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Chen S, Shang K, Chen J, Yu Z, Wei Y, He L, Ding K. Global distribution, cross-species transmission, and receptor binding of canine parvovirus-2: Risks and implications for humans. Sci Total Environ 2024; 930:172307. [PMID: 38599392 DOI: 10.1016/j.scitotenv.2024.172307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/25/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024]
Abstract
For canine parvovirus -2 (CPV-2), a zoonotic virus capable of cross-species transmission in animals, the amino acid changes of capsid protein VP2 are key factors when binding to other species' transferrin receptors (TfR). CPV-2 variants can spread from felines and canines, for example, to Carnivora, Artiodactyla, and Pholidota species, and CPV-2c variants are essential to spread from Carnivora to Artiodactyla and Pholidota species in particular. In our study, a CPV-2a variant maintained a relatively stable trend, and the proportion of CPV-2c gradually rose from 1980 to 2021. The VP2 amino acid sequence analysis showed that five amino acid mutations at 426E/D, 305H/D, and 297S may be necessary for the virus to bind to different host receptors. Meanwhile, receptor-binding loop regions and amino acid sites 87 L, 93 N, 232I, and 305Y were associated with CPV-2 cross-species transmission. The homology of TfRs in different hosts infected with CPV-2 ranged from 77.2 % to 99.0 %, and from pig to feline, canine, and humans was 80.7 %, 80.4 %, and 77.2 %, respectively. The amino acid residues of TfRs involved in the viral binding in those hosts are highly conserved, which suggests that CPV-2 may be capable of pig-to-human transmission. Our analysis of the origin, evolutionary trend, cross-species transmission dynamics, and genetic characteristics of CPV-2 when binding to host receptors provides a theoretical basis for further research on CPV-2's mechanism of cross-species transmission and for establishing an early warning and monitoring mechanism for the possible threat of CPV-2 to animal-human public security.
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Affiliation(s)
- Songbiao Chen
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang 471023, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, Henan, China
| | - Ke Shang
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang 471023, China
| | - Jian Chen
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang 471023, China
| | - Zuhua Yu
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang 471023, China
| | - Ying Wei
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang 471023, China
| | - Lei He
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang 471023, China.
| | - Ke Ding
- College of Animal Science and Technology/Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471023, China; Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang 471003, China; The Key Lab of Animal Disease and Public Health, Henan University of Science and Technology, Luoyang 471023, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, Henan, China.
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2
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Qiu X, Wang F, Sha A. Infection and transmission of henipavirus in animals. Comp Immunol Microbiol Infect Dis 2024; 109:102183. [PMID: 38640700 DOI: 10.1016/j.cimid.2024.102183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Henipavirus (HNV) is well known for two zoonotic viruses in the genus, Hendra virus (HeV) and Nipah virus (NiV), which pose serious threat to human and animal health. In August 2022, a third zoonotic virus in the genus Henipavirus, Langya virus (LayV), was discovered in China. The emergence of HeV, NiV, and LayV highlights the persistent threat of HNV to human and animal health. In addition to the above three HNVs, new species within this genus are still being discovered. Although they have not yet caused a pandemic in humans or livestock, they still have the risk of spillover as a potential threat to the health of humans and animals. It's important to understand the infection and transmission of different HNV in animals for the prevention and control of current or future HNV epidemics. Therefore, this review mainly summarizes the animal origin, animal infection and transmission of HNV that have been found worldwide, and further analyzes and summarizes the rules of infection and transmission, so as to provide a reference for relevant scientific researchers. Furthermore, it can provide a direction for epidemic prevention and control, and animal surveillance to reduce the risk of the global pandemic of HNV.
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Affiliation(s)
- Xinyu Qiu
- School of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404120, China
| | - Feng Wang
- School of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404120, China
| | - Ailong Sha
- School of Teacher Education, Chongqing Three Gorges University, Chongqing 404120, China.
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3
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Akoi Boré J, Timothy JWS, Tipton T, Kekoura I, Hall Y, Hood G, Longet S, Fornace K, Lucien MS, Fehling SK, Koivogui BK, Coggins SA, Laing ED, Broder CC, Magassouba NF, Strecker T, Rossman J, Konde K, Carroll MW. Serological evidence of zoonotic filovirus exposure among bushmeat hunters in Guinea. Nat Commun 2024; 15:4171. [PMID: 38755147 PMCID: PMC11099012 DOI: 10.1038/s41467-024-48587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Human Ebola virus (EBOV) outbreaks caused by persistent EBOV infection raises questions on the role of zoonotic spillover in filovirus epidemiology. To characterise filovirus zoonotic exposure, we collected cross-sectional serum samples from bushmeat hunters (n = 498) in Macenta Prefecture Guinea, adjacent to the index site of the 2013 EBOV-Makona spillover event. We identified distinct immune signatures (20/498, 4.0%) to multiple EBOV antigens (GP, NP, VP40) using stepwise ELISA and Western blot analysis and, live EBOV neutralisation (5/20; 25%). Using comparative serological data from PCR-confirmed survivors of the 2013-2016 EBOV outbreak, we demonstrated that most signatures (15/20) were not plausibly explained by prior EBOV-Makona exposure. Subsequent data-driven modelling of EBOV immunological outcomes to remote-sensing environmental data also revealed consistent associations with intact closed canopy forest. Together our findings suggest exposure to other closely related filoviruses prior to the 2013-2016 West Africa epidemic and highlight future surveillance priorities.
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Affiliation(s)
| | - Joseph W S Timothy
- Faulty of Infectious & Tropical Diseases, London School of Hygiene Tropical Medicine, London, UK
| | - Tom Tipton
- Centre for Human Genetics & Pandemic Sciences Inst, University of Oxford, Oxford, UK
| | - Ifono Kekoura
- Ministère de la Santé et de l'hygiène publique, Conakry, Guinea
| | - Yper Hall
- UK Health Security Agency, Porton Down, UK
| | - Grace Hood
- Centre for Human Genetics & Pandemic Sciences Inst, University of Oxford, Oxford, UK
| | - Stephanie Longet
- Centre for Human Genetics & Pandemic Sciences Inst, University of Oxford, Oxford, UK
| | - Kimberly Fornace
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | | | | | | | - Si'Ana A Coggins
- Department of Microbiology and Immunology, Uniformed Services University, MD, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University, MD, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, MD, USA
| | | | - Thomas Strecker
- Institute of Virology, Philipps University, Marburg, Germany
| | - Jeremy Rossman
- School of Bioscience, University of Kent, Canterbury, UK
| | - Kader Konde
- Centre for Training and Research on Priority Diseases including Malaria in Guinea, Conakry, Guinea
| | - Miles W Carroll
- Centre for Human Genetics & Pandemic Sciences Inst, University of Oxford, Oxford, UK.
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Weary TE, Pappas T, Tusiime P, Tuhaise S, Otali E, Emery Thompson M, Ross E, Gern JE, Goldberg TL. Common cold viruses circulating in children threaten wild chimpanzees through asymptomatic adult carriers. Sci Rep 2024; 14:10431. [PMID: 38714841 PMCID: PMC11076286 DOI: 10.1038/s41598-024-61236-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
Reverse zoonotic respiratory diseases threaten great apes across Sub-Saharan Africa. Studies of wild chimpanzees have identified the causative agents of most respiratory disease outbreaks as "common cold" paediatric human pathogens, but reverse zoonotic transmission pathways have remained unclear. Between May 2019 and August 2021, we conducted a prospective cohort study of 234 children aged 3-11 years in communities bordering Kibale National Park, Uganda, and 30 adults who were forest workers and regularly entered the park. We collected 2047 respiratory symptoms surveys to quantify clinical severity and simultaneously collected 1989 nasopharyngeal swabs approximately monthly for multiplex viral diagnostics. Throughout the course of the study, we also collected 445 faecal samples from 55 wild chimpanzees living nearby in Kibale in social groups that have experienced repeated, and sometimes lethal, epidemics of human-origin respiratory viral disease. We characterized respiratory pathogens in each cohort and examined statistical associations between PCR positivity for detected pathogens and potential risk factors. Children exhibited high incidence rates of respiratory infections, whereas incidence rates in adults were far lower. COVID-19 lockdown in 2020-2021 significantly decreased respiratory disease incidence in both people and chimpanzees. Human respiratory infections peaked in June and September, corresponding to when children returned to school. Rhinovirus, which caused a 2013 outbreak that killed 10% of chimpanzees in a Kibale community, was the most prevalent human pathogen throughout the study and the only pathogen present at each monthly sampling, even during COVID-19 lockdown. Rhinovirus was also most likely to be carried asymptomatically by adults. Although we did not detect human respiratory pathogens in the chimpanzees during the cohort study, we detected human metapneumovirus in two chimpanzees from a February 2023 outbreak that were genetically similar to viruses detected in study participants in 2019. Our data suggest that respiratory pathogens circulate in children and that adults become asymptomatically infected during high-transmission times of year. These asymptomatic adults may then unknowingly carry the pathogens into forest and infect chimpanzees. This conclusion, in turn, implies that intervention strategies based on respiratory symptoms in adults are unlikely to be effective for reducing reverse zoonotic transmission of respiratory viruses to chimpanzees.
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Affiliation(s)
- Taylor E Weary
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, USA
| | - Tressa Pappas
- Department of Paediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | | | - Emily Otali
- The Kasiisi Project, Fort Portal, Uganda
- Kibale Chimpanzee Project, Fort Portal, Uganda
| | - Melissa Emery Thompson
- Kibale Chimpanzee Project, Fort Portal, Uganda
- Department of Anthropology, University of New Mexico, Albuquerque, NM, USA
| | | | - James E Gern
- Department of Paediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, USA.
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5
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Mohapatra RK, Singh PK, Branda F, Mishra S, Kutikuppala LVS, Suvvari TK, Kandi V, Ansari A, Desai DN, Alfaresi M, Kaabi NAA, Fares MAA, Garout M, Halwani MA, Alissa M, Rabaan AA. Transmission dynamics, complications and mitigation strategies of the current mpox outbreak: A comprehensive review with bibliometric study. Rev Med Virol 2024; 34:e2541. [PMID: 38743385 DOI: 10.1002/rmv.2541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
As the mankind counters the ongoing COVID-19 pandemic by the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), it simultaneously witnesses the emergence of mpox virus (MPXV) that signals at global spread and could potentially lead to another pandemic. Although MPXV has existed for more than 50 years now with most of the human cases being reported from the endemic West and Central African regions, the disease is recently being reported in non-endemic regions too that affect more than 50 countries. Controlling the spread of MPXV is important due to its potential danger of a global spread, causing severe morbidity and mortality. The article highlights the transmission dynamics, zoonosis potential, complication and mitigation strategies for MPXV infection, and concludes with suggested 'one health' approach for better management, control and prevention. Bibliometric analyses of the data extend the understanding and provide leads on the research trends, the global spread, and the need to revamp the critical research and healthcare interventions. Globally published mpox-related literature does not align well with endemic areas/regions of occurrence which should ideally have been the scenario. Such demographic and geographic gaps between the location of the research work and the endemic epicentres of the disease need to be bridged for greater and effective translation of the research outputs to pubic healthcare systems, it is suggested.
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Affiliation(s)
- Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, Odisha, India
| | - Puneet K Singh
- School of Biotechnology, Campus-11, KIIT Deemed-to-be-University, Bhubaneswar, Odisha, India
| | - Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Snehasish Mishra
- School of Biotechnology, Campus-11, KIIT Deemed-to-be-University, Bhubaneswar, Odisha, India
| | | | - Tarun K Suvvari
- Department of Medicine, Rangaraya Medical College, Kakinada, Andhra Pradesh, India
| | - Venkataramana Kandi
- Department of Microbiology, Prathima Institute of Medical Sciences, Karimnagar, Telangana, India
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana, India
| | - Dhruv N Desai
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mubarak Alfaresi
- Department of Microbiology, National Reference Laboratory, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Pathology, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nawal A Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi, United Arab Emirates
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, United Arab Emirates
| | - Mona A Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Al Baha, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
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6
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Umar S, Muhammad S, Gao D, Chen P. SARS-CoV-2 Reverse Zoonosis Among Cats in China: A One Health Investigation. Influenza Other Respir Viruses 2024; 18:e13306. [PMID: 38698407 PMCID: PMC11065897 DOI: 10.1111/irv.13306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Affiliation(s)
- Sajid Umar
- Global Health Research Center (GHRC)Duke Kunshan UniversitySuzhouChina
- Division of Natural and Applied Sciences (DNAS)Duke Kunshan UniversitySuzhouChina
| | - Shaban Muhammad
- Global Health Research Center (GHRC)Duke Kunshan UniversitySuzhouChina
- Division of Natural and Applied Sciences (DNAS)Duke Kunshan UniversitySuzhouChina
| | - Di Gao
- MSD Animal Health ShanghaiShanghaiChina
| | - Pu Chen
- MSD Animal Health ShanghaiShanghaiChina
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7
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Lira GS, Ota VA, Melo MQS, Castiñeiras ACP, Leitão IC, Silva BO, Mariani D, Gonçalves CCA, Ribeiro LJ, Halpern M, Abreu TF, Carneiro FA, Scheid HT, Souza LAV, Rodrigues DGM, Cruz NVG, Cony A, Carvalho S, de Lima LPO, Viala VL, Caldas LA, de Souza W, Higa LM, Voloch CM, Ferreira OC, Damaso CR, Galliez RM, Faffe DS, Tanuri A, Castiñeiras TMPP. Mpox outbreak in Rio de Janeiro, Brazil: A translational approach. J Med Virol 2024; 96:e29621. [PMID: 38654686 DOI: 10.1002/jmv.29621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Mpox is a zoonotic disease historically reported in Africa. Since 2003, limited outbreaks have occurred outside Africa. In 2022, the global spread of cases with sustained interhuman transmission and unusual disease features raised public health concerns. We explore the mpox outbreak in Rio de Janeiro (RJ) state, Brazil, in an observational study of mpox-suspected cases from June to December 2022. Data collection relied on a public healthcare notification form. Diagnosis was determined by MPXV-PCR. In 46 confirmed cases, anti-OPXV IgG was determined by ELISA, and seven MPXV genomes were sequenced. A total of 3095 cases were included, 816 (26.3%) with positive MPXV-PCR results. Most positive cases were men in their 30 s and MSM. A total of 285 (34.9%) MPXV-PCR+ patients live with HIV. Eight were coinfected with varicella-zoster virus. Anogenital lesions and adenomegaly were associated with the diagnosis of mpox. Females and individuals under 18 represented 9.4% and 5.4% of all confirmed cases, respectively, showing higher PCR cycle threshold (Ct) values and fewer anogenital lesions compared to adult men. Anti-OPXV IgG was detected in 29/46 (63.0%) patients. All analyzed sequences belonged to clade IIb. In RJ state, mpox presented a diverse clinical picture, represented mainly by mild cases with low complication rates and prominent genital involvement. The incidence in females and children was higher than usually reported. The observation of a bimodal distribution of Ct values, with few positive results, may suggest the need to review the diagnostic criteria in these groups.
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Affiliation(s)
- Guilherme S Lira
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Victor A Ota
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Mariana Q S Melo
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Anna C P Castiñeiras
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Isabela C Leitão
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Bianca O Silva
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Diana Mariani
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Cássia C A Gonçalves
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Liane J Ribeiro
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Marcia Halpern
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Thalita F Abreu
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Fabiana A Carneiro
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Núcleo Multidisciplinar de Pesquisas em Biologia-NUMPEX-BIO, Campus Duque de Caxias Geraldo Cidade, Universidade Federal do Rio de Janeiro, Duque de Caxias, Brasil
| | - Helena T Scheid
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Leonardo A V Souza
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Débora G M Rodrigues
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Nádia V G Cruz
- Laboratório de Pesquisa e Biodefesa, Instituto de Biologia do Exército, Rio de Janeiro, Brasil
| | - Andrea Cony
- Laboratório Central Noel Nutes, Secretaria de Estado de Saúde do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Silvia Carvalho
- Superintendência de Emergências Em Saúde Pública, Secretaria de Estado de Saúde do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Loyze P O de Lima
- Centro de Vigilância Genômica e Avaliação Sorológica CeVIVAS, Instituto Butantan, São Paulo, Brasil
| | - Vincent L Viala
- Centro de Vigilância Genômica e Avaliação Sorológica CeVIVAS, Instituto Butantan, São Paulo, Brasil
| | - Lucio A Caldas
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Núcleo Multidisciplinar de Pesquisas em Biologia-NUMPEX-BIO, Campus Duque de Caxias Geraldo Cidade, Universidade Federal do Rio de Janeiro, Duque de Caxias, Brasil
| | - Wanderley de Souza
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem (INBEB) and Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO)s, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Luiza M Higa
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Carolina M Voloch
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Orlando C Ferreira
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Clarissa R Damaso
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Rafael M Galliez
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Débora S Faffe
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Amilcar Tanuri
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Terezinha M P P Castiñeiras
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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8
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Eskew EA, Bird BH, Ghersi BM, Bangura J, Basinski AJ, Amara E, Bah MA, Kanu MC, Kanu OT, Lavalie EG, Lungay V, Robert W, Vandi MA, Fichet-Calvet E, Nuismer SL. Reservoir displacement by an invasive rodent reduces Lassa virus zoonotic spillover risk. Nat Commun 2024; 15:3589. [PMID: 38678025 PMCID: PMC11055883 DOI: 10.1038/s41467-024-47991-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
The black rat (Rattus rattus) is a globally invasive species that has been widely introduced across Africa. Within its invasive range in West Africa, R. rattus may compete with the native rodent Mastomys natalensis, the primary reservoir host of Lassa virus, a zoonotic pathogen that kills thousands annually. Here, we use rodent trapping data from Sierra Leone and Guinea to show that R. rattus presence reduces M. natalensis density within the human dwellings where Lassa virus exposure is most likely to occur. Further, we integrate infection data from M. natalensis to demonstrate that Lassa virus zoonotic spillover risk is lower at sites with R. rattus. While non-native species can have numerous negative effects on ecosystems, our results suggest that R. rattus invasion has the indirect benefit of decreasing zoonotic spillover of an endemic pathogen, with important implications for invasive species control across West Africa.
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Affiliation(s)
- Evan A Eskew
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA.
| | - Brian H Bird
- One Health Institute, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Bruno M Ghersi
- One Health Institute, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | | | - Andrew J Basinski
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | | | - Mohamed A Bah
- Ministry of Agriculture and Forestry, Freetown, Sierra Leone
| | | | | | | | | | | | | | | | - Scott L Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
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9
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Seekings AH, Shipley R, Byrne AMP, Shukla S, Golding M, Amaya-Cuesta J, Goharriz H, Vitores AG, Lean FZX, James J, Núñez A, Breed A, Frost A, Balzer J, Brown IH, Brookes SM, McElhinney LM. Detection of SARS-CoV-2 Delta Variant (B.1.617.2) in Domestic Dogs and Zoo Tigers in England and Jersey during 2021. Viruses 2024; 16:617. [PMID: 38675958 PMCID: PMC11053977 DOI: 10.3390/v16040617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Reverse zoonotic transmission events of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been described since the start of the pandemic, and the World Organisation for Animal Health (WOAH) designated the detection of SARS-CoV-2 in animals a reportable disease. Eighteen domestic and zoo animals in Great Britain and Jersey were tested by APHA for SARS-CoV-2 during 2020-2023. One domestic cat (Felis catus), three domestic dogs (Canis lupus familiaris), and three Amur tigers (Panthera tigris altaica) from a zoo were confirmed positive during 2020-2021 and reported to the WOAH. All seven positive animals were linked with known SARS-CoV-2 positive human contacts. Characterisation of the SARS-CoV-2 variants by genome sequencing indicated that the cat was infected with an early SARS-CoV-2 lineage. The three dogs and three tigers were infected with the SARS-CoV-2 Delta variant of concern (B.1.617.2). The role of non-human species in the onward transmission and emergence of new variants of SARS-CoV-2 remain poorly defined. Continued surveillance of SARS-CoV-2 in relevant domestic and captive animal species with high levels of human contact is important to monitor transmission at the human-animal interface and to assess their role as potential animal reservoirs.
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Affiliation(s)
- Amanda H. Seekings
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- National Reference Laboratory for SARS-CoV-2 in Animals, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Rebecca Shipley
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- National Reference Laboratory for SARS-CoV-2 in Animals, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Alexander M. P. Byrne
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- Worldwide Influenza Centre, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
| | - Shweta Shukla
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- National Reference Laboratory for SARS-CoV-2 in Animals, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Megan Golding
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Joan Amaya-Cuesta
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Hooman Goharriz
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- National Reference Laboratory for SARS-CoV-2 in Animals, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Ana Gómez Vitores
- Department of Pathology and Animal Sciences, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Fabian Z. X. Lean
- Department of Pathology and Animal Sciences, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Joe James
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Alejandro Núñez
- Department of Pathology and Animal Sciences, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Alistair Breed
- Government of Jersey, Infrastructure Housing and Environment, Howard Davis Farm, La Route de la Trinité, Trinity, Jersey JE3 5JP, UK
| | - Andrew Frost
- One Health, Animal Health and Welfare Advice Team, Animal and Plant Health Agency, Nobel House, 17 Smith Square, London SW1P 3JR, UK
| | - Jörg Balzer
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Humboldtstraße 2, 70806 Kornwestheim, Germany
| | - Ian H. Brown
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Sharon M. Brookes
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Lorraine M. McElhinney
- Department of Virology, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- National Reference Laboratory for SARS-CoV-2 in Animals, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
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10
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Liu B, Zhao P, Xu P, Han Y, Wang Y, Chen L, Wu Z, Yang J. A comprehensive dataset of animal-associated sarbecoviruses. Sci Data 2023; 10:681. [PMID: 37805633 PMCID: PMC10560225 DOI: 10.1038/s41597-023-02558-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/11/2023] [Indexed: 10/09/2023] Open
Abstract
Zoonotic spillover of sarbecoviruses (SarbeCoVs) from non-human animals to humans under natural conditions has led to two large-scale pandemics, the severe acute respiratory syndrome (SARS) pandemic in 2003 and the ongoing COVID-19 pandemic. Knowledge of the genetic diversity, geographical distribution, and host specificity of SarbeCoVs is therefore of interest for pandemic surveillance and origin tracing of SARS-CoV and SARS-CoV-2. This study presents a comprehensive repository of publicly available animal-associated SarbeCoVs, covering 1,535 viruses identified from 63 animal species distributed in 43 countries worldwide (as of February 14,2023). Relevant meta-information, such as host species, sampling time and location, was manually curated and included in the dataset to facilitate further research on the potential patterns of viral diversity and ecological characteristics. In addition, the dataset also provides well-annotated sequence sets of receptor-binding domains (RBDs) and receptor-binding motifs (RBMs) for the scientific community to highlight the potential determinants of successful cross-species transmission that could be aid in risk estimation and strategic design for future emerging infectious disease control and prevention.
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Affiliation(s)
- Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Peng Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Panpan Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Yelin Han
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Yuyang Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
| | - Zhiqiang Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
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11
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Brook CE, Rozins C, Guth S, Boots M. Reservoir host immunology and life history shape virulence evolution in zoonotic viruses. PLoS Biol 2023; 21:e3002268. [PMID: 37676899 PMCID: PMC10484437 DOI: 10.1371/journal.pbio.3002268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 07/21/2023] [Indexed: 09/09/2023] Open
Abstract
The management of future pandemic risk requires a better understanding of the mechanisms that determine the virulence of emerging zoonotic viruses. Meta-analyses suggest that the virulence of emerging zoonoses is correlated with but not completely predictable from reservoir host phylogeny, indicating that specific characteristics of reservoir host immunology and life history may drive the evolution of viral traits responsible for cross-species virulence. In particular, bats host viruses that cause higher case fatality rates upon spillover to humans than those derived from any other mammal, a phenomenon that cannot be explained by phylogenetic distance alone. In order to disentangle the fundamental drivers of these patterns, we develop a nested modeling framework that highlights mechanisms that underpin the evolution of viral traits in reservoir hosts that cause virulence following cross-species emergence. We apply this framework to generate virulence predictions for viral zoonoses derived from diverse mammalian reservoirs, recapturing trends in virus-induced human mortality rates reported in the literature. Notably, our work offers a mechanistic hypothesis to explain the extreme virulence of bat-borne zoonoses and, more generally, demonstrates how key differences in reservoir host longevity, viral tolerance, and constitutive immunity impact the evolution of viral traits that cause virulence following spillover to humans. Our theoretical framework offers a series of testable questions and predictions designed to stimulate future work comparing cross-species virulence evolution in zoonotic viruses derived from diverse mammalian hosts.
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Affiliation(s)
- Cara E. Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Carly Rozins
- Department of Science, Technology, and Society, York University, Toronto, Canada
| | - Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Biosciences, University of Exeter, Penryn, United Kingdom
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12
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Kareinen L, Airas N, Kotka ST, Masika MM, Aaltonen K, Anzala O, Ogola J, Webala PW, Vapalahti O, Sironen T, Forbes KM. No Substantial Histopathologic Changes in Mops condylurus Bats Naturally Infected with Bombali Virus, Kenya. Emerg Infect Dis 2023; 29:1029-1032. [PMID: 37081584 PMCID: PMC10124661 DOI: 10.3201/eid2905.221336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
We found similar mild perivascular inflammation in lungs of Bombali virus-positive and -negative Mops condylurus bats in Kenya, indicating the virus is well-tolerated. Our findings indicate M. condylurus bats may be a reservoir host for Bombali virus. Increased surveillance of these bats will be important to reduce potential virus spread.
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13
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Cohen AA, van Doremalen N, Greaney AJ, Andersen H, Sharma A, Starr TN, Keeffe JR, Fan C, Schulz JE, Gnanapragasam PNP, Kakutani LM, West AP, Saturday G, Lee YE, Gao H, Jette CA, Lewis MG, Tan TK, Townsend AR, Bloom JD, Munster VJ, Bjorkman PJ. Mosaic RBD nanoparticles protect against challenge by diverse sarbecoviruses in animal models. Science 2022; 377:eabq0839. [PMID: 35857620 PMCID: PMC9273039 DOI: 10.1126/science.abq0839] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/29/2022] [Indexed: 12/12/2022]
Abstract
To combat future severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic nanoparticles that present randomly arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against epitopes that are conserved and relatively occluded rather than variable, immunodominant, and exposed. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD nanoparticles in mice and macaques and observed stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains, including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants, including Omicrons, and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest that mosaic-8 RBD nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.
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Affiliation(s)
- Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | | | | | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jonathan E. Schulz
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | | | - Leesa M. Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Greg Saturday
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Tiong K. Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Alain R. Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Chinese Academy of Medical Sciences, Oxford Institute, University of Oxford, Oxford OX3 9DS, UK
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Vincent J. Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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14
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15
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Clayton E, Ackerley J, Aelmans M, Ali N, Ashcroft Z, Ashton C, Barker R, Budryte V, Burrows C, Cai S, Callaghan A, Carberry J, Chatwin R, Davies I, Farlow C, Gamblin S, Iacobut A, Lambe A, Lynch F, Mihalache D, Mokbel A, Potamsetty S, Qadir Z, Soden J, Sun X, Vasile A, Wheeler O, Rohaim MA, Munir M. Structural Bases of Zoonotic and Zooanthroponotic Transmission of SARS-CoV-2. Viruses 2022; 14:418. [PMID: 35216011 PMCID: PMC8875863 DOI: 10.3390/v14020418] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/25/2022] [Accepted: 02/07/2022] [Indexed: 01/27/2023] Open
Abstract
The emergence of multiple variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the importance of possible animal-to-human (zoonotic) and human-to-animal (zooanthroponotic) transmission and potential spread within animal species. A range of animal species have been verified for SARS-CoV-2 susceptibility, either in vitro or in vivo. However, the molecular bases of such a broad host spectrum for the SARS-CoV-2 remains elusive. Here, we structurally and genetically analysed the interaction between the spike protein, with a particular focus on receptor binding domains (RBDs), of SARS-CoV-2 and its receptor angiotensin-converting enzyme 2 (ACE2) for all conceivably susceptible groups of animals to gauge the structural bases of the SARS-CoV-2 host spectrum. We describe our findings in the context of existing animal infection-based models to provide a foundation on the possible virus persistence in animals and their implications in the future eradication of COVID-19.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK; (E.C.); (J.A.); (M.A.); (N.A.); (Z.A.); (C.A.); (R.B.); (V.B.); (C.B.); (S.C.); (A.C.); (J.C.); (R.C.); (I.D.); (C.F.); (S.G.); (A.I.); (A.L.); (F.L.); (D.M.); (A.M.); (S.P.); (Z.Q.); (J.S.); (X.S.); (A.V.); (O.W.); (M.A.R.)
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16
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Lado S, Futas J, Plasil M, Loney T, Weidinger P, Camp JV, Kolodziejek J, Kannan DO, Horin P, Nowotny N, Burger PA. Crimean-Congo Hemorrhagic Fever Virus Past Infections Are Associated with Two Innate Immune Response Candidate Genes in Dromedaries. Cells 2021; 11:8. [PMID: 35011568 PMCID: PMC8750074 DOI: 10.3390/cells11010008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/15/2021] [Indexed: 12/16/2022] Open
Abstract
Dromedaries are an important livestock, used as beasts of burden and for meat and milk production. However, they can act as an intermediate source or vector for transmitting zoonotic viruses to humans, such as the Middle East respiratory syndrome coronavirus (MERS-CoV) or Crimean-Congo hemorrhagic fever virus (CCHFV). After several outbreaks of CCHFV in the Arabian Peninsula, recent studies have demonstrated that CCHFV is endemic in dromedaries and camel ticks in the United Arab Emirates (UAE). There is no apparent disease in dromedaries after the bite of infected ticks; in contrast, fever, myalgia, lymphadenopathy, and petechial hemorrhaging are common symptoms in humans, with a case fatality ratio of up to 40%. We used the in-solution hybridization capture of 100 annotated immune genes to genotype 121 dromedaries from the UAE tested for seropositivity to CCHFV. Through univariate linear regression analysis, we identified two candidate genes belonging to the innate immune system: FCAR and CLEC2B. These genes have important functions in the host defense against viral infections and in stimulating natural killer cells, respectively. This study opens doors for future research into immune defense mechanisms in an enzootic host against an important zoonotic disease.
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Affiliation(s)
- Sara Lado
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, 1160 Vienna, Austria;
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria
| | - Jan Futas
- Department of Animal Genetics, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic; (J.F.); (M.P.); (P.H.)
- RG Animal Immunogenomics, CEITEC VETUNI Brno, 61242 Brno, Czech Republic
| | - Martin Plasil
- Department of Animal Genetics, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic; (J.F.); (M.P.); (P.H.)
- RG Animal Immunogenomics, CEITEC VETUNI Brno, 61242 Brno, Czech Republic
| | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (T.L.); (N.N.)
| | - Pia Weidinger
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
| | - Jeremy V. Camp
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | - Jolanta Kolodziejek
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
| | | | - Petr Horin
- Department of Animal Genetics, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic; (J.F.); (M.P.); (P.H.)
- RG Animal Immunogenomics, CEITEC VETUNI Brno, 61242 Brno, Czech Republic
| | - Norbert Nowotny
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (T.L.); (N.N.)
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
| | - Pamela A. Burger
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, 1160 Vienna, Austria;
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17
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Singh S, McNab C, Olson RM, Bristol N, Nolan C, Bergstrøm E, Bartos M, Mabuchi S, Panjabi R, Karan A, Abdalla SM, Bonk M, Jamieson M, Werner GK, Nordström A, Legido-Quigley H, Phelan A. How an outbreak became a pandemic: a chronological analysis of crucial junctures and international obligations in the early months of the COVID-19 pandemic. Lancet 2021; 398:2109-2124. [PMID: 34762857 PMCID: PMC8575464 DOI: 10.1016/s0140-6736(21)01897-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/01/2021] [Accepted: 08/17/2021] [Indexed: 12/11/2022]
Abstract
Understanding the spread of SARS-CoV-2, how and when evidence emerged, and the timing of local, national, regional, and global responses is essential to establish how an outbreak became a pandemic and to prepare for future health threats. With that aim, the Independent Panel for Pandemic Preparedness and Response has developed a chronology of events, actions, and recommendations, from December, 2019, when the first cases of COVID-19 were identified in China, to the end of March, 2020, by which time the outbreak had spread extensively worldwide and had been characterised as a pandemic. Datapoints are based on two literature reviews, WHO documents and correspondence, submissions to the Panel, and an expert verification process. The retrospective analysis of the chronology shows a dedicated initial response by WHO and some national governments, but also aspects of the response that could have been quicker, including outbreak notifications under the International Health Regulations (IHR), presumption and confirmation of human-to-human transmission of SARS-CoV-2, declaration of a Public Health Emergency of International Concern, and, most importantly, the public health response of many national governments. The chronology also shows that some countries, largely those with previous experience with similar outbreaks, reacted quickly, even ahead of WHO alerts, and were more successful in initially containing the virus. Mapping actions against IHR obligations, the chronology shows where efficiency and accountability could be improved at local, national, and international levels to more quickly alert and contain health threats in the future. In particular, these improvements include necessary reforms to international law and governance for pandemic preparedness and response, including the IHR and a potential framework convention on pandemic preparedness and response.
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Affiliation(s)
- Sudhvir Singh
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland; Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
| | - Christine McNab
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Rose McKeon Olson
- Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nellie Bristol
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Cody Nolan
- Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Elin Bergstrøm
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Michael Bartos
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland; School of Sociology, Australian National University, Canberra, ACT, Australia
| | - Shunsuke Mabuchi
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Raj Panjabi
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Abraar Karan
- Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Salma M Abdalla
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland; Boston University School of Public Health, Boston, MA, USA
| | - Mathias Bonk
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Margaret Jamieson
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - George K Werner
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Anders Nordström
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland
| | - Helena Legido-Quigley
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland; London School of Hygiene & Tropical Medicine, London, UK; Saw Swee Hock School of Public Health, Singapore
| | - Alexandra Phelan
- The Independent Panel for Pandemic Preparedness and Response, Geneva, Switzerland; Center for Global Health Science & Security, Georgetown University, Washington, DC, USA
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18
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Shirazi R, Pozzi P, Gozlan Y, Wax M, Lustig Y, Linial M, Mendelson E, Bardenstein S, Mor O. Identification of Hepatitis E Virus Genotypes 3 and 7 in Israel: A Public Health Concern? Viruses 2021; 13:v13112326. [PMID: 34835132 PMCID: PMC8625709 DOI: 10.3390/v13112326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Hepatitis E (HEV) is an emerging cause of viral hepatitis worldwide. Swine carrying hepatitis E genotype 3 (HEV-3) are responsible for the majority of chronic viral hepatitis cases in developed countries. Recently, genotype 7 (HEV-7), isolated from a dromedary camel in the United Arab Emirates, was also associated with chronic viral hepatitis in a transplant recipient. In Israel, chronic HEV infection has not yet been reported, although HEV seroprevalence in humans is ~10%. Camels and swine are >65% seropositive. Here we report on the isolation and characterization of HEV from local camels and swine. Methods: Sera from camels (n = 142), feces from swine (n = 18) and blood from patients suspected of hepatitis E (n = 101) were collected during 2017–2020 and used to detect and characterize HEV sequences. Results: HEV-3 isolated from local swine and the camel-derived HEV-7 sequence were highly similar to HEV-3f and HEV-7 sequences (88.2% and 86.4%, respectively) related to viral hepatitis. The deduced amino acid sequences of both isolates were also highly conserved (>98%). Two patients were HEV-RNA positive; acute HEV-1 infection could be confirmed in one of them. Discussion: The absence of any reported HEV-3 and HEV-7 infection in humans remains puzzling, especially considering the reported seroprevalence rates, the similarity between HEV sequences related to chronic hepatitis and the HEV genotypes identified in swine and camels in Israel.
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Affiliation(s)
- Rachel Shirazi
- Central Virology Laboratory, Ministry of Health, Public Health Services, The Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan 52620, Israel; (R.S.); (Y.G.); (M.W.); (Y.L.); (E.M.)
| | - Paolo Pozzi
- Department of Veterinary Sciences, University of Torino, 10095 Grugliasco, Italy;
| | - Yael Gozlan
- Central Virology Laboratory, Ministry of Health, Public Health Services, The Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan 52620, Israel; (R.S.); (Y.G.); (M.W.); (Y.L.); (E.M.)
| | - Marina Wax
- Central Virology Laboratory, Ministry of Health, Public Health Services, The Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan 52620, Israel; (R.S.); (Y.G.); (M.W.); (Y.L.); (E.M.)
| | - Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Public Health Services, The Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan 52620, Israel; (R.S.); (Y.G.); (M.W.); (Y.L.); (E.M.)
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Michal Linial
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Public Health Services, The Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan 52620, Israel; (R.S.); (Y.G.); (M.W.); (Y.L.); (E.M.)
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | | | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Public Health Services, The Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan 52620, Israel; (R.S.); (Y.G.); (M.W.); (Y.L.); (E.M.)
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
- Correspondence: ; Tel.: +972-3-530-2458
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19
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Carlson CJ, Farrell MJ, Grange Z, Han BA, Mollentze N, Phelan AL, Rasmussen AL, Albery GF, Bett B, Brett-Major DM, Cohen LE, Dallas T, Eskew EA, Fagre AC, Forbes KM, Gibb R, Halabi S, Hammer CC, Katz R, Kindrachuk J, Muylaert RL, Nutter FB, Ogola J, Olival KJ, Rourke M, Ryan SJ, Ross N, Seifert SN, Sironen T, Standley CJ, Taylor K, Venter M, Webala PW. The future of zoonotic risk prediction. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200358. [PMID: 34538140 PMCID: PMC8450624 DOI: 10.1098/rstb.2020.0358] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2021] [Indexed: 01/26/2023] Open
Abstract
In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
- Colin J. Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Zoe Grange
- Public Health Scotland, Glasgow G2 6QE, UK
| | - Barbara A. Han
- Cary Institute of Ecosystem Studies, Millbrook, NY 12545, USA
| | - Nardus Mollentze
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Alexandra L. Phelan
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC 20001, USA
| | - Angela L. Rasmussen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Gregory F. Albery
- Department of Biology, Georgetown University, Washington, DC 20007, USA
| | - Bernard Bett
- Animal and Human Health Program, International Livestock Research Institute, PO Box 30709-00100, Nairobi, Kenya
| | - David M. Brett-Major
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lily E. Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tad Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70806, USA
| | - Evan A. Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | - Anna C. Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kristian M. Forbes
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Rory Gibb
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sam Halabi
- O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC 20001, USA
| | - Charlotte C. Hammer
- Centre for the Study of Existential Risk, University of Cambridge, Cambridge, UK
| | - Rebecca Katz
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Jason Kindrachuk
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9
| | - Renata L. Muylaert
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
- Department of Public Health and Community Medicine, School of Medicine, Tufts University, Boston, MA 02111, USA
| | | | | | - Michelle Rourke
- Law Futures Centre, Griffith Law School, Griffith University, Nathan, Queensland 4111, Australia
| | - Sadie J. Ryan
- Department of Geography and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Noam Ross
- EcoHealth Alliance, New York, NY 10018, USA
| | - Stephanie N. Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Tarja Sironen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Claire J. Standley
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Kishana Taylor
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Paul W. Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
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20
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Noguera Zayas LP, Rüegg S, Torgerson P. The burden of zoonoses in Paraguay: A systematic review. PLoS Negl Trop Dis 2021; 15:e0009909. [PMID: 34727113 PMCID: PMC8589157 DOI: 10.1371/journal.pntd.0009909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/12/2021] [Accepted: 10/15/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Underestimation of zoonoses is exacerbated in low and middle-income countries due mainly to inequalities with serious consequences in healthcare. This is difficult to gauge and reduce the impact of those diseases. Our study focuses on Paraguay, where the livestock industry is one of the major components of the country's economy. Therefore, the rationale of this study was to develop a case study in Paraguay to estimate the dual impact of zoonotic diseases on both the human health and animal health sector and thus determine the societal burden of such diseases. METHODOLOGY/PRINCIPAL FINDINGS We conducted a systemic review (including a meta-analysis) to assess the burden of zoonoses in Paraguay, including official reports and grey literature of disease incidence and prevalence. We estimated the Disability Adjusted Life Years (DALYs) and Zoonosis Disability Adjusted Life Years (zDALYs) to measure the difference between the current health status and the desired health situation of animals and the Paraguayan population based on 50 zoonotic diseases suggested by the WHO (World Health Organization), OIE (World Organization for Animal Health) and the National Health in Paraguay. The total DALYs represent 19,384 (95% CI: from 15,805 to 29,733), and zDALYs, 62,178 (95% CI: from 48,696 to 77,188). According to the results, the priority pathogens for DALYs are E. coli, Trypanosoma cruzi, Leishmania spp, and Toxoplasma gondii. When we include the additional animal health burden, the most important pathogens are Brucella spp, E. coli, Trypanosoma cruzi, and Fasciola hepatica for zDALYs. CONCLUSION/SIGNIFICANCE This is the first study to integrate DALYs and zDALYs with important clues related to the health status of Paraguay. Through DALYs and zDALYs, our perspective becomes more complete because we consider not only human health but also animal health. This is important for setting priorities in disease control, especially in a society where livestock contribute significantly to the economy and to human well-being.
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Affiliation(s)
- Liz Paola Noguera Zayas
- Section of Epidemiology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
- Epidemiology and Biostatistics, Life Science Zürich Graduate School, University of Zürich, Zürich, Switzerland
| | - Simon Rüegg
- Section of Epidemiology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Paul Torgerson
- Section of Epidemiology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
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21
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Abstract
Porcine endogenous retroviruses (PERVs) are integrated in the genome of all pigs, and some of them are able to infect human cells. Therefore, PERVs pose a risk for xenotransplantation, the transplantation of pig cells, tissues, or organ to humans in order to alleviate the shortage of human donor organs. Up to 2021, a huge body of knowledge about PERVs has been accumulated regarding their biology, including replication, recombination, origin, host range, and immunosuppressive properties. Until now, no PERV transmission has been observed in clinical trials transplanting pig islet cells into diabetic humans, in preclinical trials transplanting pig cells and organs into nonhuman primates with remarkable long survival times of the transplant, and in infection experiments with several animal species. Nevertheless, in order to prevent virus transmission to the recipient, numerous strategies have been developed, including selection of PERV-C-free animals, RNA interference, antiviral drugs, vaccination, and genome editing. Furthermore, at present there are no more experimental approaches to evaluate the full risk until we move to the clinic.
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Affiliation(s)
- Joachim Denner
- Department of Veterinary Medicine, Institute of Virology, Free University Berlin, 14163 Berlin, Germany
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22
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Abstract
Bats are infamous reservoirs of deadly human viruses. While retroviruses, such as the human immunodeficiency virus (HIV), are among the most significant of virus families that have jumped from animals into humans, whether bat retroviruses have the potential to infect and cause disease in humans remains unknown. Recent reports of retroviruses circulating in bat populations builds on two decades of research describing the fossil records of retroviral sequences in bat genomes and of viral metagenomes extracted from bat samples. The impact of the global COVID-19 pandemic demands that we pay closer attention to viruses hosted by bats and their potential as a zoonotic threat. Here we review current knowledge of bat retroviruses and explore the question of whether they represent a threat to humans.
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Affiliation(s)
- Joshua A. Hayward
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Gilda Tachedjian
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
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23
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Abstract
COVID-19 most likely had its origins in wildlife, and hundreds of thousands of new viruses could spill over from wildlife to humans. We are struggling to combat climate change, and we are staring down the loss of a million species. It's time to change course.
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Affiliation(s)
- John E. Scanlon AO
- Global Initiative to End Wildlife Crime, hosted by ADM Capital Foundation, Central, Hong Kong SAR, China
- * E-mail:
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24
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Andrade MDS, Campos FS, Campos AAS, Abreu FVS, Melo FL, Sevá ADP, Cardoso JDC, Dos Santos E, Born LC, da Silva CMD, Müller NFD, de Oliveira CH, da Silva AJJ, Simonini-Teixeira D, Bernal-Valle S, Mares-Guia MAMM, Albuquerque GR, Romano APM, Franco AC, Ribeiro BM, Roehe PM, de Almeida MAB. Real-Time Genomic Surveillance during the 2021 Re-Emergence of the Yellow Fever Virus in Rio Grande do Sul State, Brazil. Viruses 2021; 13:v13101976. [PMID: 34696408 PMCID: PMC8539658 DOI: 10.3390/v13101976] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 02/06/2023] Open
Abstract
The 2021 re-emergence of yellow fever in non-human primates in the state of Rio Grande do Sul (RS), southernmost Brazil, resulted in the death of many howler monkeys (genus Alouatta) and led the state to declare a Public Health Emergency of State Importance, despite no human cases reported. In this study, near-complete genomes of yellow fever virus (YFV) recovered from the outbreak were sequenced and examined aiming at a better understanding of the phylogenetic relationships and the spatio-temporal dynamics of the virus distribution. Our results suggest that the most likely sequence of events involved the reintroduction of YFV from the state of São Paulo to RS through the states of Paraná and Santa Catarina, by the end of 2020. These findings reinforce the role of genomic surveillance in determining the pathways of distribution of the virus and in providing references for the implementation of preventive measures for populations in high risk areas.
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Affiliation(s)
- Miguel de S. Andrade
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, Distrito Federal, Brazil; (M.d.S.A.); (F.L.M.); (B.M.R.)
| | - Fabrício S. Campos
- Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, Tocantins, Brazil;
| | - Aline A. S. Campos
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
| | - Filipe V. S. Abreu
- Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, Minas Gerais, Brazil; (F.V.S.A.); (C.H.d.O.); (A.J.J.d.S.)
| | - Fernando L. Melo
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, Distrito Federal, Brazil; (M.d.S.A.); (F.L.M.); (B.M.R.)
| | - Anaiá da P. Sevá
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, Bahia, Brazil; (A.d.P.S.); (D.S.-T.); (S.B.-V.); (G.R.A.)
| | - Jader da C. Cardoso
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
| | - Edmilson Dos Santos
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
| | - Lucas C. Born
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
| | - Cláudia M. D. da Silva
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
| | - Nicolas F. D. Müller
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90050-170, Rio Grande do Sul, Brazil; (N.F.D.M.); (A.C.F.); (P.M.R.)
| | - Cirilo H. de Oliveira
- Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, Minas Gerais, Brazil; (F.V.S.A.); (C.H.d.O.); (A.J.J.d.S.)
| | - Alex J. J. da Silva
- Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, Minas Gerais, Brazil; (F.V.S.A.); (C.H.d.O.); (A.J.J.d.S.)
| | - Danilo Simonini-Teixeira
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, Bahia, Brazil; (A.d.P.S.); (D.S.-T.); (S.B.-V.); (G.R.A.)
| | - Sofía Bernal-Valle
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, Bahia, Brazil; (A.d.P.S.); (D.S.-T.); (S.B.-V.); (G.R.A.)
| | - Maria A. M. M. Mares-Guia
- Flavivirus Laboratory, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil;
| | - George R. Albuquerque
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, Bahia, Brazil; (A.d.P.S.); (D.S.-T.); (S.B.-V.); (G.R.A.)
| | - Alessandro P. M. Romano
- General Coordination of Arbovirus Surveillance, Ministry of Health, Brasília 70058-900, Distrito Federal, Brazil;
| | - Ana C. Franco
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90050-170, Rio Grande do Sul, Brazil; (N.F.D.M.); (A.C.F.); (P.M.R.)
| | - Bergmann M. Ribeiro
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, Distrito Federal, Brazil; (M.d.S.A.); (F.L.M.); (B.M.R.)
| | - Paulo M. Roehe
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90050-170, Rio Grande do Sul, Brazil; (N.F.D.M.); (A.C.F.); (P.M.R.)
| | - Marco A. B. de Almeida
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
- Correspondence:
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25
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Spruill-Harrell B, Pérez-Umphrey A, Valdivieso-Torres L, Cao X, Owen RD, Jonsson CB. Impact of Predator Exclusion and Habitat on Seroprevalence of New World Orthohantavirus Harbored by Two Sympatric Rodents within the Interior Atlantic Forest. Viruses 2021; 13:1963. [PMID: 34696393 PMCID: PMC8538774 DOI: 10.3390/v13101963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding how perturbations to trophic interactions influence virus-host dynamics is essential in the face of ongoing biodiversity loss and the continued emergence of RNA viruses and their associated zoonoses. Herein, we investigated the role of predator exclusion on rodent communities and the seroprevalence of hantaviruses within the Reserva Natural del Bosque Mbaracayú (RNBM), which is a protected area of the Interior Atlantic Forest (IAF). In the IAF, two sympatric rodent reservoirs, Akodon montensis and Oligoryzomys nigripes, harbor Jaborá and Juquitiba hantavirus (JABV, JUQV), respectively. In this study, we employed two complementary methods for predator exclusion: comprehensive fencing and trapping/removal. The goal of exclusion was to preclude the influence of predation on small mammals on the sampling grids and thereby potentially reduce rodent mortality. Following baseline sampling on three grid pairs with different habitats, we closed the grids and began predator removal. By sampling three habitat types, we controlled for habitat-specific effects, which is important for hantavirus-reservoir dynamics in neotropical ecosystems. Our six-month predator exclusion experiment revealed that the exclusion of terrestrial mammalian predators had little influence on the rodent community or the population dynamics of A. montensis and O. nigripes. Instead, fluctuations in species diversity and species abundances were influenced by sampling session and forest degradation. These results suggest that seasonality and landscape composition play dominant roles in the prevalence of hantaviruses in rodent reservoirs in the IAF ecosystem.
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Affiliation(s)
- Briana Spruill-Harrell
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Anna Pérez-Umphrey
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA;
| | | | - Xueyuan Cao
- Department of Nursing-Acute/Tert Care, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Robert D. Owen
- Centro para el Desarrollo de la Investigación Científica, Asunción C.P. 1371, Paraguay;
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
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Cáceres CJ, Rajao DS, Perez DR. Airborne Transmission of Avian Origin H9N2 Influenza A Viruses in Mammals. Viruses 2021; 13:v13101919. [PMID: 34696349 PMCID: PMC8540072 DOI: 10.3390/v13101919] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/17/2022] Open
Abstract
Influenza A viruses (IAV) are widespread viruses affecting avian and mammalian species worldwide. IAVs from avian species can be transmitted to mammals including humans and, thus, they are of inherent pandemic concern. Most of the efforts to understand the pathogenicity and transmission of avian origin IAVs have been focused on H5 and H7 subtypes due to their highly pathogenic phenotype in poultry. However, IAV of the H9 subtype, which circulate endemically in poultry flocks in some regions of the world, have also been associated with cases of zoonotic infections. In this review, we discuss the mammalian transmission of H9N2 and the molecular factors that are thought relevant for this spillover, focusing on the HA segment. Additionally, we discuss factors that have been associated with the ability of these viruses to transmit through the respiratory route in mammalian species. The summarized information shows that minimal amino acid changes in the HA and/or the combination of H9N2 surface genes with internal genes of human influenza viruses are enough for the generation of H9N2 viruses with the ability to transmit via aerosol.
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27
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Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrar J, Geoghegan JL, Jiang X, Leibowitz JL, Neil SJD, Skern T, Weiss SR, Worobey M, Andersen KG, Garry RF, Rambaut A. The origins of SARS-CoV-2: A critical review. Cell 2021; 184:4848-4856. [PMID: 34480864 PMCID: PMC8373617 DOI: 10.1016/j.cell.2021.08.017] [Citation(s) in RCA: 260] [Impact Index Per Article: 86.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 01/11/2023]
Abstract
Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a "laboratory escape" scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.
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Affiliation(s)
- Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Stephen A Goldstein
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94704, USA
| | - Joel O Wertheim
- Department of Medicine, University of California-San Diego, La Jolla, CA 92093, USA
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College, London W2 1PG, UK
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peter C Doherty
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | | | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand; Institute of Environmental Science and Research, Wellington 5022, New Zealand
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University (XJTLU), Suzhou, China
| | - Julian L Leibowitz
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX 77807, USA
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Tim Skern
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Zalgen Labs, Germantown, MD 20876, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.
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Mollentze N, Babayan SA, Streicker DG. Identifying and prioritizing potential human-infecting viruses from their genome sequences. PLoS Biol 2021; 19:e3001390. [PMID: 34582436 PMCID: PMC8478193 DOI: 10.1371/journal.pbio.3001390] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 08/10/2021] [Indexed: 11/18/2022] Open
Abstract
Determining which animal viruses may be capable of infecting humans is currently intractable at the time of their discovery, precluding prioritization of high-risk viruses for early investigation and outbreak preparedness. Given the increasing use of genomics in virus discovery and the otherwise sparse knowledge of the biology of newly discovered viruses, we developed machine learning models that identify candidate zoonoses solely using signatures of host range encoded in viral genomes. Within a dataset of 861 viral species with known zoonotic status, our approach outperformed models based on the phylogenetic relatedness of viruses to known human-infecting viruses (area under the receiver operating characteristic curve [AUC] = 0.773), distinguishing high-risk viruses within families that contain a minority of human-infecting species and identifying putatively undetected or so far unrealized zoonoses. Analyses of the underpinnings of model predictions suggested the existence of generalizable features of viral genomes that are independent of virus taxonomic relationships and that may preadapt viruses to infect humans. Our model reduced a second set of 645 animal-associated viruses that were excluded from training to 272 high and 41 very high-risk candidate zoonoses and showed significantly elevated predicted zoonotic risk in viruses from nonhuman primates, but not other mammalian or avian host groups. A second application showed that our models could have identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a relatively high-risk coronavirus strain and that this prediction required no prior knowledge of zoonotic Severe Acute Respiratory Syndrome (SARS)-related coronaviruses. Genome-based zoonotic risk assessment provides a rapid, low-cost approach to enable evidence-driven virus surveillance and increases the feasibility of downstream biological and ecological characterization of viruses.
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Affiliation(s)
- Nardus Mollentze
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon A. Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel G. Streicker
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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29
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Tirera S, de Thoisy B, Donato D, Bouchier C, Lacoste V, Franc A, Lavergne A. The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts. Viruses 2021; 13:v13091690. [PMID: 34578272 PMCID: PMC8472065 DOI: 10.3390/v13091690] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/15/2021] [Indexed: 12/23/2022] Open
Abstract
Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host’s dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems.
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Affiliation(s)
- Sourakhata Tirera
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, BP 6010, 97306 Cayenne, France; (S.T.); (B.d.T.); (D.D.); (V.L.)
| | - Benoit de Thoisy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, BP 6010, 97306 Cayenne, France; (S.T.); (B.d.T.); (D.D.); (V.L.)
| | - Damien Donato
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, BP 6010, 97306 Cayenne, France; (S.T.); (B.d.T.); (D.D.); (V.L.)
| | | | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, BP 6010, 97306 Cayenne, France; (S.T.); (B.d.T.); (D.D.); (V.L.)
- Département de Virologie, Institut Pasteur, 75015 Paris, France
- Arbovirus & Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 3560, Laos
| | - Alain Franc
- UMR BIOGECO, INRAE, University Bordeaux, 33612 Cestas, France;
- Pleiade, EPC INRIA-INRAE-CNRS, University Bordeaux, 33405 Talence, France
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, BP 6010, 97306 Cayenne, France; (S.T.); (B.d.T.); (D.D.); (V.L.)
- Correspondence:
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30
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Nahata KD, Bollen N, Gill MS, Layan M, Bourhy H, Dellicour S, Baele G. On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study. Viruses 2021; 13:v13081628. [PMID: 34452492 PMCID: PMC8402743 DOI: 10.3390/v13081628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Rabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus Lyssavirus. Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 people are still estimated to die from rabies each year, leading to a global initiative to work towards the goal of zero human deaths from dog-mediated rabies by 2030, requiring scientific efforts from different research fields. The past decade has seen a much increased use of phylogeographic and phylodynamic analyses to study the evolution and spread of rabies virus. We here review published studies in these research areas, making a distinction between the geographic resolution associated with the available sequence data. We pay special attention to environmental factors that these studies found to be relevant to the spread of rabies virus. Importantly, we highlight a knowledge gap in terms of applying these methods when all required data were available but not fully exploited. We conclude with an overview of recent methodological developments that have yet to be applied in phylogeographic and phylodynamic analyses of rabies virus.
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Affiliation(s)
- Kanika D. Nahata
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
- Correspondence:
| | - Nena Bollen
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
| | - Mandev S. Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
| | - Maylis Layan
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Sorbonne Université, UMR2000, CNRS, 75015 Paris, France;
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, 75015 Paris, France;
- WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, 75015 Paris, France
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
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31
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Plowright RK, Hudson PJ. From Protein to Pandemic: The Transdisciplinary Approach Needed to Prevent Spillover and the Next Pandemic. Viruses 2021; 13:1298. [PMID: 34372504 PMCID: PMC8310336 DOI: 10.3390/v13071298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 01/10/2023] Open
Abstract
Pandemics are a consequence of a series of processes that span scales from viral biology at 10-9 m to global transmission at 106 m. The pathogen passes from one host species to another through a sequence of events that starts with an infected reservoir host and entails interspecific contact, innate immune responses, receptor protein structure within the potential host, and the global spread of the novel pathogen through the naive host population. Each event presents a potential barrier to the onward passage of the virus and should be characterized with an integrated transdisciplinary approach. Epidemic control is based on the prevention of exposure, infection, and disease. However, the ultimate pandemic prevention is prevention of the spillover event itself. Here, we focus on the potential for preventing the spillover of henipaviruses, a group of viruses derived from bats that frequently cross species barriers, incur high human mortality, and are transmitted among humans via stuttering chains. We outline the transdisciplinary approach needed to prevent the spillover process and, therefore, future pandemics.
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Affiliation(s)
- Raina K. Plowright
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, State College, PA 16802, USA;
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Wardeh M, Blagrove MSC, Sharkey KJ, Baylis M. Divide-and-conquer: machine-learning integrates mammalian and viral traits with network features to predict virus-mammal associations. Nat Commun 2021; 12:3954. [PMID: 34172731 PMCID: PMC8233343 DOI: 10.1038/s41467-021-24085-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/21/2021] [Indexed: 11/09/2022] Open
Abstract
Our knowledge of viral host ranges remains limited. Completing this picture by identifying unknown hosts of known viruses is an important research aim that can help identify and mitigate zoonotic and animal-disease risks, such as spill-over from animal reservoirs into human populations. To address this knowledge-gap we apply a divide-and-conquer approach which separates viral, mammalian and network features into three unique perspectives, each predicting associations independently to enhance predictive power. Our approach predicts over 20,000 unknown associations between known viruses and susceptible mammalian species, suggesting that current knowledge underestimates the number of associations in wild and semi-domesticated mammals by a factor of 4.3, and the average potential mammalian host-range of viruses by a factor of 3.2. In particular, our results highlight a significant knowledge gap in the wild reservoirs of important zoonotic and domesticated mammals' viruses: specifically, lyssaviruses, bornaviruses and rotaviruses.
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Affiliation(s)
- Maya Wardeh
- Department of Livestock and One Health, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK.
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK.
| | - Marcus S C Blagrove
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kieran J Sharkey
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
| | - Matthew Baylis
- Department of Livestock and One Health, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
- Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
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33
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Dróżdż M, Krzyżek P, Dudek B, Makuch S, Janczura A, Paluch E. Current State of Knowledge about Role of Pets in Zoonotic Transmission of SARS-CoV-2. Viruses 2021; 13:1149. [PMID: 34208484 PMCID: PMC8234912 DOI: 10.3390/v13061149] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Pets play a crucial role in the development of human feelings, social life, and care. However, in the era of the prevailing global pandemic of COVID-19 disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), many questions addressing the routes of the virus spread and transmission to humans are dramatically emerging. Although cases of SARS-CoV-2 infection have been found in pets including dogs, cats, and ferrets, to date there is no strong evidence for pet-to-human transmission or sustained pet-to-pet transmission of SARS-CoV-2. However, an increasing number of studies reporting detection of SARS-CoV-2 in farmed minks raises suspicion of potential viral transmission from these animals to humans. Furthermore, due to the high susceptibility of cats, ferrets, minks and hamsters to COVID-19 infection under natural and/or experimental conditions, these animals have been extensively explored as animal models to study the SARS-CoV-2 pathogenesis and transmission. In this review, we present the latest reports focusing on SARS-CoV-2 detection, isolation, and characterization in pets. Moreover, based on the current literature, we document studies aiming to broaden the knowledge about pathogenicity and transmissibility of SARS-CoV-2, and the development of viral therapeutics, drugs and vaccines. Lastly, considering the high rate of SARS-CoV-2 evolution and replication, we also suggest routes of protection against the virus.
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Affiliation(s)
- Mateusz Dróżdż
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Paweł Krzyżek
- Department of Microbiology, Wrocław Medical University, St. T. Chałubińskiego 4, 50-376 Wrocław, Poland; (P.K.); (A.J.)
| | - Barbara Dudek
- Laboratory of Microbiology, Private Health Care Institution, St. Jana Pawła II, 41-100 Siemianowice Śląskie, Poland;
| | - Sebastian Makuch
- Department of Pathology, Wrocław Medical University, St. K. Marcinkowskiego 1, 50-368 Wrocław, Poland;
| | - Adriana Janczura
- Department of Microbiology, Wrocław Medical University, St. T. Chałubińskiego 4, 50-376 Wrocław, Poland; (P.K.); (A.J.)
| | - Emil Paluch
- Department of Microbiology, Wrocław Medical University, St. T. Chałubińskiego 4, 50-376 Wrocław, Poland; (P.K.); (A.J.)
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34
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Hardmeier I, Aeberhard N, Qi W, Schoenbaechler K, Kraettli H, Hatt JM, Fraefel C, Kubacki J. Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses. PLoS One 2021; 16:e0252534. [PMID: 34133435 PMCID: PMC8208571 DOI: 10.1371/journal.pone.0252534] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.
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Affiliation(s)
| | - Nadja Aeberhard
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, Zurich, Switzerland
| | | | | | - Jean-Michel Hatt
- Clinic for Zoo Animals, Exotic Pets and Wildlife, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Jakub Kubacki
- Institute of Virology, University of Zurich, Zurich, Switzerland
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35
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Griffin BD, Chan M, Tailor N, Mendoza EJ, Leung A, Warner BM, Duggan AT, Moffat E, He S, Garnett L, Tran KN, Banadyga L, Albietz A, Tierney K, Audet J, Bello A, Vendramelli R, Boese AS, Fernando L, Lindsay LR, Jardine CM, Wood H, Poliquin G, Strong JE, Drebot M, Safronetz D, Embury-Hyatt C, Kobasa D. SARS-CoV-2 infection and transmission in the North American deer mouse. Nat Commun 2021; 12:3612. [PMID: 34127676 PMCID: PMC8203675 DOI: 10.1038/s41467-021-23848-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 05/17/2021] [Indexed: 01/08/2023] Open
Abstract
Widespread circulation of SARS-CoV-2 in humans raises the theoretical risk of reverse zoonosis events with wildlife, reintroductions of SARS-CoV-2 into permissive nondomesticated animals. Here we report that North American deer mice (Peromyscus maniculatus) are susceptible to SARS-CoV-2 infection following intranasal exposure to a human isolate, resulting in viral replication in the upper and lower respiratory tract with little or no signs of disease. Further, shed infectious virus is detectable in nasal washes, oropharyngeal and rectal swabs, and viral RNA is detectable in feces and occasionally urine. We further show that deer mice are capable of transmitting SARS-CoV-2 to naïve deer mice through direct contact. The extent to which these observations may translate to wild deer mouse populations remains unclear, and the risk of reverse zoonosis and/or the potential for the establishment of Peromyscus rodents as a North American reservoir for SARS-CoV-2 remains unknown.
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Affiliation(s)
- Bryan D Griffin
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Mable Chan
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Nikesh Tailor
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Emelissa J Mendoza
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Anders Leung
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Bryce M Warner
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Ana T Duggan
- Science Technology Cores and Services, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Estella Moffat
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Shihua He
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Lauren Garnett
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Kaylie N Tran
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Logan Banadyga
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Alixandra Albietz
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Kevin Tierney
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jonathan Audet
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Alexander Bello
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Robert Vendramelli
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Amrit S Boese
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Lisa Fernando
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - L Robbin Lindsay
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Entomology, University of Manitoba, Winnipeg, MB, Canada
| | - Claire M Jardine
- Department of Pathobiology, Canadian Wildlife Health Cooperative, Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Heidi Wood
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Guillaume Poliquin
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Pediatrics & Child Health, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Office of the Scientific Director, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - James E Strong
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Pediatrics & Child Health, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Michael Drebot
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - David Safronetz
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Carissa Embury-Hyatt
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Darwyn Kobasa
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.
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Cierniak F, von Arnim F, Heckel G, Ulrich RG, Groschup MH, Eiden M. A Putative Novel Hepatitis E Virus Genotype 3 Subtype Identified in Rabbit, Germany 2016. Viruses 2021; 13:1065. [PMID: 34205182 PMCID: PMC8228152 DOI: 10.3390/v13061065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatitis E is an emerging viral disease that is the leading cause of viral hepatitis in the world. The vast majority of hepatitis E cases in developed countries are caused by zoonotic genotypes 3 and 4 of hepatitis E virus (HEV) for which pig and wild boar and to lesser extent rabbits are the main reservoir. According to recent reports rabbits are a source of human HEV infection and highlight the risk of zoonotic foodborne transmission. Here we report the molecular analysis of a novel HEV strain identified in a rabbit during a countrywide surveillance of rabbits and hares in Germany, 2016. The analysis of the complete genome reveals characteristics of a putative novel recombinant subtype of the species Orthohepevirus A within the clade of genotype 3 but not closely related to any known subtypes. Importantly, the genome of this strain possesses a nucleotide exchange in the overlapping region of open reading frames ORF2/ORF3 interfering with a broadly applied diagnostic real-time RT-PCR. In conclusion, a new type of HEV strain was identified in a German rabbit with atypical and novel sequence characteristics.
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Affiliation(s)
- Filip Cierniak
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (F.C.); (F.v.A.); (R.G.U.); (M.H.G.)
| | - Felicitas von Arnim
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (F.C.); (F.v.A.); (R.G.U.); (M.H.G.)
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (F.C.); (F.v.A.); (R.G.U.); (M.H.G.)
- Partner Site Hamburg-Lübeck-Borstel-Riems, Deutsches Zentrum für Infektionsforschung (DZIF), 17493 Greifswald-Insel Riems, Germany
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (F.C.); (F.v.A.); (R.G.U.); (M.H.G.)
- Partner Site Hamburg-Lübeck-Borstel-Riems, Deutsches Zentrum für Infektionsforschung (DZIF), 17493 Greifswald-Insel Riems, Germany
| | - Martin Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (F.C.); (F.v.A.); (R.G.U.); (M.H.G.)
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Treagus S, Wright C, Baker-Austin C, Longdon B, Lowther J. The Foodborne Transmission of Hepatitis E Virus to Humans. Food Environ Virol 2021; 13:127-145. [PMID: 33738770 PMCID: PMC8116281 DOI: 10.1007/s12560-021-09461-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/16/2021] [Indexed: 05/04/2023]
Abstract
Globally, Hepatitis E virus (HEV) causes over 20 million cases worldwide. HEV is an emerging and endemic pathogen within economically developed countries, chiefly resulting from infections with genotype 3 (G3) HEV. G3 HEV is known to be a zoonotic pathogen, with a broad host range. The primary source of HEV within more economically developed countries is considered to be pigs, and consumption of pork products is a significant risk factor and known transmission route for the virus to humans. However, other foods have also been implicated in the transmission of HEV to humans. This review consolidates the information available regarding transmission of HEV and looks to identify gaps where further research is required to better understand how HEV is transmitted to humans through food.
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Affiliation(s)
- Samantha Treagus
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK.
- Centre for Environment Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset, DT4 8UB, UK.
| | | | - Craig Baker-Austin
- Centre for Environment Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Ben Longdon
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - James Lowther
- Centre for Environment Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset, DT4 8UB, UK
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Lado S, Elbers JP, Plasil M, Loney T, Weidinger P, Camp JV, Kolodziejek J, Futas J, Kannan DA, Orozco-terWengel P, Horin P, Nowotny N, Burger PA. Innate and Adaptive Immune Genes Associated with MERS-CoV Infection in Dromedaries. Cells 2021; 10:1291. [PMID: 34070971 PMCID: PMC8224694 DOI: 10.3390/cells10061291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/18/2022] Open
Abstract
The recent SARS-CoV-2 pandemic has refocused attention to the betacoronaviruses, only eight years after the emergence of another zoonotic betacoronavirus, the Middle East respiratory syndrome coronavirus (MERS-CoV). While the wild source of SARS-CoV-2 may be disputed, for MERS-CoV, dromedaries are considered as source of zoonotic human infections. Testing 100 immune-response genes in 121 dromedaries from United Arab Emirates (UAE) for potential association with present MERS-CoV infection, we identified candidate genes with important functions in the adaptive, MHC-class I (HLA-A-24-like) and II (HLA-DPB1-like), and innate immune response (PTPN4, MAGOHB), and in cilia coating the respiratory tract (DNAH7). Some of these genes previously have been associated with viral replication in SARS-CoV-1/-2 in humans, others have an important role in the movement of bronchial cilia. These results suggest similar host genetic pathways associated with these betacoronaviruses, although further work is required to better understand the MERS-CoV disease dynamics in both dromedaries and humans.
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Affiliation(s)
- Sara Lado
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (S.L.); (J.P.E.)
| | - Jean P. Elbers
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (S.L.); (J.P.E.)
| | - Martin Plasil
- Department of Animal Genetics, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic; (M.P.); (J.F.); (P.H.)
- RG Animal Immunogenomics, Ceitec Vetuni, 61242 Brno, Czech Republic
| | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (T.L.); (N.N.)
| | - Pia Weidinger
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
| | - Jeremy V. Camp
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | - Jolanta Kolodziejek
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
| | - Jan Futas
- Department of Animal Genetics, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic; (M.P.); (J.F.); (P.H.)
- RG Animal Immunogenomics, Ceitec Vetuni, 61242 Brno, Czech Republic
| | | | - Pablo Orozco-terWengel
- The Sir Martin Evans Building, Cardiff School of Biosciences, Cardiff University, Museum Ave, Cardiff CF10 3AX, UK;
| | - Petr Horin
- Department of Animal Genetics, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic; (M.P.); (J.F.); (P.H.)
- RG Animal Immunogenomics, Ceitec Vetuni, 61242 Brno, Czech Republic
| | - Norbert Nowotny
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (T.L.); (N.N.)
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
| | - Pamela A. Burger
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (S.L.); (J.P.E.)
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Abstract
Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding the determinants of disease emergence. Accordingly, there has been an increase in studies attempting zoonotic “risk assessment.” Herein, we demonstrate that the virological data on which these analyses are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery. Together, these shortcomings suggest that attempts to assess zoonotic risk using available virological data are likely to be inaccurate and largely only identify those host taxa that have been studied most extensively. We suggest that virus surveillance at the human–animal interface may be more productive. Determining which organisms harbour viruses that could potentially infect humans is of great topical interest. This Essay demonstrates that the data on which such zoonotic risk assessments are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery.
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Affiliation(s)
- Michelle Wille
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
- * E-mail:
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
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Gray GC, Robie ER, Studstill CJ, Nunn CL. Mitigating Future Respiratory Virus Pandemics: New Threats and Approaches to Consider. Viruses 2021; 13:637. [PMID: 33917745 PMCID: PMC8068197 DOI: 10.3390/v13040637] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Despite many recent efforts to predict and control emerging infectious disease threats to humans, we failed to anticipate the zoonotic viruses which led to pandemics in 2009 and 2020. The morbidity, mortality, and economic costs of these pandemics have been staggering. We desperately need a more targeted, cost-efficient, and sustainable strategy to detect and mitigate future zoonotic respiratory virus threats. Evidence suggests that the transition from an animal virus to a human pathogen is incremental and requires a considerable number of spillover events and considerable time before a pandemic variant emerges. This evolutionary view argues for the refocusing of public health resources on novel respiratory virus surveillance at human-animal interfaces in geographical hotspots for emerging infectious diseases. Where human-animal interface surveillance is not possible, a secondary high-yield, cost-efficient strategy is to conduct novel respiratory virus surveillance among pneumonia patients in these same hotspots. When novel pathogens are discovered, they must be quickly assessed for their human risk and, if indicated, mitigation strategies initiated. In this review, we discuss the most common respiratory virus threats, current efforts at early emerging pathogen detection, and propose and defend new molecular pathogen discovery strategies with the goal of preempting future pandemics.
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Affiliation(s)
- Gregory C. Gray
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, USA; (E.R.R.); (C.J.S.)
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA;
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore 169856, Singapore
- Global Health Center, Duke Kunshan University, Kunshan 215316, China
| | - Emily R. Robie
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, USA; (E.R.R.); (C.J.S.)
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA;
| | - Caleb J. Studstill
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, USA; (E.R.R.); (C.J.S.)
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA;
| | - Charles L. Nunn
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA;
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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Ghai RR, Carpenter A, Liew AY, Martin KB, Herring MK, Gerber SI, Hall AJ, Sleeman JM, VonDobschuetz S, Behravesh CB. Animal Reservoirs and Hosts for Emerging Alphacoronaviruses and Betacoronaviruses. Emerg Infect Dis 2021; 27:1015-1022. [PMID: 33770472 PMCID: PMC8007319 DOI: 10.3201/eid2704.203945] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The ongoing global pandemic caused by coronavirus disease has once again demonstrated the role of the family Coronaviridae in causing human disease outbreaks. Because severe acute respiratory syndrome coronavirus 2 was first detected in December 2019, information on its tropism, host range, and clinical manifestations in animals is limited. Given the limited information, data from other coronaviruses might be useful for informing scientific inquiry, risk assessment, and decision-making. We reviewed endemic and emerging infections of alphacoronaviruses and betacoronaviruses in wildlife, livestock, and companion animals and provide information on the receptor use, known hosts, and clinical signs associated with each host for 15 coronaviruses detected in humans and animals. This information can be used to guide implementation of a One Health approach that involves human health, animal health, environmental, and other relevant partners in developing strategies for preparedness, response, and control to current and future coronavirus disease threats.
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Munyua PM, Ngere I, Hunsperger E, Kochi A, Amoth P, Mwasi L, Tong S, Mwatondo A, Thornburg N, Widdowson MA, Njenga MK. Low-Level Middle East Respiratory Syndrome Coronavirus among Camel Handlers, Kenya, 2019. Emerg Infect Dis 2021; 27:1201-1205. [PMID: 33754992 PMCID: PMC8007315 DOI: 10.3201/eid2704.204458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Although seroprevalence of Middle East respiratory coronavirus syndrome is high among camels in Africa, researchers have not detected zoonotic transmission in Kenya. We followed a cohort of 262 camel handlers in Kenya during April 2018–March 2020. We report PCR-confirmed Middle East respiratory coronavirus syndrome in 3 asymptomatic handlers.
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Abstract
SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral 'genetic drift' or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wendy S. Barclay
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
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Hossain MG, Javed A, Akter S, Saha S. SARS-CoV-2 host diversity: An update of natural infections and experimental evidence. J Microbiol Immunol Infect 2021; 54:175-181. [PMID: 32624360 PMCID: PMC7315156 DOI: 10.1016/j.jmii.2020.06.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/22/2020] [Accepted: 06/11/2020] [Indexed: 01/14/2023]
Abstract
Coronavirus disease-19 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is now a pandemic threat. This virus is supposed to be spread by human to human transmission. Cellular angiotensin-converting enzyme 2 (ACE2) is the receptor of SARS-CoV-2 which is identical or similar in different species of animals such as pigs, ferrets, cats, orangutans, monkeys, and humans. Moreover, a recent study predicted that dogs might be secondary hosts during the evolution of SARS-CoV-2 from bat to human. Therefore, there is a possibility of spreading SARS-CoV-2 through domestic pets. There are now many reports of SARS-CoV-2 positive cases in dogs, cats, tigers, lion, and minks. Experimental data showed ferrets and cats are highly susceptible to SARS-CoV-2 as infected by virus inoculation and can transmit the virus directly or indirectly by droplets or airborne routes. Based on these natural infection reports and experimental data, whether the pets are responsible for SARS-CoV-2 spread to humans; needs to be deeply investigated. Humans showing clinical symptoms of respiratory infections have been undergoing for the COVID-19 diagnostic test but many infected people and few pets confirmed with SARS-CoV-2 remained asymptomatic. In this review, we summarize the natural cases of SARS-CoV-2 in animals with the latest researches conducted in this field. This review will be helpful to think insights of SARS-CoV-2 transmissions, spread, and demand for seroprevalence studies, especially in companion animals.
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Affiliation(s)
- Md Golzar Hossain
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh; Division of Virology, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.
| | - Aneela Javed
- Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan
| | - Sharmin Akter
- Department of Physiology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Sukumar Saha
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh; Department of Exploratory Clinical Research, Institute for Translational Vaccinology, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
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Burthe SJ, Schäfer SM, Asaaga FA, Balakrishnan N, Chanda MM, Darshan N, Hoti SL, Kiran SK, Seshadri T, Srinivas PN, Vanak AT, Purse BV. Reviewing the ecological evidence base for management of emerging tropical zoonoses: Kyasanur Forest Disease in India as a case study. PLoS Negl Trop Dis 2021; 15:e0009243. [PMID: 33793560 PMCID: PMC8016103 DOI: 10.1371/journal.pntd.0009243] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Zoonoses disproportionately affect tropical communities and are associated with human modification and use of ecosystems. Effective management is hampered by poor ecological understanding of disease transmission and often focuses on human vaccination or treatment. Better ecological understanding of multi-vector and multi-host transmission, social and environmental factors altering human exposure, might enable a broader suite of management options. Options may include "ecological interventions" that target vectors or hosts and require good knowledge of underlying transmission processes, which may be more effective, economical, and long lasting than conventional approaches. New frameworks identify the hierarchical series of barriers that a pathogen needs to overcome before human spillover occurs and demonstrate how ecological interventions may strengthen these barriers and complement human-focused disease control. We extend these frameworks for vector-borne zoonoses, focusing on Kyasanur Forest Disease Virus (KFDV), a tick-borne, neglected zoonosis affecting poor forest communities in India, involving complex communities of tick and host species. We identify the hierarchical barriers to pathogen transmission targeted by existing management. We show that existing interventions mainly focus on human barriers (via personal protection and vaccination) or at barriers relating to Kyasanur Forest Disease (KFD) vectors (tick control on cattle and at the sites of host (monkey) deaths). We review the validity of existing management guidance for KFD through literature review and interviews with disease managers. Efficacy of interventions was difficult to quantify due to poor empirical understanding of KFDV-vector-host ecology, particularly the role of cattle and monkeys in the disease transmission cycle. Cattle are hypothesised to amplify tick populations. Monkeys may act as sentinels of human infection or are hypothesised to act as amplifying hosts for KFDV, but the spatial scale of risk arising from ticks infected via monkeys versus small mammal reservoirs is unclear. We identified 19 urgent research priorities for refinement of current management strategies or development of ecological interventions targeting vectors and host barriers to prevent disease spillover in the future.
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Affiliation(s)
- Sarah J. Burthe
- UK Centre for Ecology & Hydrology, Edinburgh, United Kingdom
| | | | | | - Natrajan Balakrishnan
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | | | - Narayanaswamy Darshan
- Department of Health and Family Welfare Services, Government of Karnataka, Shivamogga, India
- ICMR-National Institute for Traditional Medicine, Belgavi, India
| | - Subhash L. Hoti
- ICMR-National Institute for Traditional Medicine, Belgavi, India
| | - Shivani K. Kiran
- Department of Health and Family Welfare Services, Government of Karnataka, Shivamogga, India
| | - Tanya Seshadri
- Vivekananda Gorukana Kalyana Kendra (VGKK), Chamarajanagar, India
| | - Prashanth N. Srinivas
- Ashoka Trust for Ecology and the Environment, Bengaluru, India
- DBT/Wellcome Trust India Alliance Fellow, Hyderabad, India
- Institute of Public Health, Bangalore, India
| | - Abi T. Vanak
- Ashoka Trust for Ecology and the Environment, Bengaluru, India
- DBT/Wellcome Trust India Alliance Fellow, Hyderabad, India
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Bethan V. Purse
- UK Centre for Ecology & Hydrology, Wallingford, United Kingdom
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Prince T, Smith SL, Radford AD, Solomon T, Hughes GL, Patterson EI. SARS-CoV-2 Infections in Animals: Reservoirs for Reverse Zoonosis and Models for Study. Viruses 2021; 13:494. [PMID: 33802857 PMCID: PMC8002747 DOI: 10.3390/v13030494] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 12/12/2022] Open
Abstract
The recent SARS-CoV-2 pandemic has brought many questions over the origin of the virus, the threat it poses to animals both in the wild and captivity, and the risks of a permanent viral reservoir developing in animals. Animal experiments have shown that a variety of animals can become infected with the virus. While coronaviruses have been known to infect animals for decades, the true intermediate host of the virus has not been identified, with no cases of SARS-CoV-2 in wild animals. The screening of wild, farmed, and domesticated animals is necessary to help us understand the virus and its origins and prevent future outbreaks of both COVID-19 and other diseases. There is intriguing evidence that farmed mink infections (acquired from humans) have led to infection of other farm workers in turn, with a recent outbreak of a mink variant in humans in Denmark. A thorough examination of the current knowledge and evidence of the ability of SARS-CoV-2 to infect different animal species is therefore vital to evaluate the threat of animal to human transmission and reverse zoonosis.
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Affiliation(s)
- Tessa Prince
- NIHR Health Protection Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool L69 7TX, UK; (T.S.); (G.L.H.)
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (S.L.S.); (A.D.R.)
| | - Shirley L. Smith
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (S.L.S.); (A.D.R.)
| | - Alan D. Radford
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (S.L.S.); (A.D.R.)
| | - Tom Solomon
- NIHR Health Protection Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool L69 7TX, UK; (T.S.); (G.L.H.)
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (S.L.S.); (A.D.R.)
- Walton Centre NHS Foundation Trust, Liverpool L9 7LJ, UK
| | - Grant L. Hughes
- NIHR Health Protection Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool L69 7TX, UK; (T.S.); (G.L.H.)
- Centre for Neglected Tropical Disease, Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Edward I. Patterson
- Centre for Neglected Tropical Disease, Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
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Laiton-Donato K, Ávila-Robayo P, Páez-Martinez A, Benjumea-Nieto P, Usme-Ciro JA, Pinzón-Nariño N, Giraldo I, Torres-Castellanos D, Nakazawa Y, Patel N, Wilkins K, Li Y, Davidson W, Burgado J, Satheshkumar PS, Styczynski A, Mauldin MR, Gracia-Romero M, Petersen BW. Progressive Vaccinia Acquired through Zoonotic Transmission in a Patient with HIV/AIDS, Colombia. Emerg Infect Dis 2021; 26:601-605. [PMID: 32091366 PMCID: PMC7045850 DOI: 10.3201/eid2603.191365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In March 2015, a patient in Colombia with HIV/AIDS was hospitalized for disseminated ulcers after milking cows that had vesicular lesions on their udders. Vaccinia virus was detected, and the case met criteria for progressive vaccinia acquired by zoonotic transmission. Adherence to an optimized antiretroviral regimen resulted in recovery.
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Mangombi JB, N’dilimabaka N, Lekana-Douki JB, Banga O, Maghendji-Nzondo S, Bourgarel M, Leroy E, Fenollar F, Mediannikov O. First investigation of pathogenic bacteria, protozoa and viruses in rodents and shrews in context of forest-savannah-urban areas interface in the city of Franceville (Gabon). PLoS One 2021; 16:e0248244. [PMID: 33684147 PMCID: PMC7939261 DOI: 10.1371/journal.pone.0248244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/23/2021] [Indexed: 12/29/2022] Open
Abstract
Rodents are reservoirs of numerous zoonotic diseases caused by bacteria, protozoans, or viruses. In Gabon, the circulation and maintenance of rodent-borne zoonotic infectious agents are poorly studied and are often limited to one type of pathogen. Among the three existing studies on this topic, two are focused on a zoonotic virus, and the third is focused on rodent Plasmodium. In this study, we searched for a wide range of bacteria, protozoa and viruses in different organs of rodents from the town of Franceville in Gabon. Samples from one hundred and ninety-eight (198) small mammals captured, including two invasive rodent species, five native rodent species and 19 shrews belonging to the Soricidae family, were screened. The investigated pathogens were bacteria from the Rickettsiaceae and Anaplasmataceae families, Mycoplasma spp., Bartonella spp., Borrelia spp., Orientia spp., Occidentia spp., Leptospira spp., Streptobacillus moniliformis, Coxiella burnetii, and Yersinia pestis; parasites from class Kinetoplastida spp. (Leishmania spp., Trypanosoma spp.), Piroplasmidae spp., and Toxoplasma gondii; and viruses from Paramyxoviridae, Hantaviridae, Flaviviridae and Mammarenavirus spp. We identified the following pathogenic bacteria: Anaplasma spp. (8.1%; 16/198), Bartonella spp. (6.6%; 13/198), Coxiella spp. (5.1%; 10/198) and Leptospira spp. (3.5%; 7/198); and protozoans: Piroplasma sp. (1%; 2/198), Toxoplasma gondii (0.5%; 1/198), and Trypanosoma sp. (7%; 14/198). None of the targeted viral genes were detected. These pathogens were found in Gabonese rodents, mainly Lophuromys sp., Lemniscomys striatus and Praomys sp. We also identified new genotypes: Candidatus Bartonella gabonensis and Uncultured Anaplasma spp. This study shows that rodents in Gabon harbor some human pathogenic bacteria and protozoans. It is necessary to determine whether the identified microorganisms are capable of undergoing zoonotic transmission from rodents to humans and if they may be responsible for human cases of febrile disease of unknown etiology in Gabon.
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Affiliation(s)
- Joa Braïthe Mangombi
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- Aix Marseille Univ, IRD, AP-HM, Microbes, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Nadine N’dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- Département de Biologie, Faculté des sciences, Université des Sciences et Techniques de Masuku (USTM), Franceville, Gabon
| | - Jean-Bernard Lekana-Douki
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie, Université des Sciences de la Santé (USS), Owendo, Libreville
| | - Octavie Banga
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Sydney Maghendji-Nzondo
- Département Epidémiologie-Biostatistique et Informatique Médicale (DEBIM), Université des Sciences de la Santé (USS), Owendo, Libreville
| | - Mathieu Bourgarel
- CIRAD, UMR ASTRE, Harare, Zimbabwe
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Eric Leroy
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- UMR MIVEGEC IRD-CNRS-UM, IRD, Montpellier, France
| | - Florence Fenollar
- Aix Marseille Univ, IRD, AP-HM, Microbes, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Oleg Mediannikov
- IHU Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, Microbes, MEPHI, Marseille, France
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Muga GO, Onyango-Ouma W, Sang R, Affognon H. Indigenous knowledge of Rift Valley Fever among Somali nomadic pastoralists and its implications on public health delivery approaches in Ijara sub-County, North Eastern Kenya. PLoS Negl Trop Dis 2021; 15:e0009166. [PMID: 33617555 PMCID: PMC7932528 DOI: 10.1371/journal.pntd.0009166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/04/2021] [Accepted: 01/21/2021] [Indexed: 11/28/2022] Open
Abstract
Rift Valley Fever (RVF) is a zoonotic disease whose outbreak results in heavy economic and public health burdens. In East Africa, RVF is mainly experienced in arid and semi-arid areas predominantly inhabited by the pastoralists. These areas experience sudden, dramatic epidemics of the disease at intervals of approximately 10 years, associated with widespread flooding and the resultant swarms of mosquitoes. Pastoralists’ indigenous knowledge and experience of RVF is critical for public health interventions targeting prevention and control of RVF. The study adopted a descriptive cross-sectional design combining both quantitative and qualitative methods of data collection. A total of 204 respondents participated in questionnaire survey and 15 key informants and 4 focus group discussions were interviewed and conducted respectively. In addition, secondary data mainly journal publications, books, policy documents and research reports from conferences and government departments were reviewed. Findings indicated that the Somali pastoralists possess immense knowledge of RVF including signs and symptoms, risk factors, and risk pathways associated with RVF. Ninety eight percent (98%) of respondents identified signs and symptoms such as bloody nose, diarrhea, foul smell and discharge of blood from the orifices which are consistent with RVF. Heavy rains and floods (85%) and sudden emergence of mosquito swarms (91%) were also cited as the major RVF risk factors while mosquito bites (85%), drinking raw milk and blood (78%) and contact with animal fluids during mobility, slaughter and obstetric procedures (77%) were mentioned as the RVF entry risk pathways. Despite this immense knowledge, the study found that the pastoralists did not translate the knowledge into safer health practices because of the deep-seated socio-cultural practices associated with pastoralist production system and religious beliefs. On top of these practices, food preparation and consumption practices such as drinking raw blood and milk and animal ritual sacrifices continue to account for most of the mortality and morbidity cases experienced in humans and animals during RVF outbreaks. This article concludes that pastoralists’ indigenous knowledge on RVF has implications on public health delivery approaches. Since the pastoralists’ knowledge on RVF was definitive, integrating the community into early warning systems through training on reporting mechanisms and empowering the nomads to use their mobile phone devices to report observable changes in their livestock and environment could prove very effective in providing information for timely mobilization of public health responses. Public health advocacy based on targeted and contextually appropriate health messaging and disseminated through popular communication channels in the community such as the religious leaders and local radio stations would also be needed to reverse the drivers of RVF occurrence in the study area. Rift Valley Fever is a viral disease that affects both humans and animals. It is categorized as one of the re-emerging and neglected tropical diseases that mainly affects the poor and marginalized populations that lack access to health services and are readily ignored. Humans usually get RVF through bites from infected mosquitoes. Infections also occur when humans are exposed to the body fluids, or tissues of infected animals. Hence the risk of infection is greatest when slaughtering in the context of traditional sacrificial practices. This is the major reason outbreak of RVF is commonly associated with people whose livelihoods revolve around livestock rearing. In East Africa, RVF is mainly experienced in arid and semi-arid areas predominantly inhabited by the pastoralists. These areas experience epidemics of the disease at intervals of approximately 10 years associated with Elnino events. Understanding the knowledge base of the people in terms of RVF signs and symptoms and risk factors and pathways is important for the adoption of effective prevention and control measures. This study findings suggest that even though the Somali nomads are adept at recognizing RVF, this knowledge has not been translated into appropriate health practices due to the deep-seated socio-cultural practices. Hence, there is need for health authorities to mount locally appropriate public health advocacy campaigns, empower the livestock keepers to report observable changes in livestock and environment using their mobile phone devices and promote cross-disciplinary studies on RVF.
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Affiliation(s)
- Geoffrey Otieno Muga
- Institute of Anthropology, Gender and African Studies, University of Nairobi, Nairobi, Kenya
- * E-mail:
| | - Washington Onyango-Ouma
- Institute of Anthropology, Gender and African Studies, University of Nairobi, Nairobi, Kenya
| | - Rosemary Sang
- International Centre for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
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50
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Bergner LM, Mollentze N, Orton RJ, Tello C, Broos A, Biek R, Streicker DG. Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats. Viruses 2021; 13:252. [PMID: 33562073 PMCID: PMC7914986 DOI: 10.3390/v13020252] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/25/2021] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely applied to viruses at the time of their discovery. Here, we characterized viral genomes detected through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) and used these data as a case study in evaluating zoonotic potential using molecular sequencing data. Of 58 detected viral families, including 17 which infect mammals, the only known zoonosis detected was rabies virus; however, additional genomes were detected from the families Hepeviridae, Coronaviridae, Reoviridae, Astroviridae and Picornaviridae, all of which contain human-infecting species. In phylogenetic analyses, novel vampire bat viruses most frequently grouped with other bat viruses that are not currently known to infect humans. In agreement, machine learning models built from only phylogenetic information ranked all novel viruses similarly, yielding little insight into zoonotic potential. In contrast, genome composition-based machine learning models estimated different levels of zoonotic potential, even for closely related viruses, categorizing one out of four detected hepeviruses and two out of three picornaviruses as having high priority for further research. We highlight the value of evaluating zoonotic potential beyond ad hoc consideration of phylogeny and provide surveillance recommendations for novel viruses in a wildlife host which has frequent contact with humans and domestic animals.
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Affiliation(s)
- Laura M. Bergner
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (N.M.); (R.B.); (D.G.S.)
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (R.J.O.); (A.B.)
| | - Nardus Mollentze
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (N.M.); (R.B.); (D.G.S.)
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (R.J.O.); (A.B.)
| | - Richard J. Orton
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (R.J.O.); (A.B.)
| | - Carlos Tello
- Association for the Conservation and Development of Natural Resources, Lima 15037, Peru;
- Yunkawasi, Lima 15049, Peru
| | - Alice Broos
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (R.J.O.); (A.B.)
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (N.M.); (R.B.); (D.G.S.)
| | - Daniel G. Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (N.M.); (R.B.); (D.G.S.)
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (R.J.O.); (A.B.)
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