1
|
Fujii Y, Masatani T, Nishiyama S, Takahashi T, Okajima M, Izumi F, Sakoda Y, Takada A, Ozawa M, Sugiyama M, Ito N. Molecular characterization of an avian rotavirus a strain detected from a large-billed crow (Corvus macrorhynchos) in Japan. Virology 2024; 596:110114. [PMID: 38781709 DOI: 10.1016/j.virol.2024.110114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/02/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Avian rotaviruses A (RVAs) are occasionally transmitted to animals other than the original hosts across species barriers. Information on RVAs carried by various bird species is important for identifying the origin of such interspecies transmission. In this study, to facilitate an understanding of the ecology of RVAs from wild birds, we characterized all of the genes of an RVA strain, JC-105, that was detected in a fecal sample of a large-billed crow (Corvus macrorhynchos) in Japan. All of the genes of this strain except for the VP4 and VP7 genes, which were classified as novel genotypes (P[56] and G40, respectively), were closely related to those of the avian-like RVA strain detected from a raccoon, indicating the possibility that crows had been involved in the transmission of avian RVAs to raccoons. Our findings highlight the need for further viral investigations in wild birds and mammals to understand the mechanisms of avian-to-mammal RVA transmission.
Collapse
Affiliation(s)
- Yuji Fujii
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Tatsunori Masatani
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Shoko Nishiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Tatsuki Takahashi
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Misuzu Okajima
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Fumiki Izumi
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, Hokkaido 060-0818, Japan
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Makoto Ozawa
- Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Makoto Sugiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
| | - Naoto Ito
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
| |
Collapse
|
2
|
Miura T, Kadoya SS, Miura Y, Takino H, Akiba M, Sano D, Masuda T. Pepper mild mottle virus intended for use as a process indicator for drinking water treatment: Present forms and quantitative relations to norovirus and rotavirus in surface water. WATER RESEARCH 2024; 257:121713. [PMID: 38733963 DOI: 10.1016/j.watres.2024.121713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/19/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Pepper mild mottle virus (PMMoV) has been proposed as a potential indicator of human enteric viruses in environmental water and for viral removal during drinking water treatment. To investigate the occurrence and present forms of PMMoV and quantitative relations to norovirus GII and rotavirus A (RVA) in surface waters, 147 source water samples were collected from 21 drinking water treatment plants (DWTPs) in Japan between January 2018 and January 2021, and the concentrations of viruses in suspended and dissolved fractions were measured using real-time RT-PCR. PMMoV was detected in 81-100 % of samples in each sample month and observed concentrations ranged from 3.0 to 7.0 log10 copies/L. The concentrations of PMMoV were higher in dissolved fraction compared to suspended fractions, while different partitioning was observed for NoV GII depending on seasons. The concentrations of PMMoV were basically higher than those of norovirus GII (1.9-5.3 log10 copies/L) and RVA (1.9-6.6 log10 copies/L), while in 18 samples, RVA presented higher concentrations than PMMoV. Partial regions of VP7, VP4, and VP6 of the RVA in the 18 samples were amplified using nested PCR, and the genotypes were determined using an amplicon-based next-generation sequencing approach. We found that these source water samples included not only human RVA but also various animal RVA and high genetic diversity due to the existence of animal RVA was associated with a higher RVA concentration than PMMoV. Our findings suggest that PMMoV can be used as an indicator of norovirus GII and human RVA in drinking water sources and that the indicator performance should be evaluated by comparing to zoonotic viruses as well as human viruses.
Collapse
Affiliation(s)
- Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan.
| | - Syun-Suke Kadoya
- Department of Civil and Environmental Engineering, Tohoku University, Japan; Department of Urban Engineering, The University of Tokyo, Japan
| | - Yohei Miura
- Department of Civil and Environmental Engineering, Tohoku University, Japan
| | - Hiroyuki Takino
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Michihiro Akiba
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Japan
| | | |
Collapse
|
3
|
Wu Q, Liu X, Wang J, Xu S, Zeng F, Chen L, Zhang G, Wang H. An isothermal nucleic acid amplification-based enzymatic recombinase amplification method for dual detection of porcine epidemic diarrhea virus and porcine rotavirus A. Virology 2024; 594:110062. [PMID: 38522136 DOI: 10.1016/j.virol.2024.110062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/06/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
Viral diarrhea is the predominant digestive tract sickness in piglings, resulting in substantial profit losses in the porcine industry. Porcine rotavirus A (PoRVA) and porcine epidemic diarrhea virus (PEDV) are the main causes of grave gastroenteritis and massive dysentery, especially in piglets. PoRVA and PEDV have high transmissibility, exhibit similar clinical symptoms, and frequently co-occur. Therefore, to avoid financial losses, a quick, highly efficient, objective diagnostic test for the prevention and detection of these diseases is required. Enzymatic recombinase amplification (ERA) is a novel technology based on isothermal nucleic acid amplification. It demonstrates high sensitivity and excellent specificity, with a short processing time and easy operability, compared with other in vitro nucleic acid amplification technologies. In this study, a dual ERA method to detect and distinguish between PEDV and PoRVA nucleic acids was established. The method shows high sensitivity, as the detection limits were 101 copies/μL for both viruses. To test the usefulness of this method in clinical settings, we tested 64 swine clinical samples. Our results were 100% matched with those acquired using a commercially available kit. Therefore, we have successfully developed a dual diagnostic ERA nucleic acids method for detecting and distinguishing between PEDV and PoRVA.
Collapse
Affiliation(s)
- Qianwen Wu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Xing Liu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Jingyu Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Sijia Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Fanliang Zeng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Ling Chen
- Ganzhou Quannan County Agriculture and Rural Bureau, Ganzhou, 341800, China
| | - Guihong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
| | - Heng Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
4
|
Amin AB, Cates JE, Liu Z, Wu J, Ali I, Rodriguez A, Panjwani J, Tate JE, Lopman BA, Parashar UD. Rotavirus Genotypes in the Postvaccine Era: A Systematic Review and Meta-analysis of Global, Regional, and Temporal Trends by Rotavirus Vaccine Introduction. J Infect Dis 2024; 229:1460-1469. [PMID: 37738554 PMCID: PMC11095550 DOI: 10.1093/infdis/jiad403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Even moderate differences in rotavirus vaccine effectiveness against nonvaccine genotypes may exert selective pressures on circulating rotaviruses. Whether this vaccine effect or natural temporal fluctuations underlie observed changes in genotype distributions is unclear. METHODS We systematically reviewed studies reporting rotavirus genotypes from children <5 years of age globally between 2005 and 2023. We compared rotavirus genotypes between vaccine-introducing and nonintroducing settings globally and by World Health Organization (WHO) region, calendar time, and time since vaccine introduction. RESULTS Crude pooling of genotype data from 361 studies indicated higher G2P[4], a nonvaccine genotype, prevalence in vaccine-introducing settings, both globally and by WHO region. This difference did not emerge when examining genotypes over time in the Americas, the only region with robust longitudinal data. Relative to nonintroducing settings, G2P[4] detections were more likely in settings with recent introduction (eg, 1-2 years postintroduction adjusted odds ratio [aOR], 4.39; 95% confidence interval [CI], 2.87-6.72) but were similarly likely in settings with more time elapsed since introduction, (eg, 7 or more years aOR, 1.62; 95% CI, .49-5.37). CONCLUSIONS When accounting for both regional and temporal trends, there was no substantial evidence of long-term vaccine-related selective pressures on circulating genotypes. Increased prevalence of G2P[4] may be transient after rotavirus vaccine introduction.
Collapse
Affiliation(s)
- Avnika B Amin
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Jordan E Cates
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Zihao Liu
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Joanne Wu
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Iman Ali
- Centers for Disease Control and Prevention Foundation, Atlanta, Georgia, USA
| | - Alexia Rodriguez
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Junaid Panjwani
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jacqueline E Tate
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Benjamin A Lopman
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Umesh D Parashar
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| |
Collapse
|
5
|
França Y, Medeiros RS, Viana E, de Azevedo LS, Guiducci R, da Costa AC, Luchs A. Genetic diversity and evolution of G12P[6] DS-1-like and G12P[9] AU-1-like Rotavirus strains in Brazil. Funct Integr Genomics 2024; 24:92. [PMID: 38733534 DOI: 10.1007/s10142-024-01360-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/31/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
In the early 2000s, the global emergence of rotavirus (RVA) G12P[8] genotype was noted, while G12P[6] and G12P[9] combinations remained rare in humans. This study aimed to characterize and phylogenetically analyze three Brazilian G12P[9] and four G12P[6] RVA strains from 2011 to 2020, through RT-PCR and sequencing, in order to enhance our understanding of the genetic relationship between human and animal-origin RVA strains. G12P[6] strains displayed a DS-1-like backbone, showing a distinct genetic clustering. G12P[6] IAL-R52/2020, IAL-R95/2020 and IAL-R465/2019 strains clustered with 2019 Northeastern G12P[6] Brazilian strains and a 2018 Benin strain, whereas IAL-R86/2011 strain grouped with 2010 Northern G12P[6] Brazilian strains and G2P[4] strains from the United States and Belgium. These findings suggest an African genetic ancestry and reassortments with co-circulating American strains sharing the same DS-1-like constellation. No recent zoonotic reassortment was observed, and the DS-1-like constellation detected in Brazilian G12P[6] strains does not seem to be genetically linked to globally reported intergenogroup G1/G3/G9/G8P[8] DS-1-like human strains. G12P[9] strains exhibited an AU-1-like backbone with two different genotype-lineage constellations: IAL-R566/2011 and IAL-R1151/2012 belonged to a VP3/M3.V Lineage, and IAL-R870/2013 to a VP3/M3.II Lineage, suggesting two co-circulating strains in Brazil. This genetic diversity is not observed elsewhere, and the VP3/M3.II Lineage in G12P[9] strains seems to be exclusive to Brazil, indicating its evolution within the country. All three G12P[9] AU-1-like strains were closely relate to G12P[9] strains from Paraguay (2006-2007) and Brazil (2010). Phylogenetic analysis also highlighted that all South American G12P[9] AU-1-like strains had a common origin and supports the hypothesis of their importation from Asia, with no recent introduction from globally circulating G12P[9] strains or reassortments with local G12 strains P[8] or P[6]. Notably, certain genes in the Brazilian G12P[9] AU-1-like strains share ancestry with feline/canine RVAs (VP3/M3.II, NSP4/E3.IV and NSP2/N3.II), whereas NSP1/A3.VI likely originated from artiodactyls, suggesting a history of zoonotic transmission with human strains. This genomic data adds understanding to the molecular epidemiology of G12P[6] and G12P[9] RVA strains in Brazil, offering insights into their genetic diversity and evolution.
Collapse
Affiliation(s)
- Yasmin França
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Ellen Viana
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Raquel Guiducci
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Antonio Charlys da Costa
- Medical Parasitology Laboratory (LIM/46), São Paulo Tropical Medicine Institute, University of Sao Paulo, Sao Paulo, Brazil
| | - Adriana Luchs
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil.
| |
Collapse
|
6
|
Haque W, Talha M, Rahman S, Hasan M, Alam S, Hassan Z, Moni S, Khan SH, Hossain ME, Faruque ASG, Hasan SMT, Khan SH, Ahmed T, Zaman K, Rahman M. Rotavirus trends and distribution of genotypes before and during COVID-19 pandemic era: Bangladesh, 2017-2021. J Med Virol 2024; 96:e29681. [PMID: 38773815 DOI: 10.1002/jmv.29681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 04/18/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024]
Abstract
Rotavirus gastroenteritis is accountable for an estimated 128 500 deaths among children younger than 5 years worldwide, and the majority occur in low-income countries. Although the clinical trials of rotavirus vaccines in Bangladesh revealed a significant reduction of severe rotavirus disease by around 50%, the vaccines are not yet included in the routine immunization program. The present study was designed to provide data on rotavirus diarrhea with clinical profiles and genotypes before (2017-2019) and during the COVID-19 pandemic period (2020-2021). Fecal samples were collected from 2% of the diarrheal patients at icddr,b Dhaka hospital of all ages between January 2017 and December 2021 and were tested for VP6 rotavirus antigen using ELISA. The clinical manifestations such as fever, duration of diarrhea and hospitalization, number of stools, and dehydration and so on were collected from the surveillance database (n = 3127). Of the positive samples, 10% were randomly selected for genotyping using Sanger sequencing method. A total of 12 705 fecal samples were screened for rotavirus A antigen by enzyme immunoassay. Overall, 3369 (27%) were rotavirus antigen-positive, of whom children <2 years had the highest prevalence (88.6%). The risk of rotavirus A infection was 4.2 times higher in winter than in summer. Overall, G3P[8] was the most prominent genotype (45.3%), followed by G1P[8] (32.1%), G9P[8] (6.8%), and G2P[4] (6.1%). The other unusual combinations, such as G1P[4], G1P[6], G2P[6], G3P[4], G3P[6], and G9P[6], were also present. Genetic analysis on Bangladeshi strains revealed that the selection pressure (dN/dS) was estimated as <1. The number of hospital visits showed a 37% drop during the COVID-19 pandemic relative to the years before the pandemic. Conversely, there was a notable increase in the rate of rotavirus positivity during the pandemic (34%, p < 0.00) compared to the period before COVID-19 (23%). Among the various clinical symptoms, only the occurrence of watery stool significantly increased during the pandemic. The G2P[4] strain showed a sudden rise (19%) in 2020, which then declined in 2021. In the same year, G1P[8] was more prevalent than G3P[8] (40% vs. 38%, respectively). The remaining genotypes were negligible and did not exhibit much fluctuation. This study reveals that the rotavirus burden remained high during the COVID-19 prepandemic and pandemic in Bangladesh. Considering the lack of antigenic variations between the circulating and vaccine-targeted strains, integrating the vaccine into the national immunization program could reduce the prevalence of the disease, the number of hospitalizations, and the severity of cases.
Collapse
Affiliation(s)
- Warda Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Muhammad Talha
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sezanur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mehedi Hasan
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Shaheen Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Zahid Hassan
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Sayra Moni
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sadia H Khan
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad E Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Abu S G Faruque
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - S M Tafsir Hasan
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Soroar H Khan
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Khalequz Zaman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafizur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| |
Collapse
|
7
|
Gutierrez MB, Arantes I, Bello G, Berto LH, Dutra LH, Kato RB, Fumian TM. Emergence and dissemination of equine-like G3P[8] rotavirus A in Brazil between 2015 and 2021. Microbiol Spectr 2024; 12:e0370923. [PMID: 38451227 PMCID: PMC10986506 DOI: 10.1128/spectrum.03709-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/22/2024] [Indexed: 03/08/2024] Open
Abstract
Rotavirus A (RVA) is a major cause of acute gastroenteritis globally that is classically genotyped by its two immunodominant outer capsid proteins, VP7 (G-) and VP4 (P-). Recent evidence suggests that the reassortant equine-like G3P[8] strain played a substantial role in RVA transmission in Brazil since 2015. To understand its global emergence and dissemination in Brazilian territory, stool samples collected from 11 Brazilian states (n = 919) were genotyped by RT-qPCR and proceeded to sequence the VP7 gene (n = 102, 79 being newly generated) of the G3P[8] samples with pronounced viral loads. Our phylogenetic genotyping showed that G3P[8] became the dominant strain in Brazil between 2017 and 2020, with equine-like variants representing 75%-100% of VP7 samples in this period. A Bayesian discrete phylogeographic analysis strongly suggests that the equine-like G3P[8] strain originated in Asia during the early 2010s and subsequently spread to Europe, the Caribbean, and South America. Multiple introductions were detected in Brazil between 2014 and 2017, resulting in five national clusters. The reconstruction of the effective population size of the largest Brazilian cluster showed an expansion until 2017, followed by a plateau phase until 2019 and subsequent contraction. Our study also supports that most mutations fixed during equine-like G3P[8] evolution were synonymous, suggesting that adaptive evolution was not an important driving force during viral dissemination in humans, potentially increasing its susceptibility to acquired immunity. This research emphasizes the need for comprehensive rotavirus genomic surveillance that allows close monitoring of its ever-shifting composition and informs more effective public health policies.IMPORTANCEOur original article demonstrated the origin and spread in a short time of equine-like G3P[8] in Brazil and the world. Due to its segmented genome, it allows numerous mechanisms including genetic drift and reassortment contribute substantially to the genetic diversity of rotavirus. Although the effectiveness and increasing implementation of vaccination have not been questioned, a matter of concern is its impact on the emergence of escape mutants or even the spread of unusual strains of zoonotic transmission that could drive epidemic patterns worldwide. This research emphasizes the need for comprehensive rotavirus genomic surveillance, which could facilitate the formulation of public policies aimed at preventing and mitigating its transmission.
Collapse
Affiliation(s)
| | - Ighor Arantes
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Lúcia Helena Berto
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Leonardo Hermes Dutra
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Rodrigo Bentes Kato
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| |
Collapse
|
8
|
Dias JBL, Pinheiro MS, Petrucci MP, Travassos CEPF, Mendes GS, Santos N. Rotavirus A and D circulating in commercial chicken flocks in southeastern Brazil. Vet Res Commun 2024; 48:743-748. [PMID: 37878188 DOI: 10.1007/s11259-023-10246-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/19/2023] [Indexed: 10/26/2023]
Abstract
Rotavirus (RV) outbreaks can cause significant economic losses in the livestock and poultry industries. Stool samples were collected from asymptomatic laying and broiler chickens from commercial poultry farms in the states of Rio de Janeiro and Espírito Santo in southeastern Brazil for detection of RV species A and D (RVA and RVD, respectively) by reverse transcription polymerase chain reaction. RV was detected in 10.5% (34/325) of samples: 22 (64.7%) were positive for RVA and nine (26.5%) for RVD, while three (8.8%) exhibited coinfections with both viruses. Sequence analysis of a VP6 fragment from seven RVA-positive samples identified the I11 genotype in all samples. Information regarding avian RV epidemiology is still scanty, despite the high prevalence of RV infections in several bird species and subsequent economic impact. Consequently, monitoring infections caused by avian RVs, especially in commercial birds, is essential not only to provide new and relevant information regarding the biology, epidemiology, and evolution of these viruses, but also to facilitate the implementation of preventive measures.
Collapse
Affiliation(s)
- Juliana B L Dias
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, CCS, Bl. I, Ilha do Fundão, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Mariana S Pinheiro
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, CCS, Bl. I, Ilha do Fundão, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Melissa P Petrucci
- Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Carlos E P F Travassos
- Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Gabriella S Mendes
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, CCS, Bl. I, Ilha do Fundão, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Norma Santos
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, CCS, Bl. I, Ilha do Fundão, Rio de Janeiro, RJ, 21.941-902, Brazil.
| |
Collapse
|
9
|
Snyder AJ, Agbemabiese CA, Patton JT. Production of OSU G5P[7] Porcine Rotavirus Expressing a Fluorescent Reporter via Reverse Genetics. Viruses 2024; 16:411. [PMID: 38543776 PMCID: PMC10974435 DOI: 10.3390/v16030411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 05/23/2024] Open
Abstract
Rotaviruses are a significant cause of severe, potentially life-threatening gastroenteritis in infants and the young of many economically important animals. Although vaccines against porcine rotavirus exist, both live oral and inactivated, their effectiveness in preventing gastroenteritis is less than ideal. Thus, there is a need for the development of new generations of porcine rotavirus vaccines. The Ohio State University (OSU) rotavirus strain represents a Rotavirus A species with a G5P[7] genotype, the genotype most frequently associated with rotavirus disease in piglets. Using complete genome sequences that were determined via Nanopore sequencing, we developed a robust reverse genetics system enabling the recovery of recombinant (r)OSU rotavirus. Although rOSU grew to high titers (~107 plaque-forming units/mL), its growth kinetics were modestly decreased in comparison to the laboratory-adapted OSU virus. The reverse genetics system was used to generate the rOSU rotavirus, which served as an expression vector for a foreign protein. Specifically, by engineering a fused NSP3-2A-UnaG open reading frame into the segment 7 RNA, we produced a genetically stable rOSU virus that expressed the fluorescent UnaG protein as a functional separate product. Together, these findings raise the possibility of producing improved live oral porcine rotavirus vaccines through reverse-genetics-based modification or combination porcine rotavirus vaccines that can express neutralizing antigens for other porcine enteric diseases.
Collapse
Affiliation(s)
- Anthony J. Snyder
- Department of Biology, Indiana University, 212 S. Hawthorne Drive, Simon Hall 011, Bloomington, IN 47405, USA; (A.J.S.); (C.A.A.)
| | - Chantal A. Agbemabiese
- Department of Biology, Indiana University, 212 S. Hawthorne Drive, Simon Hall 011, Bloomington, IN 47405, USA; (A.J.S.); (C.A.A.)
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra 00233, Ghana
| | - John T. Patton
- Department of Biology, Indiana University, 212 S. Hawthorne Drive, Simon Hall 011, Bloomington, IN 47405, USA; (A.J.S.); (C.A.A.)
| |
Collapse
|
10
|
Shizawa S, Fukuda F, Kikkawa Y, Oi T, Takemae H, Masuda T, Ishida H, Murakami H, Sakaguchi S, Mizutani T, Nagai M, Oba M. Genomic diversity of group A rotaviruses from wild boars and domestic pigs in Japan: wide prevalence of NSP5 carrying the H2 genotype. Arch Virol 2024; 169:63. [PMID: 38451342 DOI: 10.1007/s00705-023-05954-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/24/2023] [Indexed: 03/08/2024]
Abstract
Group A rotavirus (RVA) sequences were detected in 10.8% (23/212) and 20.7% (87/421) of fecal samples collected in 2017-2022 from wild boars and domestic pigs, using next-generation sequencing. Complete genome sequence analysis of one wild boar and 13 domestic pig RVAs revealed that six of them carried the rare H2 NSP5 genotype. Out of the 39 samples for which the NSP5 genotype could be determined, 23 (59.0%) were of genotype H2. H2 porcine RVAs consist exclusively of Japanese porcine RVAs and exhibit sequence diversity in each segment, suggesting that H2 porcine RVAs may have evolved through reassortment within the Japanese pig population.
Collapse
Affiliation(s)
- Shigeki Shizawa
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
| | - Fujiko Fukuda
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa, 920-3101, Japan
| | | | - Toru Oi
- Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
| | - Hitoshi Takemae
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Tsuneyuki Masuda
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, 794-0085, Japan
| | - Hiroho Ishida
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
| | - Hironobu Murakami
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Tetsuya Mizutani
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Makoto Nagai
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Mami Oba
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan.
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
| |
Collapse
|
11
|
Flynn TG, Olortegui MP, Kosek MN. Viral gastroenteritis. Lancet 2024; 403:862-876. [PMID: 38340741 DOI: 10.1016/s0140-6736(23)02037-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/17/2023] [Accepted: 09/18/2023] [Indexed: 02/12/2024]
Abstract
Since the discovery of norovirus in 1972 as a cause of what was contemporarily known as acute infectious non-bacterial gastroenteritis, scientific understanding of the viral gastroenteritides has continued to evolve. It is now recognised that a small number of viruses are the predominant cause of acute gastroenteritis worldwide, in both high-income and low-income settings. Although treatment is still largely restricted to the replacement of fluid and electrolytes, improved diagnostics have allowed attribution of illness, enabling both targeted treatment of individual patients and prioritisation of interventions for populations worldwide. Questions remain regarding specific genetic and immunological factors underlying host susceptibility, and the optimal clinical management of patients who are susceptible to severe or prolonged manifestations of disease. Meanwhile, the worldwide implementation of rotavirus vaccines has led to substantial reductions in morbidity and mortality, and spurred interest in vaccine development to diminish the impact of the most prevalent viruses that are implicated in this syndrome.
Collapse
Affiliation(s)
- Thomas G Flynn
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
12
|
Le LKT, Chu MNT, Tate JE, Jiang B, Bowen MD, Esona MD, Gautam R, Jaimes J, Pham TPT, Huong NT, Anh DD, Trang NV, Parashar U. Genetic diversity of G9, G3, G8 and G1 rotavirus group A strains circulating among children with acute gastroenteritis in Vietnam from 2016 to 2021. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105566. [PMID: 38316245 DOI: 10.1016/j.meegid.2024.105566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Rotavirus group A (RVA) is the most common cause of severe childhood diarrhea worldwide. The introduction of rotavirus vaccination programs has contributed to a reduction in hospitalizations and mortality caused by RVA. From 2016 to 2021, we conducted surveillance to monitor RVA prevalence and genotype distribution in Nam Dinh and Thua Thien Hue (TT Hue) provinces where a pilot Rotavin-M1 vaccine (Vietnam) implementation took place from 2017 to 2020. Out of 6626 stool samples, RVA was detected in 2164 (32.6%) by ELISA. RT-PCR using type-specific primers were used to determine the G and P genotypes of RVA-positive specimens. Whole genome sequences of a subset of 52 specimens randomly selected from 2016 to 2021 were mapped using next-generation sequencing. From 2016 to 2021, the G9, G3 and G8 strains dominated, with detected frequencies of 39%, 23%, and 19%, respectively; of which, the most common genotypes identified were G9P[8], G3P[8] and G8P[8]. G1 strains re-emerged in Nam Dinh and TT Hue (29.5% and 11.9%, respectively) from 2020 to 2021. G3 prevalence decreased from 74% to 20% in TT Hue and from 21% to 13% in Nam Dinh province between 2017 and 2021. The G3 strains consisted of 52% human typical G3 (hG3) and 47% equine-like G3 (eG3). Full genome analysis showed substantial diversity among the circulating G3 strains with different backgrounds relating to equine and feline viruses. G9 prevalence decreased sharply from 2016 to 2021 in both provinces. G8 strains peaked during 2019-2020 in Nam Dinh and TT Hue provinces (68% and 46%, respectively). Most G8 and G9 strains had no genetic differences over the surveillance period with very high nucleotide similarities of 99.2-99.9% and 99.1-99.7%, respectively. The G1 strains were not derived from the RVA vaccine. Changes in the genotype distribution and substantial diversity among circulating strains were detected throughout the surveillance period and differed between the two provinces. Determining vaccine effectiveness against circulating strains over time will be important to ensure that observed changes are due to natural secular variation and not from vaccine pressure.
Collapse
Affiliation(s)
- Ly K T Le
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam
| | - Mai N T Chu
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam
| | - Jacqueline E Tate
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Baoming Jiang
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Michael D Bowen
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Mathew D Esona
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Rashi Gautam
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Jose Jaimes
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Thao P T Pham
- Center for Research and Production of Vaccines and Biologicals, Hanoi 100000, Viet Nam
| | - Nguyen T Huong
- Center for Research and Production of Vaccines and Biologicals, Hanoi 100000, Viet Nam
| | - Dang D Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam
| | - Nguyen V Trang
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam.
| | - Umesh Parashar
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| |
Collapse
|
13
|
Okamoto A, Takemae H, Nagai M, Hashimoto S, Mizutani T, Furuya T. First report of the whole-genome sequence analysis of avian rotavirus A from Japanese chickens. Virus Genes 2024; 60:25-31. [PMID: 38102511 DOI: 10.1007/s11262-023-02040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/11/2023] [Indexed: 12/17/2023]
Abstract
Rotavirus A infects many mammalian species, including humans and causes diarrhea and gastrointestinal diseases. The virus also infects various bird species, including chickens, although information of avian rotavirus A (ARVA) infection in chicken populations in Japan is scarce. In this study, we report for the first time the whole-genome sequences of ARVA strains from Japanese chicken populations. The virus strains were inoculated to MA104 cells and cultured viruses were used to obtain the sequences with the MiSeq system, and genetic analysis demonstrated the genotype constellation of G19-P[30]-I11-R6-C6-M7-A16-N6-T8-E10-H8 of the Japanese chicken ARVA isolates. Phylogenetic analyses demonstrated that the VP1, VP2, VP3, VP4, VP7, NSP2, and NSP4 coding gene sequences of the Japanese strains were closer to those of Korean than the European ARVA strains, although such relationship was not clear for other genes. The data suggest that the Japanese ARVA strains and the ones in Korea have genetically close relationship, although the origin is not clear at this point. Further information including the whole-genome sequences of the Korean strains and sequences of other Japanese chicken ARVA strains will be necessary for elucidation of their origin.
Collapse
Affiliation(s)
- Ayana Okamoto
- Laboratory of Veterinary Infectious Diseases, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Hitoshi Takemae
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
- Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Makoto Nagai
- Department of Large Animal Clinic, Azabu University, Veterinary Teaching Hospital, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
| | - Shinichiro Hashimoto
- Wellfam Foods Corporation, 1-6-5 Kudan Minami, Chiyoda-ku, Tokyo, 102-0074, Japan
| | - Tetsuya Mizutani
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
- Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Tetsuya Furuya
- Laboratory of Veterinary Infectious Diseases, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
- Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
| |
Collapse
|
14
|
Carossino M, Vissani MA, Barrandeguy ME, Balasuriya UBR, Parreño V. Equine Rotavirus A under the One Health Lens: Potential Impacts on Public Health. Viruses 2024; 16:130. [PMID: 38257830 PMCID: PMC10819593 DOI: 10.3390/v16010130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/29/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Group A rotaviruses are a well-known cause of viral gastroenteritis in infants and children, as well as in many mammalian species and birds, affecting them at a young age. This group of viruses has a double-stranded, segmented RNA genome with high genetic diversity linked to point mutations, recombination, and, importantly, reassortment. While initial molecular investigations undertaken in the 1900s suggested host range restriction among group A rotaviruses based on the fact that different gene segments were distributed among different animal species, recent molecular surveillance and genome constellation genotyping studies conducted by the Rotavirus Classification Working Group (RCWG) have shown that animal rotaviruses serve as a source of diversification of human rotavirus A, highlighting their zoonotic potential. Rotaviruses occurring in various animal species have been linked with contributing genetic material to human rotaviruses, including horses, with the most recent identification of equine-like G3 rotavirus A infecting children. The goal of this article is to review relevant information related to rotavirus structure/genomic organization, epidemiology (with a focus on human and equine rotavirus A), evolution, inter-species transmission, and the potential zoonotic role of equine and other animal rotaviruses. Diagnostics, surveillance and the current status of human and livestock vaccines against RVA are also reviewed.
Collapse
Affiliation(s)
- Mariano Carossino
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Maria Aldana Vissani
- Escuela de Veterinaria, Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Pilar, Buenos Aires B1630AHU, Argentina; (M.A.V.); (M.E.B.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Maria E. Barrandeguy
- Escuela de Veterinaria, Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Pilar, Buenos Aires B1630AHU, Argentina; (M.A.V.); (M.E.B.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
| | - Udeni B. R. Balasuriya
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Viviana Parreño
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
| |
Collapse
|
15
|
Agbemabiese CA, Philip AA, Patton JT. Recovery of Recombinant Rotaviruses by Reverse Genetics. Methods Mol Biol 2024; 2733:249-263. [PMID: 38064037 DOI: 10.1007/978-1-0716-3533-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Rotaviruses are the primary cause of severe gastroenteritis in infants and young children throughout the world. To combat rotavirus illness, several live oral vaccines have been developed, or are under development, that are formulated from attenuated human or human-animal reassortant strains of rotavirus. While the effectiveness of these vaccines is generally high in developed countries, the same vaccines are significantly less effective in many developing countries, where the need for rotavirus vaccines is greatest. Recently, reverse genetics systems have been developed that allow modification of the segmented double-stranded (ds)RNA genome of rotavirus, including reprogramming the genome to allow expression of additional proteins that may stimulate expanded neutralizing antibody responses in vaccinated children. The use of reverse genetics systems may not only lead to the development of more potent classes of vaccines but can be used to better explore the intricacies of rotavirus molecular biology and pathogenesis. In this article, we share protocols that can be used to generate recombinant rotaviruses, including modified strains that express foreign proteins.
Collapse
Affiliation(s)
- Chantal A Agbemabiese
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Asha A Philip
- Department of Biology, Indiana University, Bloomington, IN, USA
- CSL Seqirus, Waltham, MA, USA
| | - John T Patton
- Department of Biology, Indiana University, Bloomington, IN, USA.
| |
Collapse
|
16
|
Liu W, Lin Y, Jiang J, Zhang J, Liu Q, Hu Q. Development of a 1-step TaqMan real-time PCR method for detection of the Bovine Group A Rotavirus. Diagn Microbiol Infect Dis 2023; 107:116081. [PMID: 37801886 DOI: 10.1016/j.diagmicrobio.2023.116081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND The purpose of this study was to develop a 1-step real-time quantitative fluorescence polymerase chain reaction (QF-PCR) method for detecting Bovine Group A Rotavirus (BRVA). The primers and probe were designed targeting the VP6 gene of BRVA. The standard substance was obtained through in vitro transcription. The primers, probe concentration, and annealing temperatures were optimized to determine the optimal system and conditions for the reaction. The specificity, sensitivity, and repeatability of the method were assessed and compared with a reported real-time QF-PCR method for clinical samples. RESULTS The results indicated that the detection method can achieve a sensitivity of 3.47 copies/μL and exhibit good specificity by exclusively detecting BRVA without cross-reactivity to other common pathogens in cattle and sheep. The standard curve exhibited a robust linear correlation, and the amplification efficiency was calculated to be 105%. The intra-group and inter-group coefficients of variation were less than 2%. A total of 96 clinical samples were tested and compared with the real-time QF-PCR method that was reported. The coincidence rate was 90.63% (87/96). Furthermore, the clinical samples revealed that the prevalence of BRV in cattle from Fujian Province was 85.42% (82/96). CONCLUSION This study has successfully developed a 1-step real-time QF-PCR method for BRVA, which offers an efficient and sensitive technical support for the rapid diagnosis and epidemiological investigation of BRVA.
Collapse
Affiliation(s)
- Weiwei Liu
- Institute of Animal Husbandry & Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China; College of Animal Science (College of Bee science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yusheng Lin
- Institute of Animal Husbandry & Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China; College of Animal Science (College of Bee science), Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Jinxiu Jiang
- Institute of Animal Husbandry & Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jingpeng Zhang
- Institute of Animal Husbandry & Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Qinghua Liu
- College of Animal Science (College of Bee science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qilin Hu
- Institute of Animal Husbandry & Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| |
Collapse
|
17
|
Wang Y, Liu Y, Bao H, Chen Y, Kou G, Wang M, Fu S, Huo W, Guan W, Cheng Y, Zhou X, Li X. Application of the cell-based RT-qPCR assay (C-QPA) for potency detection of the novel trivalent rotavirus vaccine in China. J Clin Lab Anal 2023; 37:e24989. [PMID: 37975330 PMCID: PMC10756945 DOI: 10.1002/jcla.24989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Because of the deficiencies of traditional methods in multivalent rotavirus vaccine potency detection, a cell-based quantitative RT-qPCR assay (C-QPA) was established and validated for specificity, precision, and accuracy. METHODS In order to further validate the robustness of this method in actual titer detection, the linear range and the practical application under different conditions were tested using monovalent and trivalent rotavirus samples and standards. RESULTS Results showed that the linear range was 2.0-6.5, 3.9-8.3, and 3.5-8.1 UI (unit of infectivity) for G2, G3, and G4, respectively. Besides, unknown sample with high titer exceeding the linear range can be calculated by dilution. The UIs of serotypes G2, G3, and G4 in monovalent and trivalent rotavirus samples showed a relative deviation ≤4.10%, and the monovalent samples of the same serotype with or without protective agents showed a relative deviation ≤4.28%; the coefficient of variation (CV) of at least 176 tests (548 individual runs) of 3 in vitro-transcribed RNA standards with certain concentrations was not higher than 6.50%; the results of the trivalent samples tested by more than 149 times in 5 years (467 individual runs) showed the CVs lower than 12.66%; 15 samples detected by one laboratory showed a CV lower than 9.83%, while other three samples tested by two independent laboratories showed a CV lower than 6.90%. CONCLUSION In summary, the C-QPA has good linearity, durability, repeatability, and reproducibility in practical application and has been proved by the authority to be widely used in the production, quality control and release of the recently licensed trivalent vaccine in China.
Collapse
Affiliation(s)
- Yunjin Wang
- Lanzhou Institute of Biological Products Co., Ltd.LanzhouChina
| | - YueYue Liu
- National Institutes for Food and Drug ControlBeijingChina
| | - Hong Bao
- Lanzhou Institute of Biological Products Co., Ltd.LanzhouChina
| | - Yueru Chen
- Lanzhou Institute of Biological Products Co., Ltd.LanzhouChina
| | - Guiying Kou
- Lanzhou Institute of Biological Products Co., Ltd.LanzhouChina
| | - Mingqiang Wang
- Lanzhou Institute of Biological Products Co., Ltd.LanzhouChina
| | - Shengfang Fu
- Lanzhou Institute of Biological Products Co., Ltd.LanzhouChina
| | - Wen Huo
- Lanzhou Institute of Biological Products Co., Ltd.LanzhouChina
| | - Wenzhu Guan
- Lanzhou Institute of Biological Products Co., Ltd.LanzhouChina
| | - Yahui Cheng
- Lanzhou Institute of Biological Products Co., Ltd.LanzhouChina
| | - Xu Zhou
- Shanghai Institute of Biological Products Co., Ltd.ShanghaiChina
| | - Xiongxiong Li
- Lanzhou Institute of Biological Products Co., Ltd.LanzhouChina
| |
Collapse
|
18
|
Morozova OV, Sashina TA, Epifanova NV, Velikzhanina EI, Novikova NA. Phylodynamic characteristics of reassortant DS-1-like G3P[8]-strains of rotavirus type A isolated in Nizhny Novgorod (Russia). Braz J Microbiol 2023; 54:2867-2877. [PMID: 37897627 PMCID: PMC10689624 DOI: 10.1007/s42770-023-01155-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Since 2013, there has been an increase in reports of the spread of a double intergroup reassortant strain of rotavirus type A (RVA) with the genotype G3P[8] and other genes belonging to the second genogroup I2-R2-C2-M2-A2-N2-T2-E2-H2. In our study, we provide a molecular genetic characterization of rotaviruses with genotype G3P[8]-I2 isolated in Nizhny Novgorod. In our study, we used RT-PCR, Sanger sequencing, RNA-PAGE methods. Phylogenetic and phylodynamic analysis were performed using the Bayesian approach. According to our study, there was a significant increase in the proportion of G3P[8] from 15% during the period of 2020-2021 to 53% during the period of 2021-2022 in Nizhny Novgorod, Russia. Phylogenetic analysis based on the VP4 gene revealed that DS-1-like RVAs isolated in Nizhny Novgorod belong to different clusters of the P[8]-3.1 lineage, with a level of variation ranging from 1.1% to 1.3%. Based on the VP6 gene, the equine-like RVAs identified by us carry genetic variants belonging to three distinct clusters of the lineage I2-V, with a variation level ranging from 2.0% to 4.5%. These data indicate the genotypic diversity of circulating DS-1-like G3 RVAs. Phylogenetic analysis of the VP7 gene allowed us to assign the isolates identified in our study to the G3-1 lineage. We estimated that the circulation of the most recent common ancestor of the spreading strains dates back to 2002. Additionally, we determined the typical level of mutations in the VP7 gene, which amounted to 2.14*10-3 substitutions/per site/per year.
Collapse
Affiliation(s)
- Olga V Morozova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia.
| | - T A Sashina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N V Epifanova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - E I Velikzhanina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N A Novikova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| |
Collapse
|
19
|
Neira V, Melgarejo C, Urzúa-Encina C, Berrios F, Valdes V, Mor S, Brito-Rodriguez B, Ramirez-Toloza GA. Identification and characterization of porcine Rotavirus A in Chilean swine population. Front Vet Sci 2023; 10:1240346. [PMID: 38026647 PMCID: PMC10652281 DOI: 10.3389/fvets.2023.1240346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
Rotavirus A (RVA) is a common cause of diarrhea in newborn pigs, leading to significant economic losses. RVA is considered a major public health concern due to genetic evolution, high prevalence, and pathogenicity in humans and animals. The objective of this study was to identify and characterize RVA in swine farms in Chile. A total of 154 samples (86 oral fluids and 68 fecal samples) were collected, from 22 swine farms. 58 (38%) samples belonging to 14 farms were found positive for RVA by real-time RT-PCR. The samples with low Ct values (21) and the two isolates were selected for whole genome sequencing. Nearly complete genomes were assembled from both isolates and partial genomes were assembled from five clinical samples. BLAST analysis confirmed that these sequences are related to human and swine-origin RVA. The genomic constellation was G5/G3-P[7]-I5-R1-C1-M1-A8-N1-T1-E1-H1. Phylogenetic analysis showed that VP4, VP1, VP2, NSP2, NSP3, NSP4, and NSP5 sequences were grouped in monophyletic clusters, suggesting a single introduction. The phylogenies for VP7, VP6, VP3, and NSP1 indicated two different origins of the Chilean sequences. The phylogenetic trees showed that most of the Chilean RVA sequences are closely related to human and swine-origin RVA detected across the world. The results highlight the potential zoonotic nature of RVA circulating in Chilean swine farms. Therefore, it is important to continue RVA whole genome sequencing globally to fully understand its complex epidemiology and early detection and characterization of zoonotic strains.
Collapse
Affiliation(s)
- Victor Neira
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Cristián Melgarejo
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Constanza Urzúa-Encina
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Felipe Berrios
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Valentina Valdes
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Sunil Mor
- Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
- Department of Veterinary and Biomedical Sciences, Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD, United States
| | | | - Galia Andrea Ramirez-Toloza
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| |
Collapse
|
20
|
Memon AM, Chen F, Khan SB, Guo X, Khan R, Khan FA, Zhu Y, He Q. Development and evaluation of polyclonal antibodies based antigen capture ELISA for detection of porcine rotavirus. Anim Biotechnol 2023; 34:1807-1814. [PMID: 35593671 DOI: 10.1080/10495398.2022.2052304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Rotaviruses are rising as zoonotic viruses worldwide, causing the lethal dehydrating diarrhea in children, piglets, and other livestock of economic importance. A simple, swift, cost-effective, highly specific, and sensitive antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) was developed for detection of porcine rotavirus-A (PoRVA) by employing rabbit (capture antibody) and murine polyclonal antibodies (detector antibody) produced against VP6 of PoRVA (RVA/Pig-tc/CHN/TM-a/2009/G9P23). Reactivity of the both polyclonal antibodies was confirmed by using an indirect ELISA, western-blot analysis and indirect fluorescence assay against rVP6 protein and PoRVA. The detection limit of AC-ELISA was found 50 ng/ml of PoRVA protein. The relative sensitivity and specificity of this in-house AC-ELISA were evaluated for detection of PoRVA from 295 porcine diarrhea samples, and results were compared with that of RT-PCR and TaqMan RT-qPCR. The relative sensitivity and specificity of AC-ELISA compared with those of TaqMan RT-qPCR were found as 94.4 and 99.2%, respectively, with the strong agreement (κ -0.58) between these two techniques. Furthermore, AC-ELISA could not detect any cross-reactivity with porcine epidemic diarrhea virus, transmissible gastro-enteritis virus, pseudo rabies virus and porcine circovirus-2. This in-house AC-ELISA efficiently detected PoRVA from clinical samples, which suggests that this technique can be used for large-scale surveillance and timely detection of rotavirus infection in the porcine farms.
Collapse
Affiliation(s)
- Atta Muhammad Memon
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Fangzhou Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Sher Bahadar Khan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaozhen Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Farhan Anwar Khan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yinxing Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qigai He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
21
|
Akari Y, Hatazawa R, Kuroki H, Ito H, Negoro M, Tanaka T, Miwa H, Sugiura K, Umemoto M, Tanaka S, Ogawa M, Ito M, Fukuda S, Murata T, Taniguchi K, Suga S, Kamiya H, Nakano T, Taniguchi K, Komoto S. Full genome-based characterization of an Asian G3P[6] human rotavirus strain found in a diarrheic child in Japan: Evidence for porcine-to-human zoonotic transmission. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105507. [PMID: 37757900 DOI: 10.1016/j.meegid.2023.105507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
Human rotavirus strains having the unconventional G3P[6] genotype have been sporadically detected in diarrheic patients in different parts of the world. However, the full genomes of only three human G3P[6] strains from Asian countries (China, Indonesia, and Vietnam) have been sequenced and characterized, and thus the exact origin and evolution of G3P[6] strains in Asia remain to be elucidated. Here, we sequenced and characterized the full genome of a G3P[6] strain (RVA/Human-wt/JPN/SO1199/2020/G3P[6]) found in a stool sample from a 3-month-old infant admitted with acute gastroenteritis in Japan. On full genomic analysis, strain SO1199 was revealed to have a unique Wa-like genogroup configuration: G3-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1. VP6 genotype I5 and NSP1 genotype A8 are commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis demonstrated that all 11 genes of strain SO1199 were closely related to those of porcine and/or porcine-like human rotaviruses and thus appeared to be of porcine origin. Thus, strain SO1199 was shown to possess a porcine-like genomic backbone and thus is likely to be the result of interspecies transmission of a porcine rotavirus strain. Of note is that all 11 genes of strain SO1199 were phylogenetically located in clusters, distinct from those of the previously identified porcine-like human G3P[6] strains from around the world including Asia, suggesting the occurrence of independent porcine-to-human zoonotic transmission events. To our knowledge, this is the first report on full genome-based characterization of a human G3P[6] strain that has emerged in Japan. Our findings revealed the diversity of unconventional human G3P[6] strains in Asia, and provide important insights into the origin and evolution of G3P[6] strains.
Collapse
Affiliation(s)
- Yuki Akari
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Riona Hatazawa
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Haruo Kuroki
- Sotobo Children's Clinic, Isumi, Chiba 299-4503, Japan
| | - Hiroaki Ito
- Department of Pediatrics, Kameda Medical Center, Kamogawa, Chiba 296-8602, Japan
| | - Manami Negoro
- Institute for Clinical Research, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Takaaki Tanaka
- Department of Pediatrics, Kawasaki Medical School, Okayama, Okayama 700-8505, Japan
| | - Haruna Miwa
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Katsumi Sugiura
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | | | - Shigeki Tanaka
- Department of Pediatrics, Mie Chuo Medical Center, Tsu, Mie 514-1101, Japan
| | - Masahiro Ogawa
- Department of Pediatrics, Mie Chuo Medical Center, Tsu, Mie 514-1101, Japan
| | - Mitsue Ito
- Department of Pediatrics, Japanese Red Cross Ise Hospital, Ise, Mie 516-8512, Japan
| | - Saori Fukuda
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Takayuki Murata
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan; Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Kiyosu Taniguchi
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Shigeru Suga
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Hajime Kamiya
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Takashi Nakano
- Department of Pediatrics, Kawasaki Medical School, Okayama, Okayama 700-8505, Japan
| | - Koki Taniguchi
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan; Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan; Division of One Health, Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu, Oita 879-5593, Japan.
| |
Collapse
|
22
|
Louge Uriarte EL, Badaracco A, Spetter MJ, Miño S, Armendano JI, Zeller M, Heylen E, Späth E, Leunda MR, Moreira AR, Matthijnssens J, Parreño V, Odeón AC. Molecular Epidemiology of Rotavirus A in Calves: Evolutionary Analysis of a Bovine G8P[11] Strain and Spatio-Temporal Dynamics of G6 Lineages in the Americas. Viruses 2023; 15:2115. [PMID: 37896894 PMCID: PMC10611311 DOI: 10.3390/v15102115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Rotavirus A (RVA) causes diarrhea in calves and frequently possesses the G6 and P[5]/P[11] genotypes, whereas G8 is less common. We aimed to compare RVA infections and G/P genotypes in beef and dairy calves from major livestock regions of Argentina, elucidate the evolutionary origin of a G8 strain and analyze the G8 lineages, infer the phylogenetic relationship of RVA field strains, and investigate the evolution and spatio-temporal dynamics of the main G6 lineages in American countries. Fecal samples (n = 422) from diarrheic (beef, 104; dairy, 137) and non-diarrheic (beef, 78; dairy, 103) calves were analyzed by ELISA and semi-nested multiplex RT-PCR. Sequencing, phylogenetic, phylodynamic, and phylogeographic analyses were performed. RVA infections were more frequent in beef (22.0%) than in dairy (14.2%) calves. Prevalent genotypes and G6 lineages were G6(IV)P[5] in beef (90.9%) and G6(III)P[11] (41.2%) or mixed genotypes (23.5%) in dairy calves. The only G8 strain was phylogenetically related to bovine and artiodactyl bovine-like strains. Re-analyses inside the G8 genotype identified G8(I) to G8(VIII) lineages. Of all G6 strains characterized, the G6(IV)P[5](I) strains from "Cuenca del Salado" (Argentina) and Uruguay clustered together. According to farm location, a clustering pattern for G6(IV)P[5] strains of beef farms was observed. Both G6 lineage strains together revealed an evolutionary rate of 1.24 × 10-3 substitutions/site/year, and the time to the most recent common ancestor was dated in 1853. The most probable ancestral locations were Argentina in 1981 for G6(III) strains and the USA in 1940 for G6(IV) strains. The highest migration rates for both G6 lineages together were from Argentina to Brazil and Uruguay. Altogether, the epidemiology, genetic diversity, and phylogeny of RVA in calves can differ according to the production system and farm location. We provide novel knowledge about the evolutionary origin of a bovine G8P[11] strain. Finally, bovine G6 strains from American countries would have originated in the USA nearly a century before its first description.
Collapse
Affiliation(s)
- Enrique L. Louge Uriarte
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Alejandra Badaracco
- Instituto Nacional de Tecnología Agropecuaria, EEA Montecarlo, Av. El Libertador Nº 2472, Montecarlo CP3384, Misiones, Argentina;
| | - Maximiliano J. Spetter
- Facultad de Ciencias Veterinarias, Departamento de Fisiopatología, Centro de Investigación Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil CP7000, Buenos Aires, Argentina; (M.J.S.); (J.I.A.)
| | - Samuel Miño
- Instituto Nacional de Tecnología Agropecuaria, EEA Cerro Azul, Ruta 14, km 836, Cerro Azul CP3313, Misiones, Argentina;
| | - Joaquín I. Armendano
- Facultad de Ciencias Veterinarias, Departamento de Fisiopatología, Centro de Investigación Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil CP7000, Buenos Aires, Argentina; (M.J.S.); (J.I.A.)
| | - Mark Zeller
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Elisabeth Heylen
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Ernesto Späth
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (E.S.); (A.C.O.)
| | - María Rosa Leunda
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Ana Rita Moreira
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Viviana Parreño
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Virología e Innovaciones Tecnológicas, Nicolas Repetto y de los Reseros s/n, Hurlingham CP1686, Buenos Aires, Argentina
| | - Anselmo C. Odeón
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (E.S.); (A.C.O.)
| |
Collapse
|
23
|
Ndebe J, Harima H, Chambaro HM, Sasaki M, Yamagishi J, Kalonda A, Shawa M, Qiu Y, Kajihara M, Takada A, Sawa H, Saasa N, Simulundu E. Prevalence and Genomic Characterization of Rotavirus A from Domestic Pigs in Zambia: Evidence for Possible Porcine-Human Interspecies Transmission. Pathogens 2023; 12:1199. [PMID: 37887715 PMCID: PMC10609906 DOI: 10.3390/pathogens12101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
Rotavirus is a major cause of diarrhea globally in animals and young children under 5 years old. Here, molecular detection and genetic characterization of porcine rotavirus in smallholder and commercial pig farms in the Lusaka Province of Zambia were conducted. Screening of 148 stool samples by RT-PCR targeting the VP6 gene revealed a prevalence of 22.9% (34/148). Further testing of VP6-positive samples with VP7-specific primers produced 12 positives, which were then Sanger-sequenced. BLASTn of the VP7 positives showed sequence similarity to porcine and human rotavirus strains with identities ranging from 87.5% to 97.1%. By next-generation sequencing, the full-length genetic constellation of the representative strains RVA/pig-wt/ZMB/LSK0137 and RVA/pig-wt/ZMB/LSK0147 were determined. Genotyping of these strains revealed a known Wa-like genetic backbone, and their genetic constellations were G4-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1 and G9-P[13]-I5-R1-C1-M1-A8-N1-T1-E1-H1, respectively. Phylogenetic analysis revealed that these two viruses might have their ancestral origin from pigs, though some of their gene segments were related to human strains. The study shows evidence of reassortment and possible interspecies transmission between pigs and humans in Zambia. Therefore, the "One Health" surveillance approach for rotavirus A in animals and humans is recommended to inform the design of effective control measures.
Collapse
Affiliation(s)
- Joseph Ndebe
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (A.T.); (H.S.); (N.S.)
| | - Hayato Harima
- Laboratory of Veterinary Public Health, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509, Japan;
| | - Herman Moses Chambaro
- Central Veterinary Research Institute (CVRI), Ministry of Fisheries and Livestock, Lusaka 10101, Zambia;
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Sapporo 001-0020, Japan;
| | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Sapporo 001-0020, Japan;
| | - Annie Kalonda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia;
| | - Misheck Shawa
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (M.S.); (M.K.)
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Sapporo 001-0020, Japan
| | - Yongjin Qiu
- National Institute of Infectious Diseases, Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, Toyama 1-23-1, Tokyo 162-8640, Japan
- Department of Virology-I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Masahiro Kajihara
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (M.S.); (M.K.)
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Sapporo 001-0020, Japan
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (A.T.); (H.S.); (N.S.)
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Sapporo 001-0020, Japan
- One Health Research Center, Hokkaido University, N18 W9, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (A.T.); (H.S.); (N.S.)
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- One Health Research Center, Hokkaido University, N18 W9, Sapporo 001-0020, Japan
- Hokkaido University, Institute for Vaccine Research and Development (HU-IVReD), N21 W11, Sapporo 001-0020, Japan
- Global Virus Network, 725 W Lombard Street, Baltimore, MD 21201, USA
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (A.T.); (H.S.); (N.S.)
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (A.T.); (H.S.); (N.S.)
- Macha Research Trust, Choma 20100, Zambia
| |
Collapse
|
24
|
Hasan MA, Suzuki M, Sakai K, Kabir MH, Miyaoka Y, Hakim H, Kadota C, Shoham D, Takehara K. Complete genome constellations of two bovine rotavirus A strains isolated in Japan reveal a unique T9 NSP3 genotype. J Vet Med Sci 2023; 85:998-1003. [PMID: 37495525 PMCID: PMC10539819 DOI: 10.1292/jvms.23-0268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023] Open
Abstract
Full genome sequencing of two bovine rotavirus A (RVA) strains isolated in Japan in 2019 revealed two genotype constellations; one had a constellation of G8-P[1]-I2-R2-C2-M2-A3-N2-T9-E2-H3. Thereupon, genotype T9 carried by RVA/Bovine-tc/JPN/AH1041/2022/G8P[1], constitutes a rare NSP3 genotype, and only two unusual Japanese bovine RVA strains have thus far been reported to carry this genotype. The other RVA/Bovine-tc/JPN/AH1207/2022/G6P[5] strain possessed a constellation of G6-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3. Phylogenetic analyses indicate that the majority of gene segments were most closely related to Japanese bovine RVAs, suggesting that both strains might have derived through multiple reassortment events from RVA strains circulating within Japanese cattle. The emergence of RVA strains in Japan and their reassortment with locally circulating atypical RVAs could have implications for current vaccination strategies.
Collapse
Affiliation(s)
- Md Amirul Hasan
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kouji Sakai
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Md Humayun Kabir
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yu Miyaoka
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hakimullah Hakim
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Chisaki Kadota
- Laboratory of Animal Health, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Dany Shoham
- Bar-Ilan University, Begin-Sadat Center for Strategic Studies, Ramat Gan, Israel
| | - Kazuaki Takehara
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Laboratory of Animal Health, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| |
Collapse
|
25
|
Cao M, Yuan F, Ma X, Ma J, Ma X, Chen H, Zhang W, Zhao J, Kuai W. Surveillance of human Group A rotavirus in Ningxia, China (2015-2021): Emergence and prevalence of G9P[8]-E2 and G3P[8]-E2 genotypes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105469. [PMID: 37331499 DOI: 10.1016/j.meegid.2023.105469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
BACKGROUND Group A rotaviruses (RVA) are the primary pathogens of acute gastroenteritis. Currently, two live attenuated RVA vaccines, LLR and RotaTeq, have been introduced into mainland China but are not included in the national immunization program. Because of the unknown genetic evolution of group A rotavirus in an all-age population in Ningxia, China, we monitored the epidemiological characteristics and circulating genotypes of RVA as a reference for developing vaccine strategies. METHODS We conducted seven years of consecutive surveillance of RVA based on stool samples from patients with acute gastroenteritis in sentinel hospitals in Ningxia, China, from 2015 to 2021. Reverse transcription quantitative polymerase chain reaction(RT-qPCR) was used to detect RVA in stool samples. Genotyping and phylogenetic analysis of VP7, VP4 and NSP4 genes were performed by reverse transcription-polymerase chain reaction(RT-PCR) and nucleotide sequence determination. RESULTS RVA was detected in 16.58% (1436/8662) of 8662 stool samples. The positive rates were 7.17% (201/2805) and 21.09% (1235/5857) in adults and children, respectively. The most affected age group was infants and children aged 12-23 months, with a positive rate of 29.53% (p < 0.05). A significant winter/spring seasonality was observed. 23.29% positive rate in 2020 was the highest in 7 years (p < 0.05). The region with the highest positive rate in the adult group was Yinchuan, and the children's group was Guyuan. A total of 9 genotype combinations were found to be distributed in Ningxia. The dominant genotype combinations in this region gradually changed from G9P[8]-E1, G3P[8]-E1, G1P[8]-E1 to G9P[8]-E1, G9P[8]-E2, and G3P[8]-E2 during these seven years. Rare strains (e.g., G9P[4]-E1, G3P[9]-E3 and G1P[8]-E2) were occasionally detected during the study. CONCLUSIONS During the study period, changes in the significant RVA circulating genotype combinations and the emergence of reassortment strains were observed, particularly the emergence and prevalence of G9P[8]-E2, G3P[8]-E2 reassortants in the region. These results indicate the importance of continuous monitoring of the molecular evolution and recombination characteristics of RVA, and should not be limited to G/P genotyping but should consider multi-gene fragment co-analysis and whole genome sequencing.
Collapse
Affiliation(s)
- Min Cao
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Fang Yuan
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Xueping Ma
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Jiangtao Ma
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Xuemin Ma
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Hui Chen
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Wei Zhang
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Jianhua Zhao
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Wenhe Kuai
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China.
| |
Collapse
|
26
|
Zhuo R, Freedman SB, Xie J, Charlton C, Plitt S, Croxen MA, Li V, Tarr GAM, Lee B, Ali S, Chui L, Luong J, Pang X. Molecular epidemiology of rotavirus among children in Western Canada: Dynamic changes in genotype prevalence in four consecutive seasons. J Med Virol 2023; 95:e29028. [PMID: 37573569 DOI: 10.1002/jmv.29028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/19/2023] [Accepted: 07/29/2023] [Indexed: 08/15/2023]
Abstract
Rotavirus molecular surveillance remains important in the postvaccine era to monitor the changes in transmission patterns, identify vaccine-induced antigenic changes and discover potentially pathogenic vaccine-related strains. The Canadian province of Alberta introduced rotavirus vaccination into its provincial vaccination schedule in June 2015. To evaluate the impact of this program on stool rotavirus positivity rate, strain diversity, and seasonal trends, we analyzed a prospective cohort of children with acute gastroenteritis recruited between December 2014 and August 2018. We identified dynamic changes in rotavirus positivity and genotype trends during pre- and post-rotavirus vaccine introduction periods. Genotypes G9P[8], G1P[8], G2P[4], and G12P[8] predominated consecutively each season with overall lower rotavirus incidence rates in 2016 and 2017. The demographic and clinical features of rotavirus gastroenteritis were comparable among wild-type rotaviruses; however, children with G12P[8] infections were older (p < 0.001). Continued efforts to monitor changes in the molecular epidemiology of rotavirus using whole genome sequence characterization are needed to further understand the impact of the selection pressure of vaccination on rotavirus evolution.
Collapse
Affiliation(s)
- Ran Zhuo
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Stephen B Freedman
- Sections of Pediatric Emergency Medicine and Gastroenterology, Departments of Pediatrics and Emergency Medicine, Alberta Children's Hospital and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jianling Xie
- Sections of Pediatric Emergency Medicine and Gastroenterology, Departments of Pediatrics and Emergency Medicine, Alberta Children's Hospital and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Carmen Charlton
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Sabrina Plitt
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
- Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Mathew A Croxen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
- Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Vincent Li
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Gillian A M Tarr
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Bonita Lee
- Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Samina Ali
- Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Jasper Luong
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| |
Collapse
|
27
|
Carossino M, Balasuriya UBR, Thieulent CJ, Barrandeguy ME, Vissani MA, Parreño V. Quadruplex Real-Time TaqMan ® RT-qPCR Assay for Differentiation of Equine Group A and B Rotaviruses and Identification of Group A G3 and G14 Genotypes. Viruses 2023; 15:1626. [PMID: 37631969 PMCID: PMC10459720 DOI: 10.3390/v15081626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Equine rotavirus A (ERVA) is the leading cause of diarrhea in foals, with G3P[12] and G14P[12] genotypes being the most prevalent. Recently, equine G3-like RVA was recognized as an emerging infection in children, and a group B equine rotavirus (ERVB) was identified as an emergent cause of foal diarrhea in the US. Thus, there is a need to adapt molecular diagnostic tools for improved detection and surveillance to identify emerging strains, understand their molecular epidemiology, and inform future vaccine development. We developed a quadruplex TaqMan® RT-qPCR assay for differentiation of ERVA and ERVB and simultaneous G-typing of ERVA strains, evaluated its analytical and clinical performance, and compared it to (1) a previously established ERVA triplex RT-qPCR assay and (2) standard RT-PCR assay and Sanger sequencing of PCR products. This quadruplex RT-qPCR assay demonstrated high sensitivity (>90%)/specificity (100%) for every target and high overall agreement (>96%). Comparison between the triplex and quadruplex assays revealed only a slightly higher sensitivity for the ERVA NSP3 target using the triplex format (p-value 0.008) while no significant differences were detected for other targets. This quadruplex RT-qPCR assay will significantly enhance rapid surveillance of both ERVA and ERVB circulating and emerging strains with potential for interspecies transmission.
Collapse
Affiliation(s)
- Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Udeni B. R. Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Côme J. Thieulent
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Maria E. Barrandeguy
- Escuela de Veterinaria, Universidad del Salvador, Buenos Aires B1630, Argentina; (M.E.B.); (M.A.V.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
| | - Maria Aldana Vissani
- Escuela de Veterinaria, Universidad del Salvador, Buenos Aires B1630, Argentina; (M.E.B.); (M.A.V.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425, Argentina
| | - Viviana Parreño
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425, Argentina
| |
Collapse
|
28
|
Gutierrez MB, de Assis RMS, de Andrade JDSR, Fialho AM, Fumian TM. Rotavirus A during the COVID-19 Pandemic in Brazil, 2020-2022: Emergence of G6P[8] Genotype. Viruses 2023; 15:1619. [PMID: 37631962 PMCID: PMC10458023 DOI: 10.3390/v15081619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/29/2023] Open
Abstract
Rotavirus A (RVA) remains a leading cause of acute gastroenteritis (AGE) hospitalizations in children worldwide. During the COVID-19 pandemic, a reduction in vaccination coverage in Brazil and elsewhere was observed, and some reports have demonstrated a reduction in AGE notifications during the pandemic. This study aims to investigate the diversity and prevalence of RVA genotypes in children and adults presenting with AGE symptoms in Brazil during the COVID-19 pandemic between 2020 and 2022. RVA was screened using RT-qPCR; then, G and P genotypes were characterized using one-step multiplex RT-PCR. A total of 2173 samples were investigated over the three-year period, and we detected RVA in 7.7% of samples (n = 167), being 15.5% in 2020, 0.5% in 2021, and 13.8% in 2022. Higher RVA prevalence was observed in the Northeastern region (19.3%) compared to the Southeastern (6.1%) and Southern regions (5.5%). The most affected age group was children aged between 0 and 6 months old; however, this was not statistically significant. Genotyping and phylogenetic analysis identified the emergence of G6P[8] during the period; moreover, it was detected in 10.6% of samples in 2020 and in 83.5% in 2022. In contrast, the prevalence of G3P[8], the previous dominant genotype, decreased from 72.3% in 2020 to 11.3% in 2022. We also identified unusual strains, such as G3P[9] and G9P[4], being sporadically detected during the period. This is the first report on the molecular epidemiology and surveillance of RVA during the COVID-19 pandemic period in Brazil. Our study provides evidence for the importance of maintaining high and sustainable levels of vaccine coverage to protect against RVA disease. Furthermore, it highlights the need to maintain nationwide surveillance in order to monitor future trends and changes in the epidemiology of RVA in Brazil.
Collapse
Affiliation(s)
| | | | | | | | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (M.B.G.)
| |
Collapse
|
29
|
Moraes MTBD, Silva MFD, Pimenta YC, Cantelli CP, Assis RMSD, Fialho AM, Bueno MG, Olivares AIO, Svensson L, Leite JPG, Nordgren J. G6P[8] Rotavirus a Possessing a Wa-like VP3 Gene from a Child with Acute Gastroenteritis Living in the Northwest Amazon Region. Pathogens 2023; 12:956. [PMID: 37513803 PMCID: PMC10385053 DOI: 10.3390/pathogens12070956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The introduction of rotavirus A (RVA) vaccines has considerably reduced the RVA-associated mortality among children under 5 years of age worldwide. The ability of RVA to reassort gives rise to different combinations of surface proteins G (glycoprotein, VP7) and P (protease sensitive, VP4) RVA types infecting children. During the epidemiological surveillance of RVA in the Northwest Amazon region, an unusual rotavirus genotype G6P[8] was detected in feces of a 2-year-old child with acute gastroenteritis (AGE) that had been vaccinated with one dose of Rotarix® (RV1). The G6P[8] sample had a DS-1-like constellation with a Wa-like VP3 gene mono-reassortment similar to equine-like G3P[8] that has been frequently detected in Brazil previously. The results presented here reinforce the evolutionary dynamics of RVA and the importance of constant molecular surveillance.
Collapse
Affiliation(s)
- Marcia Terezinha Baroni de Moraes
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
- Post-Graduate Program in Tropical Medicine, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Mauro França da Silva
- Post-Graduate Program in Tropical Medicine, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
- Technological Coordination, Tetraviral Vaccine, Immunobiological Technology Institute (Biomanguinhos), Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Yan Cardoso Pimenta
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
- Post-Graduate Program in Tropical Medicine, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Carina Pacheco Cantelli
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Rosane Maria Santos de Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Alexandre Madi Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Marina Galvão Bueno
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Alberto Ignácio Olivares Olivares
- Secretaria Estadual de Saúde de Roraima, SESAU/RR, Rua Madrid, 180-Aeroporto, Boa Vista 69310-043, Brazil
- College of Medicine, State University of Roraima, Avenida Helio Campo, s/n-Centro, Caracaraí, Boa Vista 69360-000, Brazil
| | - Lennart Svensson
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Medicine, Kalolinska Institutet, Nobels Väg 6, 171 77 Stockholm, Sweden
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Johan Nordgren
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
| |
Collapse
|
30
|
Wang J, Pan YF, Yang LF, Yang WH, Lv K, Luo CM, Wang J, Kuang GP, Wu WC, Gou QY, Xin GY, Li B, Luo HL, Chen S, Shu YL, Guo D, Gao ZH, Liang G, Li J, Chen YQ, Holmes EC, Feng Y, Shi M. Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential. Nat Commun 2023; 14:4079. [PMID: 37429936 DOI: 10.1038/s41467-023-39835-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within individual bats, and hence the frequency of virus co-infection and spillover among them. We characterize the mammal-associated viruses in 149 individual bats sampled from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high frequency of virus co-infection (simultaneous infection of bat individuals by multiple viral species) and spillover among the animals studied, which may in turn facilitate virus recombination and reassortment. Of note, we identify five viral species that are likely to be pathogenic to humans or livestock, based on phylogenetic relatedness to known pathogens or in vitro receptor binding assays. This includes a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV and SARS-CoV-2. In vitro assays indicate that this recombinant virus can utilize the human ACE2 receptor such that it is likely to be of increased emergence risk. Our study highlights the common occurrence of co-infection and spillover of bat viruses and their implications for virus emergence.
Collapse
Affiliation(s)
- Jing Wang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yuan-Fei Pan
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Fen Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Wei-Hong Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Kexin Lv
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Chu-Ming Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Juan Wang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Guo-Peng Kuang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Wei-Chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Qin-Yu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Gen-Yang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Bo Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Huan-le Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shoudeng Chen
- Molecular Imaging Center, Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China
| | - Yue-Long Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Deyin Guo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong Province, China
| | - Zi-Hou Gao
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Yun Feng
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China.
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
| |
Collapse
|
31
|
Lanzarini NM, Mannarino CF, Mata RM, Saggioro EM, Moreira JC, Miagostovich MP. Quantification and molecular characterization of intact rotavirus species A (RVA) in municipal solid waste leachate. J Appl Microbiol 2023; 134:lxad146. [PMID: 37429601 DOI: 10.1093/jambio/lxad146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
AIMS Leachate comprises a solid waste decomposition product found fresh in collection trucks or as an effluent in landfills. This study aimed to assess the occurrence, concentrations, and genetic diversity of intact rotavirus species A (RVA) in solid waste leachate. METHODS AND RESULTS Leachate samples were concentrated by ultracentrifugation, treated with propidium monoazide (PMA), and exposed to LED photolysis. Treated and untread samples were extracted using the QIAamp Fast DNA Stool mini kit, and nucleic acids were screened for RVA employing a Taqman® Real-time PCR. The PMA RT-qPCR method detected RVA in eight out of nine truck samples and in 15.40% (2/13) of the landfill leachate samples. The RVA concentrations in the PMA-treated samples ranged from 4.57 × 103 to 2.15 × 107 genomic copies (GC) 100 mL-1 in truck leachate and from 7.83 × 103 to 1.42 × 104 GC 100 mL-1 in landfill samples. Six truck leachate samples were characterized as RVA VP6 genogroup I2 by partial nucleotide sequencing. CONCLUSIONS The high intact RVA detection rates and concentrations in truck leachate samples indicate potential infectivity and comprise a warning for solid waste collectors concerning hand-to-mouth contact and the splash route.
Collapse
Affiliation(s)
- Natália Maria Lanzarini
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Camille Ferreira Mannarino
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Rafaela Marinho Mata
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Enrico Mendes Saggioro
- Environmental Health Evaluation and Promotion Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Josino Costa Moreira
- Center for Studies on Workers' Health and Human Ecology, National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| |
Collapse
|
32
|
Kim JS, Jeong HW, Park SH, Kim JA, Jin YH, Kim HS, Jung S, Lee JI, Lee JH. Genotypic shift in rotavirus associated with neonatal outbreaks in Seoul, Korea. J Clin Virol 2023; 164:105497. [PMID: 37253299 DOI: 10.1016/j.jcv.2023.105497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Rotavirus group A (RVA) is a causative agent of acute gastroenteritis among young children worldwide, despite the global expansion of rotavirus vaccination. In Korea, although the prevalence of RVA has been reduced among young children owing to vaccination, nosocomial infections still occur among neonates. OBJECTIVES The aim of this study was to investigate the molecular epidemiology of RVA strains associated with several neonatal outbreaks in Seoul from 2017 to 2020. STUDY DESIGN Clinical and environmental samples were collected and screened for the presence of RVA using ELISA and PCR targeting VP6, respectively. RVA-positive strains were genotyped via RT-PCR and subsequent sequencing of VP4 and VP7 and were phylogenetically compared with RVA strains from other countries. RESULTS During 2017-2020, a total of 15 RVA outbreaks occurred at neonatal facilities (six in hospital neonatal wards and nine in postpartum care centers) in Seoul, and only two RVA genotypes were detected: G4P[6] and G8P[6]. G8P[6] emerged in Seoul November 2018 and immediately became the predominant genotype among neonates, at least up to 2020. Phylogenetic analysis revealed that the G8P[6] genotype in this study was closely related to G8P[6] strains first identified in Korea in 2017, but differed from G8P[6] strains detected in Africa. CONCLUSIONS A novel G8P[6] genotype of RVA strains has emerged and caused outbreaks among neonates in Seoul. Continued surveillance for circulating RVA genotypes is imperative to monitor genotype changes and their potential risks to public health.
Collapse
Affiliation(s)
- Jin Seok Kim
- Emerging Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Republic of Korea.
| | - Hyo-Won Jeong
- Emerging Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Republic of Korea
| | - Sook Hyun Park
- Emerging Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Republic of Korea
| | - Jin-Ah Kim
- Emerging Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Republic of Korea
| | - Young Hee Jin
- Emerging Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Republic of Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Gyeonggi-do, Republic of Korea
| | - Soyoung Jung
- Emerging Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Republic of Korea
| | - Jae In Lee
- Emerging Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Republic of Korea
| | - Jib-Ho Lee
- Emerging Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Republic of Korea
| |
Collapse
|
33
|
Jampanil N, Kumthip K, Maneekarn N, Khamrin P. Genetic Diversity of Rotaviruses Circulating in Pediatric Patients and Domestic Animals in Thailand. Trop Med Infect Dis 2023; 8:347. [PMID: 37505643 PMCID: PMC10383398 DOI: 10.3390/tropicalmed8070347] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Rotavirus A is a highly contagious virus that causes acute gastroenteritis in humans and a wide variety of animals. In this review, we summarized the information on rotavirus described in the studies in the last decade (2008 to 2021) in Thailand, including the prevalence, seasonality, genetic diversity, and interspecies transmission. The overall prevalence of rotavirus infection in humans ranged from 15-33%. Rotavirus infection was detected throughout the year and most frequently in the dry and cold months, typically in March. The diversity of rotavirus genotypes varied year to year and from region to region. From 2008 to 2016, rotavirus G1P[8] was detected as the most predominant genotype in Thailand. After 2016, G1P[8] decreased significantly and other genotypes including G3P[8], G8P[8], and G9P[8] were increasingly detected from 2016 to 2020. Several uncommon rotavirus strains such as G1P[6], G4P[6], and G3P[10] have also been occasionally detected. In addition, most studies on rotavirus A infection in animals in Thailand from 2011 to 2021 reported the detection of rotavirus A in piglets and canine species. It was reported that rotavirus could cross the host species barrier between humans and animals through interspecies transmission and genetic reassortment mechanisms. The surveillance of rotavirus infection is crucial to identify the trend of rotavirus infection and the emergence of novel rotavirus genotypes in this country. The data provide information on rotavirus infection and the diversity of rotavirus genotypes circulating in the pre-vaccination period, and the data will be useful for the evaluation of the effectiveness of rotavirus vaccine implementation in Thailand.
Collapse
Affiliation(s)
- Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Emerging and Re-Emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Emerging and Re-Emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Emerging and Re-Emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai 50200, Thailand
| |
Collapse
|
34
|
Azevedo LS, Costa FF, Ghani MBA, Viana E, França Y, Medeiros RS, Guiducci R, Morillo SG, Primo D, Lopes RD, Gomes-Gouvêa MS, da Costa AC, Luchs A. Full genotype characterization of Brazilian canine G3P[3] strains during a 10-year survey (2012-2021) of rotavirus infection in domestic dogs and cats. Arch Virol 2023; 168:176. [PMID: 37306860 DOI: 10.1007/s00705-023-05807-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/25/2023] [Indexed: 06/13/2023]
Abstract
There is a dearth of information on the molecular epidemiology of rotaviruses in pets in Brazil. The aim of this study was to monitor rotavirus infections in household dogs and cats, determine full-genotype constellations, and obtain data on evolutionary relationships. Between 2012 and 2021, 600 fecal samples from dogs and cats (516 and 84, respectively) were collected at small animal clinics in São Paulo state, Brazil. Rotavirus screening was conducted using ELISA, PAGE, RT-PCR, sequencing, and phylogenetic analysis. Rotavirus type A (RVA) was detected in 0.5% (3/600) of the animals. No non-RVA types were detected. The three canine RVA strains were found to have a novel genetic constellation, G3-P[3] -I2-R3-C2-M3-A9-N2-T3-E3-H6, which has never been reported in dogs. As expected, all of the viral genes, except those encoding NSP2 and VP7, were closely related to the corresponding genes from canine, feline, and canine-like-human RVA strains. A novel N2 (NSP2) lineage was identified, grouping together Brazilian canine, human, rat and bovine strains, suggesting that genetic reassortment had occurred. Uruguayan G3 strains obtained from sewage contained VP7 genes that were phylogenetically close to those of the Brazilian canine strains, which suggests that these strains are widely distributed in pet populations in South American countries. For the NSP2 (I2), NSP3 (T3), NSP4 (E3), NSP5 (H6), VP1 (R3), VP3 (M3), and VP6 (I2) segments, phylogenetic analysis revealed possibly new lineages. The epidemiological and genetic data presented here point out the necessity for collaborative efforts to implement the One Health strategy in the field of RVA research and to provide an updated understanding of RVA strains circulating canines in Brazil.
Collapse
Affiliation(s)
- Lais Sampaio Azevedo
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | - Ellen Viana
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | - Yasmin França
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Raquel Guiducci
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Dieli Primo
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Michele Soares Gomes-Gouvêa
- Laboratorio de Gastroenterologia e Hepatologia Tropical-LIM07, Departamento de Gastroenterologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Laboratorio de Parasitologia Médica-LIM46, Departamento de Doenças Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Luchs
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil.
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil.
| |
Collapse
|
35
|
Manjate F, João ED, Mwangi P, Chirinda P, Mogotsi M, Messa A, Garrine M, Vubil D, Nobela N, Nhampossa T, Acácio S, Tate JE, Parashar U, Weldegebriel G, Mwenda JM, Alonso PL, Cunha C, Nyaga M, Mandomando I. Genomic characterization of the rotavirus G3P[8] strain in vaccinated children, reveals possible reassortment events between human and animal strains in Manhiça District, Mozambique. Front Microbiol 2023; 14:1193094. [PMID: 37342557 PMCID: PMC10277737 DOI: 10.3389/fmicb.2023.1193094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/20/2023] [Indexed: 06/23/2023] Open
Abstract
Mozambique introduced the rotavirus vaccine (Rotarix®; GlaxoSmithKline Biologicals, Rixensart, Belgium) in 2015, and since then, the Centro de Investigação em Saúde de Manhiça has been monitoring its impact on rotavirus-associated diarrhea and the trend of circulating strains, where G3P[8] was reported as the predominant strain after the vaccine introduction. Genotype G3 is among the most commonly detected Rotavirus strains in humans and animals, and herein, we report on the whole genome constellation of G3P[8] detected in two children (aged 18 months old) hospitalized with moderate-to-severe diarrhea at the Manhiça District Hospital. The two strains had a typical Wa-like genome constellation (I1-R1-C1-M1-A1-N1-T1-E1-H1) and shared 100% nucleotide (nt) and amino acid (aa) identities in 10 gene segments, except for VP6. Phylogenetic analysis demonstrated that genome segments encoding VP7, VP6, VP1, NSP3, and NSP4 of the two strains clustered most closely with porcine, bovine, and equine strains with identities ranging from 86.9-99.9% nt and 97.2-100% aa. Moreover, they consistently formed distinct clusters with some G1P[8], G3P[8], G9P[8], G12P[6], and G12P[8] strains circulating from 2012 to 2019 in Africa (Mozambique, Kenya, Rwanda, and Malawi) and Asia (Japan, China, and India) in genome segments encoding six proteins (VP2, VP3, NSP1-NSP2, NSP5/6). The identification of segments exhibiting the closest relationships with animal strains shows significant diversity of rotavirus and suggests the possible occurrence of reassortment events between human and animal strains. This demonstrates the importance of applying next-generation sequencing to monitor and understand the evolutionary changes of strains and evaluate the impact of vaccines on strain diversity.
Collapse
Affiliation(s)
- Filomena Manjate
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Eva D. João
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Peter Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Percina Chirinda
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Milton Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Augusto Messa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Marcelino Garrine
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Delfino Vubil
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Nélio Nobela
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Tacilta Nhampossa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde, Ministério da Saúde, Marracuene, Mozambique
| | - Sozinho Acácio
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde, Ministério da Saúde, Marracuene, Mozambique
| | - Jacqueline E. Tate
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, United States
| | - Umesh Parashar
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, United States
| | - Goitom Weldegebriel
- African Rotavirus Surveillance Network, Immunization, Vaccines, and Development Program, Regional Office for Africa, World Health Organization, Brazzaville, Democratic Republic of Congo
| | - Jason M. Mwenda
- African Rotavirus Surveillance Network, Immunization, Vaccines, and Development Program, Regional Office for Africa, World Health Organization, Brazzaville, Democratic Republic of Congo
| | - Pedro L. Alonso
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Celso Cunha
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Martin Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde, Ministério da Saúde, Marracuene, Mozambique
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
36
|
Malamba-Banda C, Mhango C, Benedicto-Matambo P, Mandolo JJ, Chinyama E, Kumwenda O, Barnes KG, Cunliffe NA, Iturriza-Gomara M, Jambo KC, Jere KC. Acute rotavirus infection is associated with the induction of circulating memory CD4 + T cell subsets. Sci Rep 2023; 13:9001. [PMID: 37268634 DOI: 10.1038/s41598-023-35681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/22/2023] [Indexed: 06/04/2023] Open
Abstract
Strong CD4+ T cell-mediated immune protection following rotavirus infection has been observed in animal models, but its relevance in humans remains unclear. Here, we characterized acute and convalescent CD4+ T cell responses in children who were hospitalized with rotavirus-positive and rotavirus-negative diarrhoea in Blantyre, Malawi. Children presenting with laboratory-confirmed rotavirus infection had higher proportions of effector and central memory T helper 2 cells during acute infection i.e., at disease presentation compared to convalescence, 28 days post-infection defined by a follow-up 28 days after acute infection. However, circulating cytokine-producing (IFN-γ and/or TNF-α) rotavirus-specific VP6-specific CD4+ T cells were rarely detectable in children with rotavirus infection at both acute and convalescent stages. Moreover, following whole blood mitogenic stimulation, the responding CD4+ T cells were predominantly non-cytokine producers of IFN-γ and/or TNF-α. Our findings demonstrate limited induction of anti-viral IFN-γ and/or TNF-α-producing CD4+ T cells in rotavirus-vaccinated Malawian children following the development of laboratory-confirmed rotavirus infection.
Collapse
Affiliation(s)
- Chikondi Malamba-Banda
- Biological Sciences Departments, Malawi University of Science and Technology, Thyolo, Malawi
- Malawi Liverpool Wellcome Research Programme (MLW), Blantyre, Malawi
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Chimwemwe Mhango
- Malawi Liverpool Wellcome Research Programme (MLW), Blantyre, Malawi
| | - Prisca Benedicto-Matambo
- Malawi Liverpool Wellcome Research Programme (MLW), Blantyre, Malawi
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jonathan J Mandolo
- Malawi Liverpool Wellcome Research Programme (MLW), Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - End Chinyama
- Malawi Liverpool Wellcome Research Programme (MLW), Blantyre, Malawi
| | - Orpha Kumwenda
- Malawi Liverpool Wellcome Research Programme (MLW), Blantyre, Malawi
| | - Kayla G Barnes
- Malawi Liverpool Wellcome Research Programme (MLW), Blantyre, Malawi
- Harvard TH Chan School of Public Health, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- University of Glasgow, Glasgow, UK
| | - Nigel A Cunliffe
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- National Institute for Health and Care Research, Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Miren Iturriza-Gomara
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kondwani C Jambo
- Malawi Liverpool Wellcome Research Programme (MLW), Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Khuzwayo C Jere
- Malawi Liverpool Wellcome Research Programme (MLW), Blantyre, Malawi.
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre, Malawi.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
- National Institute for Health and Care Research, Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK.
| |
Collapse
|
37
|
Albuquerque MA, Deus DRD, Lobo PS, Teixeira DM, Maués MAC, Cardoso JF, Silva LDD, Gabbay YB, Resque HR, Silva Soares LD, Siqueira JAM, Guerra SFS. Detection of G3 human-like rotavirus in institutionalized dogs from Brazil. Braz J Microbiol 2023; 54:1295-1301. [PMID: 37076753 PMCID: PMC10234945 DOI: 10.1007/s42770-023-00972-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/07/2023] [Indexed: 04/21/2023] Open
Abstract
Viral gastroenteritis is a common clinical problem in dogs and group A rotavirus (RVA) is one of the agents involved in this etiology. It mainly affects dogs in the first 6 months of life, and these animals are considered an important reservoir and potential transmitters of the virus to other susceptible hosts, such as humans. Among the different types of RVA, G3 is the most detected in dogs, and this genotype is also involved in infections in other animals, including humans. Thus, the present study aims to investigate the presence of RVA in samples of dogs from a public kennel. A total of 64 fecal samples from dogs with diarrhea were analyzed, collected from April 2019 to March 2020, from the kennel of the Zoonosis Control Center, located in Belém, a city in the North of Brazil. The extracted genetic material was subjected to reverse transcription followed by real-time PCR (RT-qPCR); the positives were tested by RT-PCR with a specific primer for the RVA VP7 gene, after nucleotide sequencing and phylogenetic analysis. One sample was subjected to high-performance sequencing. A positivity of 7.8% (5/64) was observed for RVA, all characterized as G3, grouping in the G3-III lineage, with greater similarity to human samples. Different regions of the RVA genome fragments were found. These results emphasize the need for animal health surveillance to better understand the global strain dispersion of RVA and elucidate possible interspecies transmission events, monitoring the genetic diversity of this pathogen.
Collapse
Affiliation(s)
| | | | - Patrícia Santos Lobo
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | - Dielle Monteiro Teixeira
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | | | - Jedson Ferreira Cardoso
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | - Luciana Damascena da Silva
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | - Yvone Benchimol Gabbay
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | - Hugo Reis Resque
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | - Luana da Silva Soares
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | | | - Sylvia Fátima Santos Guerra
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil.
| |
Collapse
|
38
|
Tran H, Friendship R, Poljak Z. Classification of group A rotavirus VP7 and VP4 genotypes using random forest. Front Genet 2023; 14:1029185. [PMID: 37323680 PMCID: PMC10267748 DOI: 10.3389/fgene.2023.1029185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction: Group A rotaviruses are major pathogens in causing severe diarrhea in young children and neonates of many different species of animals worldwide and group A rotavirus sequence data are becoming increasingly available over time. Different methods exist that allow for rotavirus genotyping, but machine learning methods have yet to be explored. Usage of machine learning algorithms such as random forest alongside alignment-based methodology may allow for both efficient and accurate classification of circulating rotavirus genotypes through the dual classification system. Methods: Random forest models were trained on positional features obtained from pairwise and multiple sequence alignment and cross-validated using methods of repeated 10-fold cross-validation thrice and leave one- out cross validation. Models were then validated on unseen data from the testing datasets to observe real-world performance. Results: All models were found to perform strongly in classification of VP7 and VP4 genotypes with high overall accuracy and kappa values during model training (0.975-0.992, 0.970-0.989) and during model testing (0.972-0.996, 0.969-0.996), respectively. Models trained on multiple sequence alignment generally had slightly higher overall accuracy and kappa values than models trained on pairwise sequence alignment method. In contrast, pairwise sequence alignment models were found to be generally faster than multiple sequence alignment models in computational speed when models do not need to be retrained. Models that used repeated 10-fold cross-validation thrice were also found to be much faster in model computational speed than models that used leave-one-out cross validation, with no noticeable difference in overall accuracy and kappa values between the cross-validation methods. Discussion: Overall, random forest models showed strong performance in the classification of both group A rotavirus VP7 and VP4 genotypes. Application of these models as classifiers will allow for rapid and accurate classification of the increasing amounts of rotavirus sequence data that are becoming available.
Collapse
|
39
|
Aksoy E, Azkur AK. Genome characterization of a Turkish bovine rotavirus field isolate by shotgun metagenomics. Arch Virol 2023; 168:159. [PMID: 37170023 DOI: 10.1007/s00705-023-05778-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
A bovine rotavirus (BRV) isolate from Kirsehir was isolated from feces of a neonatal calf with diarrhea, identified, and sequenced by shotgun sequencing. Its genotype constellation is G10-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The structural genes and the non-structural genes NSP1, NSP3, and NSP4 of the Kirsehir isolate were similar in sequence to those of BRVs identified in Turkey. However, VP2, NSP2, NSP4, and NSP5/6 showed similarity to those of rotaviruses from different animal hosts. These findings not only expand our current understanding of the diversity of rotaviruses but also contribute to our understanding of the evolution of rotaviruses at both the national and global levels and reinforce the significance of conducting further research on rotaviruses in Turkey.
Collapse
Affiliation(s)
- Emel Aksoy
- Department of Virology, Faculty of Veterinary Medicine, Kirikkale University, Kirikkale, Türkiye
| | - Ahmet Kürşat Azkur
- Department of Virology, Faculty of Veterinary Medicine, Kirikkale University, Kirikkale, Türkiye.
| |
Collapse
|
40
|
Casey-Moore MC, Mijatovic-Rustempasic S, Jaimes J, Perkins C, Riley AM, Cortese MM, Gautam R, Bowen MD. Coding-Complete Genome Sequences of G6P[14] Rotavirus Strain Detected in a Human Stool Specimen within the United States. Microbiol Resour Announc 2023:e0000823. [PMID: 37140434 DOI: 10.1128/mra.00008-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
In this study, we report the detection of a G6P[14] rotavirus strain from a human stool sample within the United States. The full genotype constellation of the G6P[14] strain was identified as G6-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3.
Collapse
Affiliation(s)
- Mary C Casey-Moore
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Slavica Mijatovic-Rustempasic
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jose Jaimes
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Charity Perkins
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ann Marie Riley
- Infectious Disease Diagnostic Laboratory, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Margaret M Cortese
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rashi Gautam
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael D Bowen
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| |
Collapse
|
41
|
Pinheiro MS, Dias JBL, Petrucci MP, Travassos CEPF, Mendes GS, Santos N. Molecular Characterization of Avian Rotaviruses F and G Detected in Brazilian Poultry Flocks. Viruses 2023; 15:v15051089. [PMID: 37243175 DOI: 10.3390/v15051089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Avian rotaviruses (RVs) are important etiologic agents of gastroenteritis in birds. In general, avian RVs are understudied; consequently, there is a paucity of information regarding these viruses. Therefore, the characterization of these viral species is highly relevant because more robust information on genetic, epidemiologic, and evolutionary characteristics can clarify the importance of these infections, and inform efficient prevention and control measures. In this study, we describe partial genome characterizations of two avian RV species, RVF and RVG, detected in asymptomatic poultry flocks in Brazil. Complete or partial sequences of at least one of the genomic segments encoding VP1, VP2, VP4, VP6, VP7, NSP1, NSP4, NSP4, or NSP5 of 23 RVF and 3 RVG strains were obtained, and demonstrated that multiple variants of both RVF and RVG circulate among Brazilian poultry. In this study, new and important information regarding the genomic characteristics of RVF and RVG is described. In addition, the circulation of these viruses in the study region and the genetic variability of the strains detected are demonstrated. Thus, the data generated in this work should help in understanding the genetics and ecology of these viruses. Nonetheless, the availability of a greater number of sequences is necessary to advance the understanding of the evolution and zoonotic potential of these viruses.
Collapse
Affiliation(s)
- Mariana S Pinheiro
- Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21947-902, Brazil
| | - Juliana B L Dias
- Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21947-902, Brazil
| | - Melissa P Petrucci
- Centro de Ciências e Tecnologias Agropecuárias, Laboratório de Sanidade Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes 28013-602, Brazil
| | - Carlos E P F Travassos
- Centro de Ciências e Tecnologias Agropecuárias, Laboratório de Sanidade Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes 28013-602, Brazil
| | - Gabriella S Mendes
- Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21947-902, Brazil
| | - Norma Santos
- Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21947-902, Brazil
| |
Collapse
|
42
|
Mwangi PN, Potgieter RL, Uwimana J, Mutesa L, Muganga N, Murenzi D, Tusiyenge L, Mwenda JM, Mogotsi MT, Rakau K, Esona MD, Steele AD, Seheri ML, Nyaga MM. The Evolution of Post-Vaccine G8P[4] Group a Rotavirus Strains in Rwanda; Notable Variance at the Neutralization Epitope Sites. Pathogens 2023; 12:658. [PMID: 37242329 PMCID: PMC10223037 DOI: 10.3390/pathogens12050658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Africa has a high level of genetic diversity of rotavirus strains, which is suggested to be a possible reason contributing to the suboptimal effectiveness of rotavirus vaccines in this region. One strain that contributes to this rotavirus diversity in Africa is the G8P[4]. This study aimed to elucidate the entire genome and evolution of Rwandan G8P[4] strains. Illumina sequencing was performed for twenty-one Rwandan G8P[4] rotavirus strains. Twenty of the Rwandan G8P[4] strains had a pure DS-1-like genotype constellation, and one strain had a reassortant genotype constellation. Notable radical amino acid differences were observed at the neutralization sites when compared with cognate regions in vaccine strains potentially playing a role in neutralization escape. Phylogenetic analysis revealed that the closest relationship was with East African human group A rotavirus (RVA) strains for five of the genome segments. Two genome sequences of the NSP4 genome segment were closely related to bovine members of the DS-1-like family. Fourteen VP1 and eleven VP3 sequences had the closest relationships with the RotaTeq™ vaccine WC3 bovine genes. These findings suggest that the evolution of VP1 and VP3 might have resulted from reassortment events with RotaTeq™ vaccine WC3 bovine genes. The close phylogenetic relationship with East African G8P[4] strains from Kenya and Uganda suggests co-circulation in these countries. These findings highlight the need for continued whole-genomic surveillance to elucidate the evolution of G8P[4] strains, especially after the introduction of rotavirus vaccination.
Collapse
Affiliation(s)
- Peter N. Mwangi
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Robyn-Lee Potgieter
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Jeannine Uwimana
- Kigali University Teaching Hospital, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda
| | - Leon Mutesa
- Kigali University Teaching Hospital, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda
- Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda
| | - Narcisse Muganga
- Kigali University Teaching Hospital, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda
| | - Didier Murenzi
- Kigali University Teaching Hospital, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda
| | - Lisine Tusiyenge
- Kigali University Teaching Hospital, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda
| | - Jason M. Mwenda
- World Health Organization, Regional Office for Africa, Brazzaville P.O. Box 06, Congo
| | - Milton T. Mogotsi
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Kebareng Rakau
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University (MEDUNSA), Pretoria 0204, South Africa
| | - Mathew D. Esona
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University (MEDUNSA), Pretoria 0204, South Africa
| | - A. Duncan Steele
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University (MEDUNSA), Pretoria 0204, South Africa
| | - Mapaseka L. Seheri
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University (MEDUNSA), Pretoria 0204, South Africa
| | - Martin M. Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| |
Collapse
|
43
|
Kumazaki M, Usuku S. Influence of herd immunity on norovirus: a long-term field study of repeated viral gastroenteritis outbreaks at the same facilities. BMC Infect Dis 2023; 23:265. [PMID: 37101126 PMCID: PMC10132420 DOI: 10.1186/s12879-023-08251-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 04/13/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Viral acute gastroenteritis (AG) is detected worldwide annually. Outbreaks caused by viruses associated with gastroenteritis have been reported repeatedly at the same facilities in Yokohama, Japan over several years. We investigated the statuses of these repeated outbreaks to consider herd immunity at the facility level. METHODS Between September 2007 and August 2017, 1459 AG outbreaks were reported at 1099 facilities. Stool samples were collected for virological testing, and the norovirus gene was amplified and sequenced to determine the genotype using the N-terminal region of the capsid. RESULTS The outbreaks were caused by norovirus, sapovirus, rotavirus A, and rotavirus C. Norovirus was consistently predominant over the 10-year period. Of 1099 facilities, 227 reported multiple outbreaks, of which norovirus-only combinations accounted for 76.2%. More outbreaks were due to different genotype combinations than the same genotype combinations. For facilities that experienced two norovirus outbreaks, the average interval between outbreaks was longer for groups with the same combinations than for groups with different genogroup or genotype combinations, although no statistically significant differences were observed. At 44 facilities, outbreaks occurred repeatedly during the same AG season, and most exhibited combinations of different norovirus genotypes or viruses. Among 49 combinations with the same norovirus genotype at the same facilities over 10 years, the most prevalent genotypes were combinations of genogroup II genotype 4 (GII.4), followed by GII.2, GII.6, GII.3, GII.14, and GI.3. The mean interval between outbreaks was 31.2 ± 26.8 months for all combinations, and the mean intervals were longer for non-GII.4 genotype cases than for GII.4 cases, and statistically significant differences were observed (t-test, P < 0.05). Additionally, these average intervals were longer for kindergarten/nursery schools and primary schools than for nursing homes for older adults (t-test, P < 0.05). CONCLUSIONS Repeated AG outbreaks at the same facilities in Yokohama during the 10-year study period included mainly norovirus combinations. Herd immunity at the facility level was maintained for at least the same AG season. Norovirus genotype-specific herd immunity was maintained for an average of 31.2 months during the study period, and these intervals differed depending on genotype.
Collapse
Affiliation(s)
- Makoto Kumazaki
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, 2-7-1 Tomiokahigashi, Kanazawa-Ku, Yokohama, Kanagawa, 236-0051, Japan.
| | - Shuzo Usuku
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, 2-7-1 Tomiokahigashi, Kanazawa-Ku, Yokohama, Kanagawa, 236-0051, Japan
| |
Collapse
|
44
|
Veletanlic V, Sartalamacchia K, Diller JR, Ogden KM. Multiple rotavirus species encode fusion-associated small transmembrane (FAST) proteins with cell type-specific activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536061. [PMID: 37066280 PMCID: PMC10104117 DOI: 10.1101/2023.04.07.536061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fusion-associated small transmembrane (FAST) proteins are viral nonstructural proteins that mediate cell-cell fusion to form multinucleated syncytia. We previously reported that human species B rotavirus NSP1-1 is a FAST protein that induces syncytia in primate epithelial cells but not rodent fibroblasts. We hypothesized that the NSP1-1 proteins of other rotavirus species could also mediate cell-cell fusion and that fusion activity might be limited to cell types derived from homologous hosts. To test this hypothesis, we predicted the structure and domain organization of NSP1-1 proteins of species B rotavirus from a human, goat, and pig, species G rotavirus from a pigeon and turkey, and species I rotavirus from a dog and cat. We cloned these sequences into plasmids and transiently expressed the NSP1-1 proteins in avian, canine, hamster, human, porcine, and simian cells. Regardless of host origin of the virus, each NSP1-1 protein induced syncytia in primate cells, while few induced syncytia in other cell types. To identify the domains that determined cell-specific fusion activity for human species B rotavirus NSP1-1, we engineered chimeric proteins containing domain exchanges with the p10 FAST protein from Nelson Bay orthoreovirus. Using the chimeric proteins, we found that the N-terminal and transmembrane domains determined the cell type specificity of fusion activity. Although the species and cell type criteria for fusion activity remain unclear, these findings suggest that rotavirus species B, G, and I NSP1-1 are functional FAST proteins whose N termini play a role in specifying the cells in which they mediate syncytia formation.
Collapse
Affiliation(s)
- Vanesa Veletanlic
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kylie Sartalamacchia
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Julia R. Diller
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kristen M. Ogden
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
45
|
Li FY, Guo YH, Sun ZL, Liu H, Zhao MC, Cui J, Jiang Y, Shen XX, Ma XJ, Feng ZS. Rapid two-stage amplification in a single tube for simultaneous detection of norovirus GII and group a rotavirus. J Clin Lab Anal 2023; 37:e24858. [PMID: 36916770 PMCID: PMC10098066 DOI: 10.1002/jcla.24858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/06/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
The most prevalent viruses currently causing diarrhea are norovirus and rotavirus, and rapid and sensitive detection methods are essential for the early diagnosis of disease. The purpose of this study was to establish a sensitive single-tube two-stage nucleic acid amplification method-reverse transcription recombinase-assisted PCR (RT-RAP)-for simultaneous detection of norovirus GII and group A Rotavirus, with the first stage consisting of isothermal reverse transcription recombinase-aided amplification (RT-RAA) and the second stage consisting of qPCR (quantitative PCR). RT-RAP is more sensitive than either RT-RAA or qRT-PCR (quantitative RT-PCR) alone. And the addition of a barrier that can be disassembled after heating enabled the detection of samples within 1 h in a single closed tube. Sensitivity was 10 copies/reaction of norovirus (Novs) GII and group A rotavirus (RVA). In parallel, two hundred fecal specimens were used to evaluate the method and compare it with a commercial fluorescent quantitative RT-PCR. The data showed kappa values of 0.957 and 0.98 (p < 0.05) for detecting Novs GII and RVA by the two methods, indicating the potential of the newly established assay to be applied to clinical and laboratory testing.
Collapse
Affiliation(s)
- Feng-Yu Li
- Hebei Medical University, Shijiazhuang, Hebei, China.,Hebei General Hospital, Shijiazhuang, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying-Hui Guo
- Department of Clinical Laboratory, Children's Hospital of Hebei Province, Shijiazhuang, Hebei, China
| | - Zhen-Lu Sun
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong Liu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong, China
| | - Meng-Chuan Zhao
- Department of Clinical Laboratory, Children's Hospital of Hebei Province, Shijiazhuang, Hebei, China
| | - Jia Cui
- Hebei General Hospital, Shijiazhuang, Hebei, China
| | - Yue Jiang
- The Third Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhi-Shan Feng
- Hebei Medical University, Shijiazhuang, Hebei, China.,Hebei General Hospital, Shijiazhuang, Hebei, China.,Hebei Medical Laboratory Clinical Medical Research Center, Shijiazhuang City, Hebei Province, China.,Hebei Key Laboratory of Molecular Medicine, Shijiazhuang City, Hebei Province, China
| |
Collapse
|
46
|
Masson L, Barbé L, Henaff F, Ahmed T, Le Moullac-Vaidye B, Peltier C, Marchand SS, Scherdel P, Vibet MA, Ruvoën-Clouet N, Elenga N, Imbert-Marcille BM, Gras-Le Guen C, Le Pendu J. Extent of the protection afforded by histo-blood group polymorphism against rotavirus gastroenteritis in metropolitan France and French Guiana. Front Microbiol 2023; 14:1141652. [PMID: 36970669 PMCID: PMC10036354 DOI: 10.3389/fmicb.2023.1141652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
Human rotaviruses attach to histo-blood group antigens glycans and null alleles of the ABO, FUT2 and FUT3 genes seem to confer diminished risk of gastroenteritis. Yet, the true extent of this protection remains poorly quantified. Here, we conducted a prospective study to evaluate the risk of consulting at the hospital in non-vaccinated pediatric patients according to the ABO, FUT2 (secretor) and FUT3 (Lewis) polymorphisms, in Metropolitan France and French Guiana. At both locations, P genotypes were largely dominated by P [8]-3, with P [6] cases exclusively found in French Guiana. The FUT2 null (nonsecretor) and FUT3 null (Lewis negative) phenotypes conferred near full protection against severe gastroenteritis due to P [8]-3 strains (OR 0.03, 95% CI [0.00–0.21] and 0.1, 95% CI [0.01–0.43], respectively in Metropolitan France; OR 0.08, 95% CI [0.01–0.52] and 0.14, 95%CI [0.01–0.99], respectively in French Guiana). Blood group O also appeared protective in Metropolitan France (OR 0.38, 95% CI [0.23–0.62]), but not in French Guiana. The discrepancy between the two locations was explained by a recruitment at the hospital of less severe cases in French Guiana than in Metropolitan France. Considering the frequencies of the null ABO, Secretor and Lewis phenotypes, the data indicate that in a Western European population, 34% (95% CI [29%; 39%]) of infants are genetically protected against rotavirus gastroenteritis of sufficient severity to lead to hospital visit.
Collapse
Affiliation(s)
- Lydie Masson
- Department of Pediatrics, University Hospital of Nantes, Nantes, France
| | - Laure Barbé
- Nantes Université, Inserm, CNRS, Immunology and New Concepts in Immunotherapy, INCIT, Nantes, France
| | - Fanny Henaff
- Department of Pediatrics, Centre Hospitalier Andrée Rosemon, Cayenne, France
| | - Tasnuva Ahmed
- Nantes Université, Inserm, CNRS, Immunology and New Concepts in Immunotherapy, INCIT, Nantes, France
- International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | | | - Cécile Peltier
- Center for Research in Transplantation and Translational Immunology, Inserm, Nantes Université, Nantes, France
| | - Sarah S Marchand
- Virology Department, University Hospital of Nantes, Nantes, France
| | - Pauline Scherdel
- Clinical Investigation Center (CIC004), Inserm, University Hospital of Nantes, Nantes, France
| | - Marie-Anne Vibet
- Clinical Research Department, University Hospital of Nantes, Nantes, France
| | - Nathalie Ruvoën-Clouet
- Nantes Université, Inserm, CNRS, Immunology and New Concepts in Immunotherapy, INCIT, Nantes, France
- Ecole Nationale Vétérinaire, Agroalimentaire et de l'Alimentation, Oniris, Nantes, France
| | - Narcisse Elenga
- Department of Pediatrics, Centre Hospitalier Andrée Rosemon, Cayenne, France
| | - Berthe-Marie Imbert-Marcille
- Center for Research in Transplantation and Translational Immunology, Inserm, Nantes Université, Nantes, France
- Virology Department, University Hospital of Nantes, Nantes, France
| | | | - Jacques Le Pendu
- Nantes Université, Inserm, CNRS, Immunology and New Concepts in Immunotherapy, INCIT, Nantes, France
- *Correspondence: Jacques Le Pendu,
| |
Collapse
|
47
|
Genomic Constellation of Human Rotavirus G8 Strains in Brazil over a 13-Year Period: Detection of the Novel Bovine-like G8P[8] Strains with the DS-1-like Backbone. Viruses 2023; 15:v15030664. [PMID: 36992373 PMCID: PMC10056101 DOI: 10.3390/v15030664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Rotavirus (RVA) G8 is frequently detected in animals, but only occasionally in humans. G8 strains, however, are frequently documented in nations in Africa. Recently, an increase in G8 detection was observed outside Africa. The aims of the study were to monitor G8 infections in the Brazilian human population between 2007 and 2020, undertake the full-genotype characterization of the four G8P[4], six G8P[6] and two G8P[8] RVA strains and conduct phylogenetic analysis in order to understand their genetic diversity and evolution. A total of 12,978 specimens were screened for RVA using ELISA, PAGE, RT-PCR and Sanger sequencing. G8 genotype represented 0.6% (15/2434) of the entirely RVA-positive samples. G8P[4] comprised 33.3% (5/15), G8P[6] 46.7% (7/15) and G8P[8] 20% (3/15). All G8 strains showed a short RNA pattern. All twelve selected G8 strains displayed a DS-1-like genetic backbone. The whole-genotype analysis on a DS-1-like backbone identified four different genotype-linage constellations. According to VP7 analysis, the Brazilian G8P[8] strains with the DS-1-like backbone strains were derived from cattle and clustered with newly DS-1-like G1/G3/G9/G8P[8] strains and G2P[4] strains. Brazilian IAL-R193/2017/G8P[8] belonged to a VP1/R2.XI lineage and were grouped with bovine-like G8P[8] strains with the DS-1-like backbone strains detected in Asia. Otherwise, the Brazilian IAL-R558/2017/G8P[8] possess a “Distinct” VP1/R2 lineage never previously described and grouped apart from any of the DS-1-like reference strains. Collectively, our findings suggest that the Brazilian bovine-like G8P[8] strains with the DS-1-like backbone strains are continuously evolving and likely reassorting with local RVA strains rather than directly relating to imports from Asia. The Brazilian G8P[6]-DS-1-like strains have been reassorted with nearby co-circulating American strains of the same DS-1 genotype constellation. However, phylogenetic analyses revealed that these strains have some genetic origin from Africa. Finally, rather than being African-born, Brazilian G8P[4]-DS-1-like strains were likely imported from Europe. None of the Brazilian G8 strains examined here exhibited signs of recent zoonotic reassortment. G8 strains continued to be found in Brazil according to their intermittent and localized pattern, thus, does not suggest that a potential emergence is taking place in the country. Our research demonstrates the diversity of G8 RVA strains in Brazil and adds to the understanding of G8P[4]/P[6]/P[8] RVA genetic diversity and evolution on a global scale.
Collapse
|
48
|
Althof N, Trojnar E, Johne R. Rotaviruses in Wild Ungulates from Germany, 2019-2022. Microorganisms 2023; 11:microorganisms11030566. [PMID: 36985140 PMCID: PMC10058221 DOI: 10.3390/microorganisms11030566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/30/2023] Open
Abstract
Rotavirus A (RVA) is an important cause of diarrhea in humans and animals. However, RVA in wild animals has only scarcely been investigated so far. Here, the presence of RVA in wild ungulates hunted between 2019 and 2022 in Brandenburg, Germany, was investigated using real-time RT-PCR and sequencing of RT-PCR products. By analyzing intestinal contents, RVA-RNA was detected in 1.0% (2/197) of wild boar (Sus scrofa), 1.3% (2/152) of roe deer (Capreolus capreolus), and 2.1% (2/95) of fallow deer (Dama dama) but not in 28 red deer (Cervus elaphus) samples. Genotyping identified G3P[13] strains in wild boar, which were closely related to previously described pig and wild boar strains. Genotype G10P[15] strains, closely related to strains from roe deer, sheep, or cattle, were found in roe deer. The strains of fallow deer represented genotype G3P[3], clustering in a group containing different strains from several hosts. The results indicated a low prevalence of RVA in wild ungulates in Germany. Associations of specific genotypes with certain ungulate species seem to exist but should be confirmed by analyses of more samples in the future.
Collapse
Affiliation(s)
- Nadine Althof
- German Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Eva Trojnar
- German Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Reimar Johne
- German Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| |
Collapse
|
49
|
Mwangi PN, Potgieter RL, Simwaka J, Mpabalwani EM, Mwenda JM, Mogotsi MT, Magagula N, Esona MD, Steele AD, Seheri ML, Nyaga MM. Genomic Analysis of G2P[4] Group A Rotaviruses in Zambia Reveals Positive Selection in Amino Acid Site 7 of Viral Protein 3. Viruses 2023; 15:v15020501. [PMID: 36851715 PMCID: PMC9965253 DOI: 10.3390/v15020501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
The G2P[4] genotype is among the rotavirus strains that circulate commonly in humans. Several countries have reported its immediate upsurge after the introduction of rotavirus vaccination, raising concern about sub-optimal vaccine effectiveness against this genotype in the long term. This study aimed to gain insight into the evolution of post-vaccine Zambian G2P[4] group A rotavirus (RVA) strains and their overall genetic make-up by analysis of sequence alignments at the amino acid (AA) level. Twenty-nine Zambian G2P[4] rotavirus strains were subjected to whole-genome sequencing using the Illumina MiSeq® platform. All the strains exhibited the typical DS-1-like genotype constellation, and the nucleotide sequences of the 11 genome segments showed high nucleotide similarities (>97%). Phylogenetic analyses together with representative global G2P[4] RVA showed that Zambian strains clustered into human lineages IV (for VP2, VP4, VP7, NSP1, and NSP5), V (for VP1, VP3, VP6, NSP2, and NSP3), and XXIII (for NSP4). The AA differences between the lineages where the study strains clustered and lineages of global reference strains were identified and analyzed. Selection pressure analysis revealed that AA site seven in the Viral Protein 3 (VP3) genome segment was under positive selection. This site occurs in the region of intrinsic disorder in the VP3 protein, and Zambian G2P[4] strains could potentially be utilizing this intrinsically disordered region to survive immune pressure. The Zambian G2P[4] strains from 2012 to 2016 comprised the G2P[4] strains that have been circulating globally since the early 2000s, highlighting the epidemiological fitness of these contemporary G2P[4] strains. Continuous whole-genome surveillance of G2P[4] strains remains imperative to understand their evolution during the post-vaccination period.
Collapse
Affiliation(s)
- Peter N. Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Robyn-Lee Potgieter
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Julia Simwaka
- Institute of Basic and Biomedical Sciences, Department of Biomedical Sciences, The Levy Mwanawasa Medical University, Lusaka 10101, Zambia
| | - Evans M. Mpabalwani
- Department of Paediatrics and Child Health, School of Medicine, University of Zambia, Ridgeway, Lusaka RW50000, Zambia
| | - Jason M. Mwenda
- World Health Organization, Regional Office for Africa, Brazzaville P.O. Box 06, Congo
| | - Milton T. Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Nonkululeko Magagula
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - Mathew D. Esona
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - A. Duncan Steele
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - Mapaseka L. Seheri
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
- Correspondence:
| |
Collapse
|
50
|
Amin AB, Tate JE, Waller LA, Lash TL, Lopman BA. Monovalent Rotavirus Vaccine Efficacy Against Different Rotavirus Genotypes: A Pooled Analysis of Phase II and III Trial Data. Clin Infect Dis 2023; 76:e1150-e1156. [PMID: 36031386 PMCID: PMC10169401 DOI: 10.1093/cid/ciac699] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/15/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Rotavirus vaccine performance appears worse in countries with high rotavirus genotype diversity. Evidence suggests diminished vaccine efficacy (VE) against G2P[4], which is heterotypic with existing monovalent rotavirus vaccine formulations. Most studies assessing genotype-specific VE have been underpowered and inconclusive. METHODS We pooled individual-level data from 10 Phase II and III clinical trials of rotavirus vaccine containing G1 and P[8] antigens (RV1) conducted between 2000 and 2012. We estimated VE against both any-severity and severe (Vesikari score ≥11) rotavirus gastroenteritis (RVGE) using binomial and multinomial logistic regression models for non-specific VE against any RVGE, genotype-specific VE, and RV1-typic VE against genotypes homotypic, partially heterotypic, or fully heterotypic with RV1 antigens. We adjusted models for concomitant oral poliovirus and RV1 vaccination and the country's designated child mortality stratum. RESULTS Analysis included 87 644 infants from 22 countries in the Americas, Europe, Africa, and Asia. For VE against severe RVGE, non-specific VE was 91% (95% confidence interval [CI]: 87-94%). Genotype-specific VE ranged from 96% (95% CI: 89-98%) against G1P[8] to 71% (43-85%) against G2P[4]. RV1-typic VE was 92% (95% CI: 84-96%) against partially heterotypic genotypes but 83% (67-91%) against fully heterotypic genotypes. For VE against any-severity RVGE, non-specific VE was 82% (95% CI: 75-87%). Genotype-specific VE ranged from 94% (95% CI: 86-97%) against G1P[8] to 63% (41-77%) against G2P[4]. RV1-typic VE was 83% (95% CI: 72-90%) against partially heterotypic genotypes but 63% (40-77%) against fully heterotypic genotypes. CONCLUSIONS RV1 VE is comparatively diminished against fully heterotypic genotypes including G2P[4].
Collapse
Affiliation(s)
- Avnika B Amin
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA.,Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Jacqueline E Tate
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lance A Waller
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Timothy L Lash
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Benjamin A Lopman
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| |
Collapse
|