distribution of rabies viruses (RABVs) were scattered. Here, we explore the evolution and distribution of this deadly virus from a novel panorama view. Multiple bioinformatic software tools were employed to analyze the phylogenetic diversity, evolution, spatiotemporal, and distribution of RABVs. The analyses were based on 1,202 qualified full-length genomes of RABVs and numerous literatures. Of the 10 distinct phylogenetic clades of RABV that we identified, more frequent intra- and inter-clade recombination occurs in the sequences of Asian-SEA, Arctic, and Cosmopolitan clades isolated from China, while according to existing sequence information, RABV might originate from bats (posterior probability, PP = 0.75, PP = 0.60 inferred from N and L genes, separately) in North America (PP = 0.57, PP = 0.62 inferred from N and L genes, separately). Due to the difference in evolutionary rate of N (2.22 × 10-4 subs/site/year, 95% HPD 1.99-2.47 × 10-4 subs/site/year) and L genes (1.67 × 10-4 subs/site/year, 95% HPD 1.59-1.74 × 10-4 subs/site/year), the root age was 1,406.6 (95% HPD 1,291.2-1,518.2) and 1,122.7 (95% HPD 1,052.4-1,193.9) inferred from N and L genes, separately. Among other findings, Mephitidae plays an important role in the interspecific transmission and communication of RABV, which we found tends to spread to populations genetically proximate to the host. We also identified amino acids under positive selection in different genes of different clades as well as single nucleotide variation sites important for different lineages. IMPORTANCE Rabies virus is widely distributed all over the world, and wild animals are its largest potential reservoir. Our study offers a panorama view about evolution and distribution of rabies viruses and emphasizes the need to monitor the transmission dynamics of animal rabies.
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Affiliation(s)
- Gen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yue Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hong-Ling He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Chang-Yi Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xin Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yu Xiao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhi-Bin Yan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ying Chu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jun Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao-Feng Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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22
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Hausharter J, Rashid S, Wessely J, Strutzenberger P, Moser D, Gattringer A, Fiedler K, Hülber K, Dullinger S. Niche breadth explains the range size of European-centred butterflies, but dispersal ability does not. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2023; 32:1535-1548. [PMID: 38505836 PMCID: PMC10946795 DOI: 10.1111/geb.13717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 03/21/2024]
Abstract
Aim The breadth of ecological niches and dispersal abilities have long been discussed as important determinants of species' range sizes. However, studies directly comparing the relative effects of both factors are rare, taxonomically biased and revealed inconsistent results. Location Europe. Time Period Cenozoic. Major Taxa Butterflies, Lepidoptera. Methods We relate climate, diet and habitat niche breadth and two indicators of dispersal ability, wingspan and a dispersal tendency index, to the global range size of 369 European-centred butterfly species. The relative effects of these five predictors and their variation across the butterfly phylogeny were assessed by means of phylogenetic generalized least squares models and phylogenetically weighted regressions respectively. Results Climate niche breadth was the most important single predictor, followed by habitat and diet niche breadth, while dispersal tendency and wingspan showed no relation to species' range size. All predictors together explained 59% of the variation in butterfly range size. However, the effects of each predictor varied considerably across families and genera. Main Conclusions Range sizes of European-centred butterflies are strongly correlated with ecological niche breadth but apparently independent of dispersal ability. The magnitude of range size-niche breadth relationships is not stationary across the phylogeny and is often negatively correlated across the different dimensions of the ecological niche. This variation limits the generalizability of range size-trait relationships across broad taxonomic groups.
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Affiliation(s)
- Johannes Hausharter
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Sonia Rashid
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Vienna Doctoral School of Ecology and Evolution (VDSEE)University of ViennaViennaAustria
| | - Johannes Wessely
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | | | - Dietmar Moser
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Department of Biological Diversity and Nature ConservationEnvironment Agency AustriaViennaAustria
| | - Andreas Gattringer
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Konrad Fiedler
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Karl Hülber
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Stefan Dullinger
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
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23
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Moreira FRR, de Menezes MT, Salgado-Benvindo C, Whittaker C, Cox V, Chandradeva N, de Paula HHS, Martins AF, Chagas RRD, Brasil RDV, Cândido DDS, Herlinger AL, Ribeiro MDO, Arruda MB, Alvarez P, Tôrres MCDP, Dorigatti I, Brady O, Voloch CM, Tanuri A, Iani F, de Souza WM, Cardozo SV, Faria NR, Aguiar RS. Epidemiological and genomic investigation of chikungunya virus in Rio de Janeiro state, Brazil, between 2015 and 2018. PLoS Negl Trop Dis 2023; 17:e0011536. [PMID: 37769008 PMCID: PMC10564160 DOI: 10.1371/journal.pntd.0011536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 10/10/2023] [Accepted: 07/17/2023] [Indexed: 09/30/2023] Open
Abstract
Since 2014, Brazil has experienced an unprecedented epidemic caused by chikungunya virus (CHIKV), with several waves of East-Central-South-African (ECSA) lineage transmission reported across the country. In 2018, Rio de Janeiro state, the third most populous state in Brazil, reported 41% of all chikungunya cases in the country. Here we use evolutionary and epidemiological analysis to estimate the timescale of CHIKV-ECSA-American lineage and its epidemiological patterns in Rio de Janeiro. We show that the CHIKV-ECSA outbreak in Rio de Janeiro derived from two distinct clades introduced from the Northeast region in mid-2015 (clade RJ1, n = 63/67 genomes from Rio de Janeiro) and mid-2017 (clade RJ2, n = 4/67). We detected evidence for positive selection in non-structural proteins linked with viral replication in the RJ1 clade (clade-defining: nsP4-A481D) and the RJ2 clade (nsP1-D531G). Finally, we estimate the CHIKV-ECSA's basic reproduction number (R0) to be between 1.2 to 1.6 and show that its instantaneous reproduction number (Rt) displays a strong seasonal pattern with peaks in transmission coinciding with periods of high Aedes aegypti transmission potential. Our results highlight the need for continued genomic and epidemiological surveillance of CHIKV in Brazil, particularly during periods of high ecological suitability, and show that selective pressures underline the emergence and evolution of the large urban CHIKV-ECSA outbreak in Rio de Janeiro.
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Affiliation(s)
- Filipe Romero Rebello Moreira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
| | - Mariane Talon de Menezes
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clarisse Salgado-Benvindo
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
| | - Victoria Cox
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
| | - Nilani Chandradeva
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
| | - Hury Hellen Souza de Paula
- Departamento de Saúde, Programa de Pós-graduação em Biomedicina Translacional, Universidade do Grande Rio (UNIGRANRIO), Duque de Caxias, Rio de Janeiro, Brazil
| | - André Frederico Martins
- Departamento de Saúde, Programa de Pós-graduação em Biomedicina Translacional, Universidade do Grande Rio (UNIGRANRIO), Duque de Caxias, Rio de Janeiro, Brazil
| | - Raphael Rangel das Chagas
- Departamento de Saúde, Programa de Pós-graduação em Biomedicina Translacional, Universidade do Grande Rio (UNIGRANRIO), Duque de Caxias, Rio de Janeiro, Brazil
| | - Rodrigo Decembrino Vargas Brasil
- Departamento de Saúde, Programa de Pós-graduação em Biomedicina Translacional, Universidade do Grande Rio (UNIGRANRIO), Duque de Caxias, Rio de Janeiro, Brazil
| | - Darlan da Silva Cândido
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alice Laschuk Herlinger
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marisa de Oliveira Ribeiro
- Institute of Technology in Immunobiology Bio-Manguinhos, Oswaldo Cruz Foundation/ Fiocruz, Rio de Janeiro, Brazil
| | - Monica Barcellos Arruda
- Institute of Technology in Immunobiology Bio-Manguinhos, Oswaldo Cruz Foundation/ Fiocruz, Rio de Janeiro, Brazil
| | - Patricia Alvarez
- Institute of Technology in Immunobiology Bio-Manguinhos, Oswaldo Cruz Foundation/ Fiocruz, Rio de Janeiro, Brazil
| | | | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
| | - Oliver Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Carolina Moreira Voloch
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Felipe Iani
- Fundação Ezequiel Dias (FUNED), Belo Horizonte, Minas Gerais, Brazil
| | - William Marciel de Souza
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sergian Vianna Cardozo
- Departamento de Saúde, Programa de Pós-graduação em Biomedicina Translacional, Universidade do Grande Rio (UNIGRANRIO), Duque de Caxias, Rio de Janeiro, Brazil
| | - Nuno Rodrigues Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Renato Santana Aguiar
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Instituto D’or, Rio de Janeiro, Rio de Janeiro, Brazil
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24
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Billard E, Barro M, Sérémé D, Bangratz M, Wonni I, Koala M, Kassankogno AI, Hébrard E, Thébaud G, Brugidou C, Poulicard N, Tollenaere C. Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot. Virus Evol 2023; 9:vead049. [PMID: 37649958 PMCID: PMC10465090 DOI: 10.1093/ve/vead049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023] Open
Abstract
The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at a local scale remains scarce, in spite of potential implications for crop protection. Here, we describe a 5-year (2015-9) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon, and Karfiguela). It confirmed one irrigated site as a disease hotspot and also found one rainfed lowland (RL) site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a 5-m distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site scale (ca. 520 ha) and also within various specific fields (25 m side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20 per cent or less in 2015-6 to more than 65 per cent in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found, however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at the highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at a small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation under controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.
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Affiliation(s)
- Estelle Billard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Mariam Barro
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Drissa Sérémé
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Martine Bangratz
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Moustapha Koala
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Abalo Itolou Kassankogno
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Eugénie Hébrard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Gaël Thébaud
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Christophe Brugidou
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Charlotte Tollenaere
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
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25
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Byrne AMP, James J, Mollett BC, Meyer SM, Lewis T, Czepiel M, Seekings AH, Mahmood S, Thomas SS, Ross CS, Byrne DJF, McMenamy MJ, Bailie V, Lemon K, Hansen RDE, Falchieri M, Lewis NS, Reid SM, Brown IH, Banyard AC. Investigating the Genetic Diversity of H5 Avian Influenza Viruses in the United Kingdom from 2020-2022. Microbiol Spectr 2023; 11:e0477622. [PMID: 37358418 PMCID: PMC10433820 DOI: 10.1128/spectrum.04776-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/27/2023] [Indexed: 06/27/2023] Open
Abstract
Since 2020, the United Kingdom and Europe have experienced annual epizootics of high-pathogenicity avian influenza virus (HPAIV). The first epizootic, during the autumn/winter of 2020-2021, involved six H5Nx subtypes, although H5N8 HPAIV dominated in the United Kingdom. While genetic assessments of the H5N8 HPAIVs within the United Kingdom demonstrated relative homogeneity, there was a background of other genotypes circulating at a lower degree with different neuraminidase and internal genes. Following a small number of detections of H5N1 in wild birds over the summer of 2021, the autumn/winter of 2021-2022 saw another European H5 HPAIV epizootic that dwarfed the prior epizootic. This second epizootic was dominated almost exclusively by H5N1 HPAIV, although six distinct genotypes were defined. We have used genetic analysis to evaluate the emergence of different genotypes and proposed reassortment events that have been observed. The existing data suggest that the H5N1 viruses circulating in Europe during late 2020 continued to circulate in wild birds throughout 2021, with minimal adaptation, but then went on to reassort with AIVs in the wild bird population. We have undertaken an in-depth genetic assessment of H5 HPAIVs detected in the United Kingdom over two winter seasons and demonstrate the utility of in-depth genetic analyses in defining the diversity of H5 HPAIVs circulating in avian species, the potential for zoonotic risk, and whether incidents of lateral spread can be defined over independent incursions of infections from wild birds. This provides key supporting data for mitigation activities. IMPORTANCE High-pathogenicity avian influenza virus (HPAIV) outbreaks devastate avian species across all sectors, having both economic and ecological impacts through mortalities in poultry and wild birds, respectively. These viruses can also represent a significant zoonotic risk. Since 2020, the United Kingdom has experienced two successive outbreaks of H5 HPAIV. While H5N8 HPAIV was predominant during the 2020-2021 outbreak, other H5 subtypes were also detected. The following year, there was a shift in the subtype dominance to H5N1 HPAIV, but multiple H5N1 genotypes were detected. Through the thorough utilization of whole-genome sequencing, it was possible to track and characterize the genetic evolution of these H5 HPAIVs in United Kingdom poultry and wild birds. This enabled us to assess the risk posed by these viruses at the poultry-wild bird and the avian-human interfaces and to investigate the potential lateral spread between infected premises, a key factor in understanding the threat to the commercial sector.
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Affiliation(s)
- Alexander M. P. Byrne
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Joe James
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
- WOAH/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, United Kingdom
| | - Benjamin C. Mollett
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Stephanie M. Meyer
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
- WOAH/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, United Kingdom
| | - Thomas Lewis
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
- WOAH/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, United Kingdom
| | - Magdalena Czepiel
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
- WOAH/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, United Kingdom
| | - Amanda H. Seekings
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Sahar Mahmood
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Saumya S. Thomas
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Craig S. Ross
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Dominic J. F. Byrne
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | | | - Valerie Bailie
- Agri-Food and Bioscience Institute, Belfast, United Kingdom
| | - Ken Lemon
- Agri-Food and Bioscience Institute, Belfast, United Kingdom
| | - Rowena D. E. Hansen
- Veterinary Exotics and Notifiable Disease Unit, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Marco Falchieri
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Nicola S. Lewis
- Department of Pathology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Scott M. Reid
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Ian H. Brown
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
- WOAH/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, United Kingdom
| | - Ashley C. Banyard
- Virology Department, Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
- WOAH/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, United Kingdom
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Zeller MA, Ma J, Wong FY, Tum S, Hidano A, Holt H, Chhay T, Sorn S, Koeut D, Seng B, Chao S, Ng GGK, Yan Z, Chou M, Rudge JW, Smith GJD, Su YCF. The genomic landscape of swine influenza A viruses in Southeast Asia. Proc Natl Acad Sci U S A 2023; 120:e2301926120. [PMID: 37552753 PMCID: PMC10438389 DOI: 10.1073/pnas.2301926120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/07/2023] [Indexed: 08/10/2023] Open
Abstract
Swine are a primary source for the emergence of pandemic influenza A viruses. The intensification of swine production, along with global trade, has amplified the transmission and zoonotic risk of swine influenza A virus (swIAV). Effective surveillance is essential to uncover emerging virus strains; however gaps remain in our understanding of the swIAV genomic landscape in Southeast Asia. More than 4,000 nasal swabs were collected from pigs in Cambodia, yielding 72 IAV-positive samples by RT-qPCR and 45 genomic sequences. We unmasked the cocirculation of multiple lineages of genetically diverse swIAV of pandemic concern. Genomic analyses revealed a novel European avian-like H1N2 swIAV reassortant variant with North American triple reassortant internal genes, that emerged approximately seven years before its first detection in pigs in 2021. Using phylogeographic reconstruction, we identified south central China as the dominant source of swine viruses disseminated to other regions in China and Southeast Asia. We also identified nine distinct swIAV lineages in Cambodia, which diverged from their closest ancestors between two and 15 B.P., indicating significant undetected diversity in the region, including reverse zoonoses of human H1N1/2009 pandemic and H3N2 viruses. A similar period of cryptic circulation of swIAVs occurred in the decades before the H1N1/2009 pandemic. The hidden diversity of swIAV observed here further emphasizes the complex underlying evolutionary processes present in this region, reinforcing the importance of genomic surveillance at the human-swine interface for early warning of disease emergence to avoid future pandemics.
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Affiliation(s)
- Michael A. Zeller
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Jordan Ma
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Sothyra Tum
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Arata Hidano
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Hannah Holt
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Ty Chhay
- Livestock Development for Community Livelihood, Phnom Penh120108, Cambodia
| | - San Sorn
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Dina Koeut
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Bunnary Seng
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Sovanncheypo Chao
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Giselle G. K. Ng
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Zhuang Yan
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Monidarin Chou
- University of Health Sciences, Phnom Penh120210, Cambodia
| | - James W. Rudge
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore169857, Singapore
- SingHealth Duke-NUS Global Health Institute,SingHealth Duke-NUS Academic Medical Centre, Singapore169857, Singapore
- Duke Global Health Institute, Duke University, Durham, NC27708
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
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Junqueira DM, Tochetto C, Anderson TK, Gava D, Haach V, Cantão ME, Baker ALV, Schaefer R. Human-to-swine introductions and onward transmission of 2009 H1N1 pandemic influenza viruses in Brazil. Front Microbiol 2023; 14:1243567. [PMID: 37614592 PMCID: PMC10442540 DOI: 10.3389/fmicb.2023.1243567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/27/2023] [Indexed: 08/25/2023] Open
Abstract
Introduction Once established in the human population, the 2009 H1N1 pandemic virus (H1N1pdm09) was repeatedly introduced into swine populations globally with subsequent onward transmission among pigs. Methods To identify and characterize human-to-swine H1N1pdm09 introductions in Brazil, we conducted a large-scale phylogenetic analysis of 4,141 H1pdm09 hemagglutinin (HA) and 3,227 N1pdm09 neuraminidase (NA) gene sequences isolated globally from humans and swine between 2009 and 2022. Results Phylodynamic analysis revealed that during the period between 2009 and 2011, there was a rapid transmission of the H1N1pdm09 virus from humans to swine in Brazil. Multiple introductions of the virus were observed, but most of them resulted in self-limited infections in swine, with limited onward transmission. Only a few sustained transmission clusters were identified during this period. After 2012, there was a reduction in the number of human-to-swine H1N1pdm09 transmissions in Brazil. Discussion The virus underwent continuous antigenic drift, and a balance was established between swine-to-swine transmission and extinction, with minimal sustained onward transmission from humans to swine. These results emphasize the dynamic interplay between human-to-swine transmission, antigenic drift, and the establishment of swine-to-swine transmission in shaping the evolution and persistence of H1N1pdm09 in swine populations.
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Affiliation(s)
- Dennis Maletich Junqueira
- Laboratório de Bioinformática e Evolução de Vírus, Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas (CCNE), Universidade Federal de Santa Maria (UFSM), Santa Maria, Brazil
| | | | - Tavis K. Anderson
- Virus and Prion Research Unit, United States Department of Agriculture, National Animal Disease Center, Agricultural Research Service, Ames, IA, United States
| | | | - Vanessa Haach
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Amy L. Vincent Baker
- Virus and Prion Research Unit, United States Department of Agriculture, National Animal Disease Center, Agricultural Research Service, Ames, IA, United States
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Matio Kemkuignou B, Lambert C, Stadler M, Kouam Fogue S, Marin-Felix Y. Unprecedented Antimicrobial and Cytotoxic Polyketides from Cultures of Diaporthe africana sp. nov. J Fungi (Basel) 2023; 9:781. [PMID: 37504769 PMCID: PMC10381184 DOI: 10.3390/jof9070781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/20/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023] Open
Abstract
Four unprecedented polyketides named isoprenylisobenzofuran B (2), isoprenylisobenzofuran C1/C2 (3), diaporisoindole F1/F2 (4), and isochromophilonol A1/A2 (7) were isolated from ethyl acetate extracts of the newly described endophytic fungus Diaporthe africana. Additionally, the previously reported cyclic depsipeptide eucalactam B (1) was also identified, along with the known compounds diaporisoindole A/B (5), tenellone B (6) and beauvericin (8). The taxonomic identification of the fungus was accomplished using a polyphasic approach combining multi-gene phylogenetic analysis and microscopic morphological characters. The structures 1-8 were determined by a detailed analysis of their spectral data, namely high-resolution electrospray ionization mass spectrometry (HR-ESIMS), 1D/2D nuclear magnetic resonance (NMR) spectroscopy, as well as electronic circular dichroism (ECD) spectra. In addition, chemical methods such as Marfey's analysis were also employed to determine the stereochemistry in compound 1. All the compounds obtained were evaluated for antimicrobial and in vitro cytotoxic properties. Compounds 3-8 were active against certain fungi and Gram-positive bacteria with MIC values of 8.3 to 66.6 µg/mL. In addition, 3-5 displayed cytotoxic effects (22.0 ≤ IC50 ≤ 59.2 µM) against KB3.1 and L929 cell lines, whereas compounds 6-8 inhibited the growth of seven mammalian cancer cell lines with IC50 ranging from 17.7 to 49.5 µM (6), 0.9 to 12.9 µM (7) and 1.9 to 4.3 µM (8).
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Affiliation(s)
- Blondelle Matio Kemkuignou
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research (DZIF), Partner Site Hannover/Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Christopher Lambert
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research (DZIF), Partner Site Hannover/Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research (DZIF), Partner Site Hannover/Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Simeon Kouam Fogue
- Department of Chemistry, Higher Teacher Training College, University of Yaoundé I, Yaoundé P.O. Box 47, Cameroon
| | - Yasmina Marin-Felix
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research (DZIF), Partner Site Hannover/Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
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Campos PE, Pruvost O, Boyer K, Chiroleu F, Cao TT, Gaudeul M, Baider C, Utteridge TMA, Becker N, Rieux A, Gagnevin L. Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history. Nat Commun 2023; 14:4306. [PMID: 37474518 PMCID: PMC10359311 DOI: 10.1038/s41467-023-39950-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).
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Affiliation(s)
- Paola E Campos
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | | | - Thuy Trang Cao
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
- Herbier national, Muséum national d'Histoire naturelle, CP39, 57 rue Cuvier, 75005, Paris, France
| | - Cláudia Baider
- The Mauritius Herbarium, Agricultural Services, Ministry of Agro-Industry and Food Security, R.E. Vaughan Building (MSIRI Compound), Reduit, 80835, Mauritius
| | | | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
- CIRAD, UMR PHIM, Montpellier, France.
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30
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Tafazoli A, Mikros J, Khaghani F, Alimardani M, Rafigh M, Hemmati M, Siamoglou S, Golińska AK, Kamiński KA, Niemira M, Miltyk W, Patrinos GP. Pharmacovariome scanning using whole pharmacogene resequencing coupled with deep computational analysis and machine learning for clinical pharmacogenomics. Hum Genomics 2023; 17:62. [PMID: 37452347 PMCID: PMC10347842 DOI: 10.1186/s40246-023-00508-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND This pilot study aims to identify and functionally assess pharmacovariants in whole exome sequencing data. While detection of known variants has benefited from pharmacogenomic-dedicated bioinformatics tools before, in this paper we have tested novel deep computational analysis in addition to artificial intelligence as possible approaches for functional analysis of unknown markers within less studied drug-related genes. METHODS Pharmacovariants from 1800 drug-related genes from 100 WES data files underwent (a) deep computational analysis by eight bioinformatic algorithms (overall containing 23 tools) and (b) random forest (RF) classifier as the machine learning (ML) approach separately. ML model efficiency was calculated by internal and external cross-validation during recursive feature elimination. Protein modelling was also performed for predicted highly damaging variants with lower frequencies. Genotype-phenotype correlations were implemented for top selected variants in terms of highest possibility of being damaging. RESULTS Five deleterious pharmacovariants in the RYR1, POLG, ANXA11, CCNH, and CDH23 genes identified in step (a) and subsequent analysis displayed high impact on drug-related phenotypes. Also, the utilization of recursive feature elimination achieved a subset of 175 malfunction pharmacovariants in 135 drug-related genes that were used by the RF model with fivefold internal cross-validation, resulting in an area under the curve of 0.9736842 with an average accuracy of 0.9818 (95% CI: 0.89, 0.99) on predicting whether a carrying individuals will develop adverse drug reactions or not. However, the external cross-validation of the same model indicated a possible false positive result when dealing with a low number of observations, as only 60 important variants in 49 genes were displayed, giving an AUC of 0.5384848 with an average accuracy of 0.9512 (95% CI: 0.83, 0.99). CONCLUSION While there are some technologies for functionally assess not-interpreted pharmacovariants, there is still an essential need for the development of tools, methods, and algorithms which are able to provide a functional prediction for every single pharmacovariant in both large-scale datasets and small cohorts. Our approaches may bring new insights for choosing the right computational assessment algorithms out of high throughput DNA sequencing data from small cohorts to be used for personalized drug therapy implementation.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy With the Division of Laboratory Medicine, Medical University of Bialystok, 15-089, Białystok, Poland
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Kraków, Poland
| | - John Mikros
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Faeze Khaghani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Guilan University of Medical Sciences, Rasht, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahboobeh Rafigh
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahboobeh Hemmati
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | | | - Karol A Kamiński
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Białystok, Poland
- Department of Cardiology, Medical University of Bialystok, Białystok, Poland
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, Białystok, Poland
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy With the Division of Laboratory Medicine, Medical University of Bialystok, 15-089, Białystok, Poland.
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
- Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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31
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Li YQ, Ghafari M, Holbrook AJ, Boonen I, Amor N, Catalano S, Webster JP, Li YY, Li HT, Vergote V, Maes P, Chong YL, Laudisoit A, Baelo P, Ngoy S, Mbalitini SG, Gembu GC, Musaba AP, Goüy de Bellocq J, Leirs H, Verheyen E, Pybus OG, Katzourakis A, Alagaili AN, Gryseels S, Li YC, Suchard MA, Bletsa M, Lemey P. The evolutionary history of hepaciviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547218. [PMID: 37425679 PMCID: PMC10327235 DOI: 10.1101/2023.06.30.547218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.
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Affiliation(s)
- YQ Li
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - M Ghafari
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AJ Holbrook
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - I Boonen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - N Amor
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Catalano
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - JP Webster
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - YY Li
- College of Life Sciences, Linyi University, Linyi, 276000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - HT Li
- College of Life Sciences, Liaocheng University, Liaocheng, 252000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - V Vergote
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - P Maes
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - YL Chong
- Animal Resource Science and Management Group, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak (UNIMAS), 94300, Malaysia
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, 999077, China
| | - A Laudisoit
- EcoHealth Alliance, New York, NY 10018, USA
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - P Baelo
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - S Ngoy
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - SG Mbalitini
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - GC Gembu
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Akawa P Musaba
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - J Goüy de Bellocq
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - H Leirs
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - E Verheyen
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - OG Pybus
- Department of Biology, University of Oxford, Oxford, OX1, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - A Katzourakis
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AN Alagaili
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Gryseels
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - YC Li
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - MA Suchard
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - M Bletsa
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - P Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
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32
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González JB, Lambert CA, Foley AM, Hajek AE. First report of Colletotrichum fioriniae infections in brown marmorated stink bugs, Halyomorpha halys. J Invertebr Pathol 2023:107939. [PMID: 37236421 DOI: 10.1016/j.jip.2023.107939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023]
Abstract
An epizootic caused by fungal pathogens occurred among Halyomorpha halys, brown marmorated stink bugs, while they were overwintering, with infections also occurring after overwintering. We report that one of the two pathogens responsible was Collectotrichum fioriniae (Marcelino & Gouli), Pennycook; a species well known as a plant pathogen and endophyte and which has only previously been reported naturally infecting elongate hemlock scales, Fiorinia externa. To prove pathogenicity, H. halys adults challenged with conidia died from infections and the fungus subsequently produced conidia externally on cadavers.
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Affiliation(s)
- Jennifer B González
- Biology Department, Nazareth College, Rochester, New York 14618 USA; Department of Environmental Studies, Dartmouth College, Hanover, New Hampshire 03755 USA
| | - Chloe A Lambert
- Biology Department, Nazareth College, Rochester, New York 14618 USA
| | | | - Ann E Hajek
- Department of Entomology, Cornell University, Ithaca, New York 14853-2601 USA.
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Wang H, Guo H, Hein VG, Xu Y, Yu S, Wang X. The evolutionary dynamics history of canine distemper virus through analysis of the hemagglutinin gene during 1930-2020. EUR J WILDLIFE RES 2023; 69:56. [PMID: 37252648 PMCID: PMC10198785 DOI: 10.1007/s10344-023-01685-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/19/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023]
Abstract
Canine distemper virus (CDV) is a lethal viral disease of carnivores which is considered to be a serious threat to domestic and wild species. Despite the widespread use of vaccines, CDV still occurs in vaccinated animals and current vaccines does not guarantee complete protection. In this study, a total of 286 hemagglutinin (H) gene sequences of the virus isolated in 25 countries during 90 years (1930-2020) were analyzed by Bayesian maximum likelihood analysis to estimate the population dynamics. We identified the most recent common ancestor (TMRCA) of the virus in 1868 in the USA which arrived in continental Europe in 1948, and from there, the virus spread rapidly to other continents. The Canidae family was identified as the original host as well as a source of the subsequent spread. We identified 11 lineages of geographic co-circulating strains globally. The effective population size experienced a two-phase-exponential growth between 2000-2005 and 2010-2012. Our findings provide a novel insight into the epidemic history of canine distemper virus which may facilitate more effective disease management. This study uses a large set of sequencing data on the H gene of CDV to identify distinct lineages of the virus, track its geographic spread over time, analyze its likelihood of transmission within and between animal families, and provide suggestions for improved strategies to combat the virus. Supplementary Information The online version contains supplementary material available at 10.1007/s10344-023-01685-z.
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Affiliation(s)
- Haoning Wang
- Heilongjiang Cold Region Wetland Ecology and Environment Research Key Laboratory, School of Geography and Tourism, Harbin University, 109 Zhongxing Road, Harbin, 150086 Heilongjiang Province People’s Republic of China
- School of Geography and Tourism, Harbin University, Harbin, 150086 Heilongjiang Province People’s Republic of China
- The Key Laboratory of Wildlife Diseases and Biosecurity Management of Heilongjiang Province, Harbin, Heilongjiang Province People’s Republic of China
- Collage of Wildlife and Protected Area, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040 Heilongjiang People’s Republic of China
| | - Hong Guo
- Heilongjiang Cold Region Wetland Ecology and Environment Research Key Laboratory, School of Geography and Tourism, Harbin University, 109 Zhongxing Road, Harbin, 150086 Heilongjiang Province People’s Republic of China
- School of Geography and Tourism, Harbin University, Harbin, 150086 Heilongjiang Province People’s Republic of China
| | - Van Gils Hein
- Department of Geography, Geoinformatics & Meteorology, University of Pretoria, Pretoria, 0002 Gauteng Province Republic of South Africa
| | - Yanchun Xu
- Collage of Wildlife and Protected Area, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040 Heilongjiang People’s Republic of China
| | - Shaopeng Yu
- Heilongjiang Cold Region Wetland Ecology and Environment Research Key Laboratory, School of Geography and Tourism, Harbin University, 109 Zhongxing Road, Harbin, 150086 Heilongjiang Province People’s Republic of China
- School of Geography and Tourism, Harbin University, Harbin, 150086 Heilongjiang Province People’s Republic of China
| | - Xiaolong Wang
- The Key Laboratory of Wildlife Diseases and Biosecurity Management of Heilongjiang Province, Harbin, Heilongjiang Province People’s Republic of China
- Collage of Wildlife and Protected Area, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040 Heilongjiang People’s Republic of China
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Rossi G, Shih BBJ, Egbe NF, Motta P, Duchatel F, Kelly RF, Ndip L, Sander M, Tanya VN, Lycett SJ, Bronsvoort BM, Muwonge A. Unraveling the epidemiology of Mycobacterium bovis using whole-genome sequencing combined with environmental and demographic data. Front Vet Sci 2023; 10:1086001. [PMID: 37266384 PMCID: PMC10230100 DOI: 10.3389/fvets.2023.1086001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/14/2023] [Indexed: 06/03/2023] Open
Abstract
When studying the dynamics of a pathogen in a host population, one crucial question is whether it transitioned from an epidemic (i.e., the pathogen population and the number of infected hosts are increasing) to an endemic stable state (i.e., the pathogen population reached an equilibrium). For slow-growing and slow-evolving clonal pathogens such as Mycobacterium bovis, the causative agent of bovine (or animal) and zoonotic tuberculosis, it can be challenging to discriminate between these two states. This is a result of the combination of suboptimal detection tests so that the actual extent of the pathogen prevalence is often unknown, as well as of the low genetic diversity, which can hide the temporal signal provided by the accumulation of mutations in the bacterial DNA. In recent years, the increased availability, efficiency, and reliability of genomic reading techniques, such as whole-genome sequencing (WGS), have significantly increased the amount of information we can use to study infectious diseases, and therefore, it has improved the precision of epidemiological inferences for pathogens such as M. bovis. In this study, we use WGS to gain insights into the epidemiology of M. bovis in Cameroon, a developing country where the pathogen has been reported for decades. A total of 91 high-quality sequences were obtained from tissue samples collected in four abattoirs, 64 of which were with complete metadata. We combined these with environmental, demographic, ecological, and cattle movement data to generate inferences using phylodynamic models. Our findings suggest M. bovis in Cameroon is slowly expanding its epidemiological range over time; therefore, endemic stability is unlikely. This suggests that animal movement plays an important role in transmission. The simultaneous prevalence of M. bovis in co-located cattle and humans highlights the risk of such transmission being zoonotic. Therefore, using genomic tools as part of surveillance would vastly improve our understanding of disease ecology and control strategies.
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Affiliation(s)
- Gianluigi Rossi
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Barbara Bo-Ju Shih
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| | - Nkongho Franklyn Egbe
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Paolo Motta
- The Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Bangkok, Thailand
| | - Florian Duchatel
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| | - Robert Francis Kelly
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Lucy Ndip
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, Cameroon
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | | | | | - Samantha J. Lycett
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Barend Mark Bronsvoort
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Adrian Muwonge
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
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Rajkhowa TK, Zodinpuii D, Bhutia LD, Islam SJ, Gogoi A, Hauhnar L, Kiran J, Choudhary OP. Emergence of a novel genotype of class II New Castle Disease virus in North Eastern States of India. Gene 2023; 864:147315. [PMID: 36842725 DOI: 10.1016/j.gene.2023.147315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Outbreaks of New Castle Disease from three north eastern states of India were confirmed by clinico-pathological examination followed by reverse transcription-PCR detection of F gene of ND Virus (NDV). Irrespective of vaccination, the outbreaks resulted 90-100% mortality in the affected flocks. The analysis of fusion protein sequences from ten field isolates revealed them as the velogenic or highly virulent strain. Phylogenetic analyses based on the complete F gene nucleotide sequences of the isolates have characterized only one of the isolate (OK149201) in the genotype XIII.2.2. The rest of the nine isolates are depicted in a distinct monophyletic group with average nucleotide distances from the other 20 genotypes ranged from 10.90 - 20.70. The nine isolates were further divided into two sub branches with the bootstrap support value of 100% at the nodes that define the two subgroups with an average evolutionary nucleotide distance of 6.00between the isolates in the two subgroups. As per the recommendation put forth in recently updated unified phylogenetic classification system for NDV, our findings clearly indicates emergence of a novel genotype of class II NDV in the biodiversity hot spot region of NER, India. The isolates in the newly identified genotype is designated with next available Roman numerals XXII. Further, the two subgroups within the genotype are designated as XXII.1 and XXII.2.
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Affiliation(s)
- Tridib Kumar Rajkhowa
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram 796014, India.
| | - Doris Zodinpuii
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram 796014, India
| | | | - Sikder Jabidur Islam
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram 796014, India
| | - Amrit Gogoi
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University (I), Jalukie, Peren, Nagaland 797110, India
| | - Lalthapuii Hauhnar
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram 796014, India
| | - J Kiran
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram 796014, India
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram 796014, India
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Cedeño-Sanchez M, Schiefelbein R, Stadler M, Voglmayr H, Bensch K, Lambert C. Redisposition of apiosporous genera Induratia and Muscodor in the Xylariales, following the discovery of an authentic strain of Induratia apiospora. BOTANICAL STUDIES 2023; 64:8. [PMID: 37052736 PMCID: PMC10102272 DOI: 10.1186/s40529-023-00372-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The genus Induratia is based on Induratia apiospora, a xylarialean pyrenomycete from New Zealand with clypeate uniperitheciate stromata, hyaline apiospores and a nodulisporium-like anamorph. However, because of the lack of DNA data from the generic type, its phylogenetic affinities have remained unresolved. Recently, two fungal species with teleomorphs strikingly similar to Induratia were discovered in Thailand. However, they did not produce an anamorph and were found to be phylogenetically close to the species classified within the hyphomycete genus Muscodor, which was described after Induratia. Therefore, in 2020 the species of Muscodor were transferred to Induratia, and a new family Induratiaceae was proposed. RESULTS We have encountered an unpublished ex-holotype strain of Induratia apiospora among the holdings of the ATCC collection, enabling detailed morphological and molecular phylogenetic investigations. We observed the characteristic nodulisporium-like anamorph described in the original publication. Phylogenetic analyses of multigene sequence data revealed a close relationship of Induratia apiospora to the Barrmaeliaceae, while a close relationship to the Induratia species formerly classified within Muscodor was rejected. CONCLUSIONS We here classify Induratia apiospora within the Barrmaeliaceae and consider Induratiaceae to be synonymous with the former. As the holotype specimen of Induratia apiospora is apparently lost, an isotype specimen from WSP is selected as lectotype. We also propose that the genus Muscodor is resurrected within the Xylariaceae, and formally transfer several Induratia species to Muscodor.
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Affiliation(s)
- Marjorie Cedeño-Sanchez
- Department Microbial Drugs, Helmholtz-Centre for Infection Research GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Rahel Schiefelbein
- Department Microbial Drugs, Helmholtz-Centre for Infection Research GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz-Centre for Infection Research GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Hermann Voglmayr
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
- Department of Forest and Soil Sciences, Institute of Forest Entomology, Forest Pathology and Forest Protection, BOKU-University of Natural Resources and Life Sciences, Franz- Schwackhöfer-Haus, Peter-Jordan-Straße 82/I, 1190, Vienna, Austria
| | - Konstanze Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Christopher Lambert
- Department Microbial Drugs, Helmholtz-Centre for Infection Research GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany.
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.
- Department of Cell Biology, Helmholtz-Centre for Infection Research GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany.
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Wang Q, Zhang J, Wang H, Wang Z, Li Q, Zhao G, Zheng M, Wen J. Estimates of genomic inbreeding and identification of candidate regions in Beijing-You chicken populations. Anim Genet 2023; 54:155-165. [PMID: 36541281 DOI: 10.1111/age.13286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/09/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022]
Abstract
Runs of homozygosity (ROHs) has become an effective method for analysing inbreeding in livestock populations. Moreover, ROHs is well-suited to detect signatures of selection via ROH islands. This study aimed to investigate the occurrence and distribution of ROHs, compare the genomic inbreeding coefficients and identify the genomic regions with high ROH frequencies in different Beijing-You chicken (BY) populations, including a random conservation population (BY_R), a pedigree conservation population (BY_P), and a commercial population obtained from the market (BY_C). Among them, BY_R in 2010 and 2019 were BY_R1 and BY_R2 respectively. A total of 27 916 ROHs were identified. The average number of ROHs per individual across the three BY populations ranged from 213 (BY_P) to 161 (BY_C), and the average length of ROHs ranged from 0.432 Mb (BY_R2) to 0.451 Mb (BY_P). The highest inbreeding coefficient calculated based on ROHs (FROH ) was 0.1 in BY_P, whereas the lowest FROH was 0.0743 in BY_C. In addition, the inbreeding coefficient of BY_R2 (FROH = 0.0798) was higher than that of BY_R1 (FROH = 0.0579). Furthermore, the highest proportion of long ROH fragments (>4 Mb) was observed in BY_P and BY_C. This study showed the top 10 ROH islands of each population, and these ROH islands harboured 53 genes, some of which were related to limb development, body size and immune response. These findings contribute to the understanding of genetic diversity and population demography, and might help improve breeding and conservation strategies for BY populations.
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Affiliation(s)
- Qiao Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Jin Zhang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Hailong Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Zixuan Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Qinghe Li
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Guiping Zhao
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Maiqing Zheng
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Jie Wen
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
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Hossain I, Parvin R, Rahman MM, Begum JA, Chowdhury EH, Islam MR, Diel DG, Nooruzzaman M. Comparative pathogenicity of a genotype XXI.1.2 pigeon Newcastle disease virus isolate in pigeons and chickens. Microb Pathog 2023; 178:106068. [PMID: 36933579 DOI: 10.1016/j.micpath.2023.106068] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/20/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Here, we performed molecular and pathogenic characterization of a Newcastle disease virus (NDV) isolate from pigeons in Bangladesh. Molecular phylogenetic analysis based on the complete fusion gene sequences classified the three study isolates into genotype XXI (sub-genotype XXI.1.2) together with recent NDV isolates obtained from pigeons in Pakistan (2014-2018). The Bayesian Markov Chain Monte Carlo analysis revealed that the ancestor of Bangladeshi pigeon NDVs and the viruses from sub-genotype XXI.1.2 existed in the late 1990s. Pathogenicity testing using mean embryo death time pathotyped the viruses as mesogenic, while all isolates carried multiple basic amino acid residues at the fusion protein cleavage site. Experimental infection of chickens and pigeons revealed no or minimum clinical signs in chickens, while a relatively high morbidity (70%) and mortality (60%) were observed in pigeons. The infected pigeons showed extensive and systemic lesions including hemorrhagic and/or vascular changes in the conjunctiva, respiratory and digestive system and brain, and atrophy in the spleen, while only mild congestion in the lungs was noticed in the inoculated chickens. Histologically, consolidation in the lungs with collapsed alveoli and edema around the blood vessels, hemorrhages in the trachea, severe hemorrhages and congestion, focal aggregation of mononuclear cells, and single hepatocellular necrosis in the liver, severe congestion, multifocal tubular degeneration, and necrosis, as well as mononuclear cell infiltration in the renal parenchyma, encephalomalacia with severe neuronal necrosis with neuronophagia were noticed in the brain in infected pigeons. In contrast, only slight congestion was found in lungs of the infected chickens. qRT-PCR revealed the replication of the virus in both pigeons and chickens; however, higher viral RNA loads were observed in oropharyngeal and cloacal swabs, respiratory tissues, and spleen of infected pigeons than the chickens. In conclusion, genotype XXI.1.2 NDVs are circulating in the pigeon population of Bangladesh since 1990s, produce high mortality in pigeons with pneumonia, hepatocellular necrosis, renal tubular degeneration, and neuronal necrosis in pigeons, and may infect chickens without overt signs of clinical disease and are likely to shed viruses via the oral or cloacal routes.
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Affiliation(s)
- Ismail Hossain
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Rokshana Parvin
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Mohammad Mijanur Rahman
- Department of Livestock Services, Ministry of Fisheries and Livestock, Krishi Khamar Sarak, Dhaka, Bangladesh
| | - Jahan Ara Begum
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Emdadul Haque Chowdhury
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Mohammad Rafiqul Islam
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Mohammed Nooruzzaman
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh; Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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de Oliveira CH, Andrade MS, Campos FS, da C. Cardoso J, Gonçalves-dos-Santos ME, Oliveira RS, Aquino-Teixeira SM, Campos AAS, Almeida MAB, Simonini-Teixeira D, da P. Sevá A, Temponi AOD, Magalhães FM, da Silva Menezes AS, Lopes BT, Almeida HP, Pedroso AL, Gonçalves GP, Chaves DCC, de Menezes GG, Bernal-Valle S, Müller NFD, Janssen L, dos Santos E, Mares-Guia MA, Albuquerque GR, Romano APM, Franco AC, Ribeiro BM, Roehe PM, Lourenço-de-Oliveira R, de Abreu FVS. Yellow Fever Virus Maintained by Sabethes Mosquitoes during the Dry Season in Cerrado, a Semiarid Region of Brazil, in 2021. Viruses 2023; 15:757. [PMID: 36992466 PMCID: PMC10058068 DOI: 10.3390/v15030757] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
In recent decades, waves of yellow fever virus (YFV) from the Amazon Rainforest have spread and caused outbreaks in other regions of Brazil, including the Cerrado, a savannah-like biome through which YFV usually moves before arriving at the Atlantic Forest. To identify the vectors involved in the maintenance of the virus in semiarid environments, an entomological survey was conducted after confirmation of yellow fever (YF) epizootics at the peak of the dry season in the Cerrado areas of the state of Minas Gerais. In total, 917 mosquitoes from 13 taxa were collected and tested for the presence of YFV. Interestingly, mosquitoes of the Sabethes genus represented 95% of the diurnal captured specimens, displaying a peak of biting activity never previously recorded, between 4:30 and 5:30 p.m. Molecular analysis identified three YFV-positive pools, two from Sabethes chloropterus-from which near-complete genomes were generated-and one from Sa. albiprivus, whose low viral load prevented sequencing. Sa. chloropterus was considered the primary vector due to the high number of copies of YFV RNA and the high relative abundance detected. Its bionomic characteristics allow its survival in dry places and dry time periods. For the first time in Brazil, Sa. albiprivus was found to be naturally infected with YFV and may have played a role as a secondary vector. Despite its high relative abundance, fewer copies of viral RNA were found, as well as a lower Minimum Infection Rate (MIR). Genomic and phylogeographic analysis showed that the virus clustered in the sub-lineage YFVPA-MG, which circulated in Pará in 2017 and then spread into other regions of the country. The results reported here contribute to the understanding of the epidemiology and mechanisms of YFV dispersion and maintenance, especially in adverse weather conditions. The intense viral circulation, even outside the seasonal period, increases the importance of surveillance and YFV vaccination to protect human populations in affected areas.
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Affiliation(s)
- Cirilo H. de Oliveira
- Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, MG, Brazil
| | - Miguel S. Andrade
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, DF, Brazil
- Department of Molecular Biology, Sabin Diagnóstico e Saúde, Brasília 70632-340, DF, Brazil
| | - Fabrício S. Campos
- Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, TO, Brazil
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil
| | - Jader da C. Cardoso
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, RS, Brazil
| | | | - Ramon Silva Oliveira
- Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, MG, Brazil
| | | | - Aline AS Campos
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, RS, Brazil
| | - Marco AB Almeida
- Pan American Health Organization, World Health Organization Office in Brazil, Brasília 70800-400, DF, Brazil
| | - Danilo Simonini-Teixeira
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Anaiá da P. Sevá
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Andrea Oliveira Dias Temponi
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Fernando Maria Magalhães
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Agna Soares da Silva Menezes
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Bartolomeu Teixeira Lopes
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Hermes P. Almeida
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Ana Lúcia Pedroso
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Giovani Pontel Gonçalves
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Danielle Costa Capistrano Chaves
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Givaldo Gomes de Menezes
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Sofía Bernal-Valle
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Nicolas FD Müller
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil
| | - Luis Janssen
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, DF, Brazil
| | - Edmilson dos Santos
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, RS, Brazil
| | - Maria A. Mares-Guia
- Flavivirus Laboratory, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - George R. Albuquerque
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Alessandro PM Romano
- General Coordination of Arbovirus Surveillance, Ministry of Health, Brasília 70058-900, DF, Brazil
| | - Ana C. Franco
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil
| | - Bergmann M. Ribeiro
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, DF, Brazil
| | - Paulo M. Roehe
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil
| | - Ricardo Lourenço-de-Oliveira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
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A comprehensive phylogeny and revised taxonomy illuminate the origin and diversification of the global radiation of Papilio (Lepidoptera: Papilionidae). Mol Phylogenet Evol 2023; 183:107758. [PMID: 36907224 DOI: 10.1016/j.ympev.2023.107758] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
The swallowtail genus Papilio (Lepidoptera: Papilionidae) is species rich, distributed worldwide, and has broad morphological habits and ecological niches. Because of its elevated species richness, it has been historically difficult to reconstruct a densely sampled phylogeny for this clade. Here we provide a taxonomic working list for the genus, resulting in 235 Papilio species, and assemble a molecular dataset of seven gene fragments representing ca. 80% of the currently described diversity. Phylogenetic analyses reconstructed a robust tree with highly supported relationships within subgenera, although a few nodes in the early history of the Old World Papilio remain unresolved. Contrasting with previous results, we found that Papilio alexanor is sister to all Old World Papilio and that the subgenus Eleppone is no longer monotypic. The latter includes the recently described Fijian Papilio natewa with the Australian Papilio anactus and is sister to subgenus Araminta (formerly included in subgenus Menelaides) occurring in Southeast Asia. Our phylogeny also includes rarely studied (P. antimachus, P. benguetana) or endangered species (P. buddha, P. chikae). Taxonomic changes resulting from this study are elucidated. Molecular dating and biogeographic analyses indicate that Papilio originated ca. 30 million years ago (Oligocene), in a northern region centered on Beringia. A rapid early Miocene radiation in the Paleotropics is revealed within Old World Papilio, potentially explaining their low early branch support. Most subgenera originated in the early to middle Miocene followed by synchronous southward biogeographic dispersals and repeated local extirpations in northern latitudes. This study provides a comprehensive phylogenetic framework for Papilio with clarification of subgeneric systematics and species taxonomic changes enumerated, which will facilitate further studies to address questions on their ecology and evolutionary biology using this model clade.
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Olawoye IB, Oluniyi PE, Oguzie JU, Uwanibe JN, Kayode TA, Olumade TJ, Ajogbasile FV, Parker E, Eromon PE, Abechi P, Sobajo TA, Ugwu CA, George UE, Ayoade F, Akano K, Oyejide NE, Nosamiefan I, Fred-Akintunwa I, Adedotun-Sulaiman K, Brimmo FB, Adegboyega BB, Philip C, Adeleke RA, Chukwu GC, Ahmed MI, Ope-Ewe OO, Otitoola SG, Ogunsanya OA, Saibu MF, Sijuwola AE, Ezekiel GO, John OG, Akin-John JO, Akinlo OO, Fayemi OO, Ipaye TO, Nwodo DC, Omoniyi AE, Omwanghe IB, Terkuma CA, Okolie J, Ayo-Ale O, Ikponmwosa O, Benevolence E, Naregose GO, Patience AE, Blessing O, Micheal A, Jacqueline A, Aiyepada JO, Ebhodaghe P, Racheal O, Rita E, Rosemary GE, Solomon E, Anieno E, Edna Y, Chris AO, Donatus AI, Ogbaini-Emovon E, Tatfeng MY, Omunakwe HE, Bob-Manuel M, Ahmed RA, Onwuamah CK, Shaibu JO, Okwuraiwe A, Ataga AE, Bock-Oruma A, Daramola F, Yusuf IF, Fajola A, Ntia NA, Ekpo JJ, Moses AE, Moore-Igwe BW, Fakayode OE, Akinola M, Kida IM, Oderinde BS, Wudiri ZW, Adeyemi OO, Akanbi OA, Ahumibe A, Akinpelu A, Ayansola O, Babatunde O, Omoare AA, Chukwu C, Mba NG, Omoruyi EC, Olisa O, Akande OK, Nwafor IE, Ekeh MA, Ndoma E, Ewah RL, Duruihuoma RO, Abu A, Odeh E, Onyia V, Ojide CK, Okoro S, Igwe D, Ogah EO, Khan K, Ajayi NA, Ugwu CN, Ukwaja KN, Ugwu NI, Abejegah C, Adedosu N, Ayodeji O, Liasu AA, Isamotu RO, Gadzama G, Petros BA, Siddle KJ, Schaffner SF, Akpede G, Erameh CO, Baba MM, Oladiji F, Audu R, Ndodo N, Fowotade A, Okogbenin S, Okokhere PO, Park DJ, Mcannis BL, Adetifa IM, Ihekweazu C, Salako BL, Tomori O, Happi AN, Folarin OA, Andersen KG, Sabeti PC, Happi CT. Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria. Nat Commun 2023; 14:811. [PMID: 36781860 PMCID: PMC9924892 DOI: 10.1038/s41467-023-36449-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates.
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Affiliation(s)
- Idowu B Olawoye
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Judith U Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Jessica N Uwanibe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Tolulope A Kayode
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Testimony J Olumade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Fehintola V Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Priscilla Abechi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Tope A Sobajo
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Chinedu A Ugwu
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Uwem E George
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Femi Ayoade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kazeem Akano
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Nicholas E Oyejide
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iguosadolo Nosamiefan
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iyanuoluwa Fred-Akintunwa
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kemi Adedotun-Sulaiman
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Farida B Brimmo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Babatunde B Adegboyega
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Courage Philip
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Richard A Adeleke
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Grace C Chukwu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Muhammad I Ahmed
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oludayo O Ope-Ewe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Shobi G Otitoola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olusola A Ogunsanya
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Mudasiru F Saibu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Ayotunde E Sijuwola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Grace O Ezekiel
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G John
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Julie O Akin-John
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwasemilogo O Akinlo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olanrewaju O Fayemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Testimony O Ipaye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Deborah C Nwodo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Abolade E Omoniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iyobosa B Omwanghe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Christabel A Terkuma
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Johnson Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olubukola Ayo-Ale
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Odia Ikponmwosa
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Ebo Benevolence
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Osiemi Blessing
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Airende Micheal
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - John O Aiyepada
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Omiunu Racheal
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Esumeh Rita
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Giwa E Rosemary
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Ekanem Anieno
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Yerumoh Edna
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Aire O Chris
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Mirabeau Y Tatfeng
- Department of Medical Laboratory Science, Niger Delta University, Amassoma, Bayelsa State, Nigeria
| | - Hannah E Omunakwe
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Rivers State, Nigeria
| | - Mienye Bob-Manuel
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Rivers State, Nigeria
| | - Rahaman A Ahmed
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Chika K Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Joseph O Shaibu
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Azuka Okwuraiwe
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Anthony E Ataga
- Molecular Laboratory, Regional Centre for Biotechnology and Bioresources Research, University of Port Harcourt, Port Harcourt, Rivers State, Nigeria
| | | | - Funmi Daramola
- Clinical Health, SPDC, Port Harcourt, Rivers State, Nigeria
| | | | - Akinwumi Fajola
- Regional Community Health, SPDC, Port Harcourt, Rivers State, Nigeria
| | | | - Julie J Ekpo
- Department of Medical Microbiology and Parasitology, University of Uyo, Uyo, Akwa Ibom State, Nigeria
| | - Anietie E Moses
- Department of Medical Microbiology and Parasitology, University of Uyo, Uyo, Akwa Ibom State, Nigeria
| | | | | | - Monilade Akinola
- WHO Polio Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | - Ibrahim M Kida
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Bamidele S Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Zara W Wudiri
- Department of Community Medicine, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | - Oluwapelumi O Adeyemi
- Department of Medical Microbiology and Parasitology. Faculty of Basic Clinical Sciences. College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | | | | | | | | | | | | | - Nwando G Mba
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Ewean C Omoruyi
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olasunkanmi Olisa
- Biorepository Clinical Virology Laboratory, University of Ibadan, Ibadan, Nigeria
| | - Olatunji K Akande
- Biorepository Clinical Virology Laboratory, University of Ibadan, Ibadan, Nigeria
| | - Ifeanyi E Nwafor
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Matthew A Ekeh
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Erim Ndoma
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Richard L Ewah
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Rosemary O Duruihuoma
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Augustine Abu
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Elizabeth Odeh
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Venatius Onyia
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Chiedozie K Ojide
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Sylvanus Okoro
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Daniel Igwe
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Emeka O Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kamran Khan
- Department of Medicine, University of Toronto, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Nnennaya A Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Collins N Ugwu
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kingsley N Ukwaja
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ngozi I Ugwu
- Haematology Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | | | | | | | - Galadima Gadzama
- Department of Medical Microbiology, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | | | | | | | - George Akpede
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Marycelin M Baba
- WHO Polio Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Femi Oladiji
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Rosemary Audu
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | | | - Adeola Fowotade
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | | | | | - Danny J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | | | | | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Anise N Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Onikepe A Folarin
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
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Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G. Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus Evol 2023; 9:vead010. [PMID: 36860641 PMCID: PMC9969415 DOI: 10.1093/ve/vead010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/06/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Bayesian phylogeographic inference is a powerful tool in molecular epidemiological studies, which enables reconstruction of the origin and subsequent geographic spread of pathogens. Such inference is, however, potentially affected by geographic sampling bias. Here, we investigated the impact of sampling bias on the spatiotemporal reconstruction of viral epidemics using Bayesian discrete phylogeographic models and explored different operational strategies to mitigate this impact. We considered the continuous-time Markov chain (CTMC) model and two structured coalescent approximations (Bayesian structured coalescent approximation [BASTA] and marginal approximation of the structured coalescent [MASCOT]). For each approach, we compared the estimated and simulated spatiotemporal histories in biased and unbiased conditions based on the simulated epidemics of rabies virus (RABV) in dogs in Morocco. While the reconstructed spatiotemporal histories were impacted by sampling bias for the three approaches, BASTA and MASCOT reconstructions were also biased when employing unbiased samples. Increasing the number of analyzed genomes led to more robust estimates at low sampling bias for the CTMC model. Alternative sampling strategies that maximize the spatiotemporal coverage greatly improved the inference at intermediate sampling bias for the CTMC model, and to a lesser extent, for BASTA and MASCOT. In contrast, allowing for time-varying population sizes in MASCOT resulted in robust inference. We further applied these approaches to two empirical datasets: a RABV dataset from the Philippines and a SARS-CoV-2 dataset describing its early spread across the world. In conclusion, sampling biases are ubiquitous in phylogeographic analyses but may be accommodated by increasing the sample size, balancing spatial and temporal composition in the samples, and informing structured coalescent models with reliable case count data.
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Affiliation(s)
| | | | | | | | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, 25-28 rue du Docteur Roux, Paris 75014, France,WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Université Paris Cité, 28 rue du Docteur Roux, Paris 75724, France
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43
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Ribeiro IP, Delatorre E, de Abreu FVS, dos Santos AAC, Furtado ND, Ferreira-de-Brito A, de Pina-Costa A, Neves MSAS, de Castro MG, Motta MDA, Brasil P, Lourenço-de-Oliveira R, Bonaldo MC. Ecological, Genetic, and Phylogenetic Aspects of YFV 2017-2019 Spread in Rio de Janeiro State. Viruses 2023; 15:v15020437. [PMID: 36851651 PMCID: PMC9961572 DOI: 10.3390/v15020437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/23/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
In Brazil, a yellow fever (YF) outbreak was reported in areas considered YF-free for decades. The low vaccination coverage and the increasing forest fragmentation, with the wide distribution of vector mosquitoes, have been related to yellow fever virus (YFV) transmission beyond endemic areas since 2016. Aiming to elucidate the molecular and phylogenetic aspects of YFV spread on a local scale, we generated 43 new YFV genomes sampled from humans, non-human primates (NHP), and primarily, mosquitoes from highly heterogenic areas in 15 localities from Rio de Janeiro (RJ) state during the YFV 2016-2019 outbreak in southeast Brazil. Our analysis revealed that the genetic diversity and spatial distribution of the sylvatic transmission of YFV in RJ originated from at least two introductions and followed two chains of dissemination, here named the YFV RJ-I and YFV RJ-II clades. They moved with similar dispersal speeds from the north to the south of the RJ state in parallel directions, separated by the Serra do Mar Mountain chain, with YFV RJ-I invading the north coast of São Paulo state. The YFV RJ-I clade showed a more significant heterogeneity across the entire polyprotein. The YFV RJ-II clade, with only two amino acid polymorphisms, mapped at NS1 (I1086V), present only in mosquitoes at the same locality and NS4A (I2176V), shared by all YFV clade RJ-II, suggests a recent clustering of YFV isolates collected from different hosts. Our analyses strengthen the role of surveillance, genomic analyses of YVF isolated from other hosts, and environmental studies into the strategies to forecast, control, and prevent yellow fever outbreaks.
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Affiliation(s)
- Ieda Pereira Ribeiro
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Edson Delatorre
- Laboratório de Genômica Evolutiva e Ambiental, Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre 29500-000, ES, Brazil
| | - Filipe Vieira Santos de Abreu
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
- Instituto Federal do Norte de Minas Gerais, Salinas 39560-000, MG, Brazil
| | - Alexandre Araújo Cunha dos Santos
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Nathália Dias Furtado
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Anielly Ferreira-de-Brito
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Anielle de Pina-Costa
- Laboratório de Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
- Faculdade de Medicina de Teresópolis, Centro Universitário Serra dos Órgãos, UNIFESO, Teresópolis 25955-001, RJ, Brazil
| | | | - Márcia Gonçalves de Castro
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Monique de Albuquerque Motta
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Patricia Brasil
- Laboratório de Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Ricardo Lourenço-de-Oliveira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
- Correspondence: (R.L.-d.-O.); (M.C.B.)
| | - Myrna Cristina Bonaldo
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
- Correspondence: (R.L.-d.-O.); (M.C.B.)
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Zhang G, Li B, Raghwani J, Vrancken B, Jia R, Hill SC, Fournié G, Cheng Y, Yang Q, Wang Y, Wang Z, Dong L, Pybus OG, Tian H. Bidirectional Movement of Emerging H5N8 Avian Influenza Viruses Between Europe and Asia via Migratory Birds Since Early 2020. Mol Biol Evol 2023; 40:msad019. [PMID: 36703230 PMCID: PMC9922686 DOI: 10.1093/molbev/msad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 01/28/2023] Open
Abstract
Migratory birds play a critical role in the rapid spread of highly pathogenic avian influenza (HPAI) H5N8 virus clade 2.3.4.4 across Eurasia. Elucidating the timing and pattern of virus transmission is essential therefore for understanding the spatial dissemination of these viruses. In this study, we surveyed >27,000 wild birds in China, tracked the year-round migration patterns of 20 bird species across China since 2006, and generated new HPAI H5N8 virus genomic data. Using this new data set, we investigated the seasonal transmission dynamics of HPAI H5N8 viruses across Eurasia. We found that introductions of HPAI H5N8 viruses to different Eurasian regions were associated with the seasonal migration of wild birds. Moreover, we report a backflow of HPAI H5N8 virus lineages from Europe to Asia, suggesting that Europe acts as both a source and a sink in the global HPAI virus transmission network.
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Affiliation(s)
- Guogang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Jayna Raghwani
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Ru Jia
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Guillaume Fournié
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Yanchao Cheng
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Qiqi Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Yuxin Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
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45
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Namuddu A, Seal S, van Brunschot S, Malka O, Kabaalu R, Morin S, Omongo C, Colvin J. Distribution of Bemisia tabaci in different agro-ecological regions in Uganda and the threat of vector-borne pandemics into new cassava growing areas. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2023.1068109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Previous studies in sub-Saharan Africa have showed the spread of cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) pandemics into different cassava growing regions by high Bemisia tabaci populations. Studies did indicate that there were stark differences in some whitefly species, yet they have not looked extensively across agroecologies. Members of B. tabaci species complex termed sub-Saharan Africa 1 (SSA1) and SSA2 have been linked to the spread of CMD and CBSD viruses. During the period of a severe CMD pandemic in the 1990s, SSA2 was the most predominant until the resurgence of SSA1, particularly SSA1-subgroup1 (SSA1-SG1) from the early 2000s to date. Cassava being a drought resilient crop has become an important food security crop and has been introduced into new areas and regions. Considering the role B. tabaci in the spread of cassava virus pandemics into neighboring regions, we investigated the genetic diversity and distribution of B. tabaci in nine different agro-ecological regions of Uganda in 2017. Adult whiteflies were collected from cassava and 33 other host plants from cassava-growing areas, those with limited cassava and areas with no cassava, where it is being introduced as a food security crop. The partial sequences of the mitochondrial cytochrome oxidase 1 (mtCO1) gene (657 bp) were used to determine the phylogenetic relationships between the sampled B. tabaci. Cassava B. tabaci SSA1 (-SG1, -SG2, -Hoslundia (previously called SSA1-SG1/2), -SG3), SSA2 and SSA3; non-cassava B. tabaci SSA6, SSA10, SSA11, SSA12, SSA13, MED-ASL, MED-Q1, MEAM1, Indian Ocean; and other Bemisia species, Bemisia afer and Bemisia Uganda1 were identified in the study. SSA3, one of the key B. tabaci species that occurs on cassava in West Africa, was identified for the first time in Uganda. The SSA1-SG1 was widely distributed, predominated on cassava and was found on 17 other host-plants. The ability of SSA1-SG1 to exist in environments with limited or no cassava growing poses the risk of continued spread of virus pandemics. Therefore, measures must be put in place to prevent the introduction of diseased materials into new areas, since the vectors exist.
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46
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Paliocha M, Schubert M, Preston JC, Fjellheim S. Independent recruitment of FRUITFULL-like transcription factors in the convergent origins of vernalization-responsive grass flowering. Mol Phylogenet Evol 2023; 179:107678. [PMID: 36535518 DOI: 10.1016/j.ympev.2022.107678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Flowering in response to low temperatures (vernalization) has evolved multiple times independently across angiosperms as an adaptation to match reproductive development with the short growing season of temperate habitats. Despite the context of a generally conserved flowering time network, evidence suggests that the genes underlying vernalization responsiveness are distinct across major plant clades. Whether different or similar mechanisms underlie vernalization-induced flowering at narrower (e.g., family-level) phylogenetic scales is not well understood. To test the hypothesis that vernalization responsiveness has evolved convergently in temperate species of the grass family (Poaceae), we carried out flowering time experiments with and without vernalization in several representative species from different subfamilies. We then determined the likelihood that vernalization responsiveness evolved through parallel mechanisms by quantifying the response of Pooideae vernalization pathway FRUITFULL (FUL)-like genes to extended periods of cold. Our results demonstrate that vernalization-induced flowering has evolved multiple times independently in at least five grass subfamilies, and that different combinations of FUL-like genes have been recruited to this pathway on several occasions.
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Affiliation(s)
- Martin Paliocha
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, N-1432 Ås, Norway.
| | - Marian Schubert
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, N-1432 Ås, Norway.
| | - Jill Christine Preston
- Department of Plant Biology, College of Agriculture and Life Sciences, The University of Vermont, Burlington, VT 05405, USA.
| | - Siri Fjellheim
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, N-1432 Ås, Norway.
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47
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Morales ME, Goloboff PA. New TNT routines for parallel computing with MPI. Mol Phylogenet Evol 2023; 178:107643. [PMID: 36216302 DOI: 10.1016/j.ympev.2022.107643] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 11/21/2022]
Abstract
Phylogenetic inference, which involves time-consuming calculations, is a field where parallelization can speed up the resolution of many problems. TNT (a widely used program for phylogenetic analysis under parsimony) allows parallelization under the PVM system (Parallel Virtual Machine). However, as the basic aspects of the implementation remain unpublished, few studies have taken advantage of the parallelization routines of TNT. In addition, the PVM system is deprecated by many system administrators. One of the most common standards for high performance computing is now MPI (Message Passing Interface). To facilitate the use of the parallel analyses offered by TNT, this paper describes the basic aspects of the implementation, as well as a port of the parallelization interface of TNT into MPI. The use of the new routines is illustrated by reanalysis of seven significant datasets, either recent phylogenomic datasets with many characters (up to 2,509,064 characters) or datasets with large numbers of taxa (up to 13,921 taxa). Versions of TNT including the MPI functionality are available at: http://www.lillo.org.ar/phylogeny/tnt/.
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Affiliation(s)
- Martín E Morales
- Unidad Ejecutora Lillo (Fundación Miguel Lillo - Consejo Nacional de Investigaciones Científicas y Técnicas), Miguel Lillo 251, S. M. de Tucumán 4000, Argentina
| | - Pablo A Goloboff
- Unidad Ejecutora Lillo (Fundación Miguel Lillo - Consejo Nacional de Investigaciones Científicas y Técnicas), Miguel Lillo 251, S. M. de Tucumán 4000, Argentina; American Museum of Natural History, Central Park West at 79th Street, New York, United States.
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48
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Goatley CHR, Tornabene L. Tempestichthys bettyae, a new genus and species of ocean sleeper (Gobiiformes, Thalasseleotrididae) from the central Coral Sea. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2090633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Christopher H. R. Goatley
- Function, Evolution and Anatomy Research (FEAR) Lab, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia
- School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, USA
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, USA
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49
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Rojas-Cruz AF, Gallego-Gómez JC, Bermúdez-Santana CI. RNA structure-altering mutations underlying positive selection on Spike protein reveal novel putative signatures to trace crossing host-species barriers in Betacoronavirus. RNA Biol 2022; 19:1019-1044. [PMID: 36102368 PMCID: PMC9481089 DOI: 10.1080/15476286.2022.2115750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Similar to other RNA viruses, the emergence of Betacoronavirus relies on cross-species viral transmission, which requires careful health surveillance monitoring of protein-coding information as well as genome-wide analysis. Although the evolutionary jump from natural reservoirs to humans may be mainly traced-back by studying the effect that hotspot mutations have on viral proteins, it is largely unexplored if other impacts might emerge on the structured RNA genome of Betacoronavirus. In this survey, the protein-coding and viral genome architecture were simultaneously studied to uncover novel insights into cross-species horizontal transmission events. We analysed 1,252,952 viral genomes of SARS-CoV, MERS-CoV, and SARS-CoV-2 distributed across the world in bats, intermediate animals, and humans to build a new landscape of changes in the RNA viral genome. Phylogenetic analyses suggest that bat viruses are the most closely related to the time of most recent common ancestor of Betacoronavirus, and missense mutations in viral proteins, mainly in the S protein S1 subunit: SARS-CoV (G > T; A577S); MERS-CoV (C > T; S746R and C > T; N762A); and SARS-CoV-2 (A > G; D614G) appear to have driven viral diversification. We also found that codon sites under positive selection on S protein overlap with non-compensatory mutations that disrupt secondary RNA structures in the RNA genome complement. These findings provide pivotal factors that might be underlying the eventual jumping the species barrier from bats to intermediate hosts. Lastly, we discovered that nearly half of the Betacoronavirus genomes carry highly conserved RNA structures, and more than 90% of these RNA structures show negative selection signals, suggesting essential functions in the biology of Betacoronavirus that have not been investigated to date. Further research is needed on negatively selected RNA structures to scan for emerging functions like the potential of coding virus-derived small RNAs and to develop new candidate antiviral therapeutic strategies.
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Affiliation(s)
- Alexis Felipe Rojas-Cruz
- Theoretical and Computational RNomics Group, Department of Biology, Faculty of Sciences, National University of Colombia, Bogota Colombia
| | - Juan Carlos Gallego-Gómez
- Molecular and Translational Medicine Group, Faculty of Medicine, University of Antioquia, Medellin Colombia
| | - Clara Isabel Bermúdez-Santana
- Theoretical and Computational RNomics Group, Department of Biology, Faculty of Sciences, National University of Colombia, Bogota Colombia
- Center of Excellence in Scientific Computing, National University of Colombia, Bogota Colombia
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50
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Ghorbani A, Khataeipour SJ, Solbakken MH, Huebert DNG, Khoddami M, Eslamloo K, Collins C, Hori T, Jentoft S, Rise ML, Larijani M. Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish. BMC Biol 2022; 20:293. [PMID: 36575514 PMCID: PMC9795746 DOI: 10.1186/s12915-022-01489-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/30/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Antibody affinity maturation in vertebrates requires the enzyme activation-induced cytidine deaminase (AID) which initiates secondary antibody diversification by mutating the immunoglobulin loci. AID-driven antibody diversification is conserved across jawed vertebrates since bony and cartilaginous fish. Two exceptions have recently been reported, the Pipefish and Anglerfish, in which the AID-encoding aicda gene has been lost. Both cases are associated with unusual reproductive behavior, including male pregnancy and sexual parasitism. Several cold water fish in the Atlantic cod (Gadinae) family carry an aicda gene that encodes for a full-length enzyme but lack affinity-matured antibodies and rely on antibodies of broad antigenic specificity. Hence, we examined the functionality of their AID. RESULTS By combining genomics, transcriptomics, immune responsiveness, and functional enzymology of AID from 36 extant species, we demonstrate that AID of that Atlantic cod and related fish have extremely lethargic or no catalytic activity. Through ancestral reconstruction and functional enzymology of 71 AID enzymes, we show that this enzymatic inactivation likely took place relatively recently at the emergence of the true cod family (Gadidae) from their ancestral Gadiformes order. We show that this AID inactivation is not only concordant with the previously shown loss of key adaptive immune genes and expansion of innate and cell-based immune genes in the Gadiformes but is further reflected in the genomes of these fish in the form of loss of AID-favored sequence motifs in their immunoglobulin variable region genes. CONCLUSIONS Recent demonstrations of the loss of the aicda gene in two fish species challenge the paradigm that AID-driven secondary antibody diversification is absolutely conserved in jawed vertebrates. These species have unusual reproductive behaviors forming an evolutionary pressure for a certain loss of immunity to avoid tissue rejection. We report here an instance of catalytic inactivation and functional loss of AID rather than gene loss in a conventionally reproducing vertebrate. Our data suggest that an expanded innate immunity, in addition to lower pathogenic pressures in a cold environment relieved the pressure to maintain robust secondary antibody diversification. We suggest that in this unique scenario, the AID-mediated collateral genome-wide damage would form an evolutionary pressure to lose AID function.
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Affiliation(s)
- Atefeh Ghorbani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - S. Javad Khataeipour
- grid.25055.370000 0000 9130 6822Department of Computer Science, Faculty of Science, Memorial University of Newfoundland, St. John’s, Canada
| | - Monica H. Solbakken
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David N. G. Huebert
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Minasadat Khoddami
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Khalil Eslamloo
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Cassandra Collins
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Tiago Hori
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Sissel Jentoft
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Matthew L. Rise
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Mani Larijani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
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