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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.
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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
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2
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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.
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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
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3
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Doan YH, Dennis FE, Takemae N, Haga K, Shimizu H, Appiah MG, Lartey BL, Damanka SA, Hayashi T, Suzuki T, Kageyama T, Armah GE, Katayama K. Emergence of Intergenogroup Reassortant G9P[4] Strains Following Rotavirus Vaccine Introduction in Ghana. Viruses 2023; 15:2453. [PMID: 38140694 PMCID: PMC10747750 DOI: 10.3390/v15122453] [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: 11/22/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023] Open
Abstract
Rotavirus (RVA) is a leading cause of childhood gastroenteritis. RVA vaccines have reduced the global disease burden; however, the emergence of intergenogroup reassortant strains is a growing concern. During surveillance in Ghana, we observed the emergence of G9P[4] RVA strains in the fourth year after RVA vaccine introduction. To investigate whether Ghanaian G9P[4] strains also exhibited the DS-1-like backbone, as seen in reassortant G1/G3/G8/G9 strains found in other countries in recent years, this study determined the whole genome sequences of fifteen G9P[4] and two G2P[4] RVA strains detected during 2015-2016. The results reveal that the Ghanaian G9P[4] strains exhibited a double-reassortant genotype, with G9-VP7 and E6-NSP4 genes on a DS-1-like backbone (G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2). Although they shared a common ancestor with G9P[4] DS-1-like strains from other countries, further intra-reassortment events were observed among the original G9P[4] and co-circulating strains in Ghana. In the post-vaccine era, there were significant changes in the distribution of RVA genotype constellations, with unique strains emerging, indicating an impact beyond natural cyclical fluctuations. However, reassortant strains may exhibit instability and have a limited duration of appearance. Current vaccines have shown efficacy against DS-1-like strains; however, ongoing surveillance in fully vaccinated children is crucial for addressing concerns about long-term effectiveness.
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Affiliation(s)
- Yen Hai Doan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.H.D.)
| | - Francis Ekow Dennis
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nobuhiro Takemae
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.H.D.)
| | - Kei Haga
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Michael Gyasi Appiah
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Belinda Larteley Lartey
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Susan Afua Damanka
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Takaya Hayashi
- Department of Molecular Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8549, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Pathogenesis, Infection and Host Response, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8549, Japan
| | - Tsutomu Kageyama
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.H.D.)
| | - George Enyimah Armah
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Kazuhiko Katayama
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
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4
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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.
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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.)
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5
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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.
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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.
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6
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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.
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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
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7
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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.
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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.
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8
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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.
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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
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Abstract
Rotaviruses are the most common viral agents associated with foal diarrhea. Between 2014 and 2017, the annual prevalence of rotavirus in diarrheic foals ranged between 18 and 28% in Haryana (India). Whole-genome sequencing of two equine rotavirus A (ERVA) isolates (RVA/Horse-wt/IND/ERV4/2017 and RVA/Horse-wt/IND/ERV6/2017) was carried out to determine the genotypic constellations (GCs) of ERVAs. The GCs of both the isolates were G3-P[3]-I8-R3-C3-M3-A9-N3-T3-E3-H6, a unique combination reported for ERVAs so far. Both the isolates carried VP6 of genotype I8, previously unreported from equines. Upon comparison with RVAs of other species, the GC of both isolates was identical to that of a bat rotavirus strain, MSLH14, isolated from China in 2012. The nucleotide sequences of the genes encoding VP3, NSP2, and NSP3 shared >95.81% identity with bat RVA strains isolated from Africa (Gabon). The genes encoding VP1, VP2, VP7, NSP1, and NSP4 shared 94.82% to 97.12% nucleotide identities with the human strains which have zoonotic links to bats (RCH272 and MS2015-1-0001). The VP6 genes of both strains were distinct and had the highest similarity of only 87.08% with that of CMH222, a human strain of bat origin. The phylogenetic analysis and lineage studies revealed that VP7 of both isolates clustered in a new lineage (lineage X) of the G3 genotype with bat, human, and alpaca strains. Similarly, VP4 clustered in a distinct P[3] lineage. These unusual findings highlight the terra incognita of the genomic diversity of equine rotaviruses and support the need for the surveillance of RVAs in animals and humans with a "one health" approach. IMPORTANCE Rotaviruses are globally prevalent diarrheal pathogens in young animals including foals, piglets, calves, goats, sheep, cats, and dogs along with humans. The genome of rotaviruses consists of 11 segments, which enables them to undergo reshuffling by reassortment of segments from multiple species during mixed infections. In this study, the prevalence of equine rotaviruses was 32.11% in organized equine farms of North India. The complete genome analysis of two ERVA isolates revealed an unusual genomic constellation, which was previously reported only in a bat RVA strain. A segment-wise phylogenetic analysis revealed that most segments of both isolates were highly similar either to bat or to bat-like human rotaviruses. The occurrence of unusual bat-like rotaviruses in equines emphasizes the need of extensive surveillance of complete genomes of both animal and human rotaviruses with a "one health" approach.
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Brnić D, Čolić D, Kunić V, Maltar-Strmečki N, Krešić N, Konjević D, Bujanić M, Bačani I, Hižman D, Jemeršić L. Rotavirus A in Domestic Pigs and Wild Boars: High Genetic Diversity and Interspecies Transmission. Viruses 2022; 14:v14092028. [PMID: 36146832 PMCID: PMC9503859 DOI: 10.3390/v14092028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/05/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Rotavirus A (RVA) is an important pathogen for porcine health. In comparison to humans, RVA in domestic animals and especially in wildlife is under researched. Therefore, the aim of the present study was to investigate the prevalence, genetic diversity, molecular epidemiology and interspecies transmission of RVA in domestic pigs and wild boars. During the three consecutive RVA seasons (2018–2021) we collected 445 and 441 samples from domestic pigs and wild boars, respectively. Samples were tested by real-time RT-PCR, and RVA-positive samples were genotyped in VP7 and VP4 segments. Our results report an RVA prevalence of 49.9% in domestic pigs and 9.3% in wild boars. Outstanding RVA genetic diversity was observed in VP7 and VP4 segments, especially in domestic pigs exhibiting a striking 23 different RVA combinations (G5P[13] and G9P[23] prevailed). Interspecies transmission events were numerous between domestic pigs and wild boars, sharing G3, G5, G6, G9, G11 and P[13] genotypes. Furthermore, our data indicate that such transmission events involved even bovines (G6, P[11]) and, intriguingly, humans (G1P[8]). This study contributes to the basic knowledge that may be considered important for vaccine development and introduction, as a valuable and currently missing tool for efficient pig health management in the EU.
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Affiliation(s)
- Dragan Brnić
- Virology Department, Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-6123-674
| | - Daniel Čolić
- Virology Department, Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Valentina Kunić
- Virology Department, Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Nadica Maltar-Strmečki
- Laboratory for Electron Spin Spectroscopy, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Nina Krešić
- Virology Department, Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Dean Konjević
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Miljenko Bujanić
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Ivica Bačani
- Animal Feed Factory Ltd., Dr. Ivana Novaka 11, 40000 Čakovec, Croatia
| | - Dražen Hižman
- Belje Agro-Vet plus Ltd., Kokingrad 4, Mece, 31326 Darda, Croatia
- Rusagro, LLC “Tambovsky bacon”, Bazarnaya 104, 392036 Tambov, Russia
| | - Lorena Jemeršić
- Virology Department, Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
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11
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Lucien MAB, Esona MD, Pierre M, Joseph G, Rivière C, Leshem E, Aliabadi N, Desormeaux AM, Andre-Alboth J, Fitter DL, Grant-Greene Y, Tate J, Boncy J, Patel R, Burnett E, Juin S, Parashar UD, Bowen MD. Diversity of rotavirus strains circulating in Haiti before and after introduction of monovalent vaccine. IJID REGIONS 2022; 4:146-151. [PMID: 35923644 PMCID: PMC9340491 DOI: 10.1016/j.ijregi.2022.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022]
Abstract
Rotaviruses are the most common cause of acute gastroenteritis among children. In Haiti, the most frequent genotype in the pre-vaccine period was G12P[8]. Equine-like G3P[8] strains dominated most years following vaccine introduction.
Background Haiti introduced a monovalent human group A rotavirus (RVA) vaccine (Rotarix) into its routine infant immunization program in April 2014. The goal of the surveillance program was to characterize RVA strains circulating in Haiti before and after RVA vaccine introduction. Methods Stool samples were collected from children <5 years old presenting with acute gastroenteritis at 16 hospitals in Haiti. RVA antigen enzyme immunoassay (EIA) testing was performed, and G and P genotypes were determined for positive specimens. In this study, genotype data for samples collected from May 2012 through April 2014 (the pre-vaccine introduction era) and May 2014 through July 2019 (post-vaccine introduction era) were analyzed. Results A total of 809 specimens were tested by the Centers for Disease Control and Prevention. During the pre-vaccine introduction era (May 2012 through April 2014), G12P[8] was the predominant genotype, detected in 88–94% of specimens. There was a high prevalence of the equine-like G3P[8] genotype among Haitian children with RVA after vaccine introduction. Conclusions The predominance of equine-like G3P[8] in three of five RVA seasons post-vaccine introduction suggests possible vaccine-specific selection pressure in Haiti. These temporal variations in RVA genotype predominance will require continued monitoring in Haiti as the vaccination program continues.
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Affiliation(s)
- Mentor Ali Ber Lucien
- Laboratoire National de Santé Publique, Port-au-Prince, Haiti
- Corresponding author: Mentor Ali Ber Lucien, Laboratoire National de Santé Publique, Port-au-Prince, Haiti.
| | - Mathew D. Esona
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), CDC, Atlanta, Georgia, USA
| | | | - Gerard Joseph
- Laboratoire National de Santé Publique, Port-au-Prince, Haiti
| | | | - Eyal Leshem
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), CDC, Atlanta, Georgia, USA
| | - Negar Aliabadi
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), CDC, Atlanta, Georgia, USA
| | | | | | | | | | - Jacqueline Tate
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), CDC, Atlanta, Georgia, USA
| | - Jacques Boncy
- Laboratoire National de Santé Publique, Port-au-Prince, Haiti
| | | | - Eleanor Burnett
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), CDC, Atlanta, Georgia, USA
| | | | - Umesh D. Parashar
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), CDC, Atlanta, Georgia, USA
| | - Michael D. Bowen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), CDC, Atlanta, Georgia, USA
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12
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Rotavirus Strain Trends in United States, 2009–2016: Results from the National Rotavirus Strain Surveillance System (NRSSS). Viruses 2022; 14:v14081775. [PMID: 36016397 PMCID: PMC9414880 DOI: 10.3390/v14081775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Before the introduction of vaccines, group A rotaviruses (RVA) were the leading cause of acute gastroenteritis in children worldwide. The National Rotavirus Strain Surveillance System (NRSSS) was established in 1996 by the Centers for Disease Control and Prevention (CDC) to perform passive RVA surveillance in the USA. We report the distribution of RVA genotypes collected through NRSSS during the 2009–2016 RVA seasons and retrospectively examine the genotypes detected through the NRSSS since 1996. During the 2009–2016 RVA seasons, 2134 RVA-positive fecal specimens were sent to the CDC for analysis of the VP7 and VP4 genes by RT-PCR genotyping assays and sequencing. During 2009–2011, RVA genotype G3P[8] dominated, while G12P[8] was the dominant genotype during 2012–2016. Vaccine strains were detected in 1.7% of specimens and uncommon/unusual strains, including equine-like G3P[8] strains, were found in 1.9%. Phylogenetic analyses showed limited VP7 and VP4 sequence variation within the common genotypes with 1–3 alleles/lineages identified per genotype. A review of 20 years of NRSSS surveillance showed two changes in genotype dominance, from G1P[8] to G3P[8] and then G3P[8] to G12P[8]. A better understanding of the long-term effects of vaccine use on epidemiological and evolutionary dynamics of circulating RVA strains requires continued surveillance.
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13
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Gainor K, Ghosh S. A comprehensive review of viruses in terrestrial animals from the Caribbean islands of Greater and Lesser Antilles. Transbound Emerg Dis 2022; 69:e1299-e1325. [PMID: 35578793 DOI: 10.1111/tbed.14595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 11/26/2022]
Abstract
Viruses pose a major threat to animal health worldwide, causing significant mortalities and morbidities in livestock, companion animals and wildlife, with adverse implications on human health, livelihoods, food safety and security, regional/national economies, and biodiversity. The Greater and Lesser Antilles consist of a cluster of islands between the North and South Americas and is habitat to a wide variety of animal species. This review is the first to put together decades of information on different viruses circulating in companion animals, livestock, and wildlife from the Caribbean islands of Greater and Lesser Antilles. Although animal viral diseases have been documented in the Caribbean region since the 1940s, we found that studies on different animal viruses are limited, inconsistent, and scattered. Furthermore, a significant number of the reports were based on serological assays, yielding preliminary data. The available information was assessed to identify knowledge gaps and limitations, and accordingly, recommendations were made, with the overall goal to improve animal health and production, and combat zoonoses in the region. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kerry Gainor
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts, West Indies
| | - Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts, West Indies
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14
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Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016-2018. Virus Res 2022; 313:198715. [PMID: 35247484 DOI: 10.1016/j.virusres.2022.198715] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022]
Abstract
Species A Rotaviruses (RVA) still play a major role in causing acute diarrhea in children under five years old worldwide. Currently, an 11-gene classification system is used to designate the full genotypic constellations of circulating strains. Viral proteins and non-structural proteins in the order VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 are represented by the genotypes Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx, respectively. In Benin, ROTAVAC® vaccine was introduced into the Expanded Programme on Immunization in December 2019. To monitor circulating RVA strains for changes that may affect vaccine performance, in-depth analysis of strains prior to vaccine introduction are needed. Here we report, the whole-gene characterization (11 ORFs) for 72 randomly selected RVA strains of common and unusual genotypes collected in Benin from the 2016-2018 seasons. The sequenced strains were 15 G1P[8], 20 G2P[4], 5 G9P[8], 14 G12P[8], 9 G3P[6], 2 G1P[6], 3 G2P[6], 2 G9P[4], 1 G12P[6], and 1 G1G9P[8]/P[4]. The study strains exhibited two genetic constellations designed as Wa-like G1/G9/G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and DS-1-like G2/G3/G12-P[4]/P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Genotype G9P[4] strains possessed a DS-1-like genetic constellation with an E6 NSP4 gene, G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2. The mixed genotype showed both Wa-like and DS-1-like profiles with a T6 NSP3 gene G1/G9P[8]/[4]-I1/I2-R1/R2-C1/C2-M1/M2-A1/A2-N1/N2-T1/T6-E1/E6-H1/H2. At the allelic level, the analysis of the Benin strains, reference strains (with known alleles), vaccine strains (with known alleles) identified 2-13 and 1-17 alleles for DS-1-like and Wa-like strains, respectively. Most of the study strains clustered into previously defined alleles, but we defined 3 new alleles for the VP7 (G3=1 new allele and G12=2 new alleles) and VP4 (P[4]=1 new allele and P[6]=2 new alleles) genes which formed the basis of the VP7 and VP4 gene clusters, respectively. For the remaining 9 genes, 0-6 new alleles were identified for both Wa-like and DS-1-like strains. This analysis of whole genome sequences of RVA strains circulating in Benin described genetic point mutations and reassortment events as well as novel alleles. Further detailed studies on these new alleles are needed and these data can also provide a baseline for studies on RVA in the post-vaccination period.
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15
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Simsek C, Bloemen M, Jansen D, Beller L, Descheemaeker P, Reynders M, Van Ranst M, Matthijnssens J. High Prevalence of Coinfecting Enteropathogens in Suspected Rotavirus Vaccine Breakthrough Cases. J Clin Microbiol 2021; 59:e0123621. [PMID: 34586890 PMCID: PMC8601229 DOI: 10.1128/jcm.01236-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/21/2021] [Indexed: 12/15/2022] Open
Abstract
Despite the global use of rotavirus vaccines, vaccine breakthrough cases remain a pediatric health problem. In this study, we investigated suspected rotavirus vaccine breakthrough cases using next-generation sequencing (NGS)-based viral metagenomics (n = 102) and a panel of semiquantitative reverse transcription-PCR (RT-qPCR) (n = 92) targeting known enteric pathogens. Overall, we identified coinfections in 80% of the cases. Enteropathogens such as adenovirus (32%), enterovirus (15%), diarrheagenic Escherichia coli (1 to 14%), astrovirus (10%), Blastocystis spp. (10%), parechovirus (9%), norovirus (9%), Clostridioides (formerly Clostridium) difficile (9%), Dientamoeba fragilis (9%), sapovirus (8%), Campylobacter jejuni (4%), and Giardia lamblia (4%) were detected. Except for a few reassortant rotavirus strains, unusual genotypes or genotype combinations were not present. However, in addition to well-known enteric viruses, divergent variants of enteroviruses and nonclassic astroviruses were identified using NGS. We estimated that in 31.5% of the patients, rotavirus was likely not the cause of gastroenteritis, and in 14.1% of the patients, it contributed together with another pathogen(s) to disease. The remaining 54.4% of the patients likely had a true vaccine breakthrough infection. The high prevalence of alternative enteropathogens in the suspected rotavirus vaccine breakthrough cases suggests that gastroenteritis is often the result of a coinfection and that rotavirus vaccine effectiveness might be underestimated in clinical and epidemiological studies.
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Affiliation(s)
- Ceren Simsek
- KU Leuven—University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Mandy Bloemen
- KU Leuven—University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Daan Jansen
- KU Leuven—University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Leen Beller
- KU Leuven—University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Patrick Descheemaeker
- Department of Laboratory Medicine, Medical Microbiology, AZ Sint-Jan Brugge-Oostende AV, Bruges, Belgium
| | - Marijke Reynders
- Department of Laboratory Medicine, Medical Microbiology, AZ Sint-Jan Brugge-Oostende AV, Bruges, Belgium
| | - Marc Van Ranst
- KU Leuven—University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven—University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
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16
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Development of a Real-Time Reverse Transcription-PCR Assay To Detect and Quantify Group A Rotavirus Equine-Like G3 Strains. J Clin Microbiol 2021; 59:e0260220. [PMID: 34432486 DOI: 10.1128/jcm.02602-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Since 2013, group A rotavirus strains characterized as novel DS-1-like intergenogroup reassortant "equine-like G3" strains have emerged and spread across 5 continents among human populations in at least 14 countries. Here, we report a novel one-step TaqMan quantitative real-time reverse transcription-PCR assay developed to genotype and quantify the viral load for samples containing rotavirus equine-like G3 strains. Using a universal G forward primer and a newly designed reverse primer and TaqMan probe, we developed and validated an assay with a linear dynamic range of 227 to 2.3 × 109 copies per reaction and a limit of detection of 227 copies. The percent positive agreement, percent negative agreement, and precision of our assay were 100.00%, 99.63%, and 100.00%, respectively. This assay can simultaneously detect and quantify the viral load for samples containing DS-1-like intergenogroup reassortant equine-like G3 strains with high sensitivity and specificity, faster turnaround time, and decreased cost. It will be valuable for high-throughput screening of stool samples collected to monitor equine-like G3 strain prevalence and circulation among human populations throughout the world.
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Whole Genome Analysis of Human Rotaviruses Reveals Single Gene Reassortant Rotavirus Strains in Zambia. Viruses 2021; 13:v13091872. [PMID: 34578453 PMCID: PMC8472975 DOI: 10.3390/v13091872] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 12/28/2022] Open
Abstract
Rotarix® vaccine was implemented nationwide in Zambia in 2013. In this study, four unusual strains collected in the post-vaccine period were subjected to whole genome sequencing and analysis. The four strains possessed atypical genotype constellations, with at least one reassortant genome segment within the constellation. One of the strains (UFS-NGS-MRC-DPRU4749) was genetically and phylogenetically distinct in the VP4 and VP1 gene segments. Pairwise analyses demonstrated several amino acid disparities in the VP4 antigenic sites of this strain compared to that of Rotarix®. Although the impact of these amino acid disparities remains to be determined, this study adds to our understanding of the whole genomes of reassortant strains circulating in Zambia following Rotarix® vaccine introduction.
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18
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Gutierrez MB, de Figueiredo MR, Fialho AM, Cantelli CP, Miagostovich MP, Fumian TM. Nosocomial acute gastroenteritis outbreak caused by an equine-like G3P[8] DS-1-like rotavirus and GII.4 Sydney[P16] norovirus at a pediatric hospital in Rio de Janeiro, Brazil, 2019. Hum Vaccin Immunother 2021; 17:4654-4660. [PMID: 34402714 DOI: 10.1080/21645515.2021.1963169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Worldwide, rotavirus (RVA) and norovirus are considered major etiological agents of acute gastroenteritis (AGE) in pediatric population admitted to hospitals. This study describes the investigation of nosocomial infections caused by emergent RVA and norovirus strains reported at a pediatric hospital in southern Brazil in May 2019. This outbreak affected 30 people among children and adults. Nine stool samples (eight children and one nurse) were obtained and analyzed by RT-qPCR to detect and quantify RVA and norovirus. Positive samples were genotyped by sequencing and subjected to phylogenetic analysis. We detected RVA in 44.4% (4/9) and norovirus in 55.5% (5/9) at high viral loads, ranging from 3.5 × 107 to 6.1 × 107 and 3.2 × 102 to 3.2 × 109 genome copies/g of stool, respectively. Co-infections were not observed. RVA VP4 and VP7 gene sequencing in combination with polyacrylamide gel electrophoresis identified the circulation of equine-like G3P[8] DS-1-like, and the partial sequencing of the other nine genes revealed that strains possessed I2-R2-C2-M2-A2-N1-T2-E2-H2 genotype background. The emergent recombinant norovirus variant, GII.4 Sydney[P16], was identified by ORF1-2 sequencing. Active surveillance and effective prevention measures should be constantly reinforced to avoid the spread of nosocomial viral infections into hospitals, which could severely affect pediatric patients admitted with underlying health conditions.
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Affiliation(s)
- Meylin B Gutierrez
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Mirza Rocha de Figueiredo
- Department of Hospital Epidemiology and Surveillance Centre, The National Institute of Women, Children and Adolescents Health Fernandes Figueira (IFF), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Alexandre Madi Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Carina Pacheco Cantelli
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
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19
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Silva Serra AC, Júnior EC, Cruz JF, Lobo PS, Júnior ET, Bandeira RS, Bezerra DA, Mascarenhas JD, Santos Guerra SF, Soares LS. Molecular analysis of G3P[6] rotavirus in the Amazon region of Brazil: evidence of reassortment with equine-like strains. Future Microbiol 2021; 16:847-862. [PMID: 34318682 DOI: 10.2217/fmb-2020-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To perform a molecular analysis of rotavirus A (RVA) G3P[6] strains detected in 2012 and 2017 in the Amazon region of Brazil. Materials & methods: Eighteen RVA G3P[6] strains were collected from children aged under 10 years hospitalized with acute gastroenteritis, and partial sequencing of each segment genome was performed using Sanger sequencing. Results: Phylogenetic analysis showed that all G3P[6] strains had a DS-1-like genotype constellation. Two strains had the highest nucleotide identities with equine-like G3P[6]/G3P[8] genotypes. Several amino acid alterations in VP4 and VP7 neutralizing epitopes of equine-like RVA G3P[6] strains were observed in comparison with vaccine strains. Conclusion: These findings suggest that equine-like RVA G3P[6] strains have been circulating in the Amazon region of Brazil as a result of direct importation, and support natural RVA evolutionary mechanisms.
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Affiliation(s)
- Ana C Silva Serra
- Program in Virology, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Edivaldo Cs Júnior
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Jonas F Cruz
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Patrícia S Lobo
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Edvaldo Tp Júnior
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Renato S Bandeira
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Delana Am Bezerra
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Joana Dp Mascarenhas
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Sylvia F Santos Guerra
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Luana S Soares
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
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20
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Burnett E, Juin S, Esona MD, Desormeaux AM, Aliabadi N, Pierre M, Andre-Alboth J, Leshem E, Etheart MD, Patel R, Dely P, Fitter D, Jean-Denis G, Kalou M, Katz MA, Bowen MD, Grant-Greene Y, Boncy J, Parashar UD, Joseph GA, Tate JE. Effectiveness of monovalent rotavirus vaccine against hospitalizations due to all rotavirus and equine-like G3P[8] genotypes in Haiti 2014-2019. Vaccine 2021; 39:4458-4462. [PMID: 34187708 PMCID: PMC8474148 DOI: 10.1016/j.vaccine.2021.06.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Rotavirus vaccines are effective in preventing severe rotavirus. Haiti introduced 2-dose monovalent (G1P[8]) rotavirus vaccine recommended for infants at 6 and 10 weeks of age in 2014. We calculated the effectiveness of rotavirus vaccine against hospitalization for acute gastroenteritis in Haiti. METHODS We enrolled children 6-59 months old admitted May 2014-September 2019 for acute watery diarrhea at any sentinel surveillance hospital. Stool was tested for rotavirus using enzyme immunoassay (EIA) and genotyped with multiplex one-step RT-PCR assay and Sanger sequencing for stratification by genotype. We used a case-negative design where cases were children positive for rotavirus and controls were negative for rotavirus. Only children eligible for vaccination were included and a child was considered vaccinated if vaccine was given ≥ 14 days before enrollment. We used unconditional logistic regression to calculate odds ratios and calculated 2-dose and 1-dose vaccine effectiveness (VE) as (1 - odds ratio) * 100. RESULTS We included 129 (19%) positive cases and 543 (81%) negative controls. Among cases, 77 (60%) were positive for equine-like G3P[8]. Two doses of rotavirus vaccine were 66% (95% CI: 44, 80) effective against hospitalizations due to any strain of rotavirus and 64% (95% CI: 33, 81) effective against hospitalizations due to the equine-like G3P[8] genotype. CONCLUSIONS These findings are comparable to other countries in the Americas region. To the best of our knowledge, this is the first VE estimate both against the equine-like G3P[8] genotype and from a Caribbean country. Overall, these results support rotavirus vaccine use and demonstrate the importance of complete vaccination.
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Affiliation(s)
| | | | | | | | | | | | - Jocelyn Andre-Alboth
- Ministry of Public Health and Population - Laboratoire National de Sante Publique, Port-au-Prince, Haiti
| | - Eyal Leshem
- Division of Viral Diseases, NCIRD, CDC, USA; Sheba Medical Center and Tel Aviv University, Tel Aviv, Israel
| | | | | | - Patrick Dely
- Ministry of Public Health and Population - Directorate of Epidemiology, Laboratory and Research (DELR), Port-au-Prince, Haiti
| | | | | | | | | | | | | | - Jacques Boncy
- Ministry of Public Health and Population - Laboratoire National de Sante Publique, Port-au-Prince, Haiti
| | | | - Gerard A Joseph
- Ministry of Public Health and Population - Laboratoire National de Sante Publique, Port-au-Prince, Haiti
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21
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Burke RM, Groom HC, Naleway AL, Katz EM, Salas B, Mattison CP, Donald J, Tsaknaridis L, Biggs C, Bowen MD, Tate JE, Parashar UD, Schmidt M, Hall AJ. Rotavirus Vaccine Is Effective Against Rotavirus Gastroenteritis Resulting in Outpatient Care: Results From the Medically Attended Acute Gastroenteritis (MAAGE) Study. Clin Infect Dis 2021; 72:2000-2005. [PMID: 32322882 DOI: 10.1093/cid/ciaa466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/20/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Rotavirus is a common cause of severe pediatric acute gastroenteritis. Two vaccines are licensed in the United States and have demonstrated high effectiveness against moderate to severe disease. However, fewer data are available on rotavirus vaccine effectiveness (VE) against milder disease. METHODS We leveraged active surveillance data from Kaiser Permanente Northwest to calculate rotavirus VE against medically attended rotavirus illness among age-eligible children. We utilized a test-negative case-control design and applied 4 distinct case definitions based on reverse transcription-quantitative real-time PCR (qRT-PCR) assay and enzyme immunoassay (EIA) test results. VE was calculated as 100 × (1 - odds ratio), and models were adjusted for age group. RESULTS The VE analysis population comprised 842 children, 799 (95%) of whom had mild disease requiring at most a clinic visit and 698 (83%) of whom were fully vaccinated against rotavirus. Age-adjusted VE was 70% (95% confidence interval [CI], 37-86%) against disease defined solely by qRT-PCR results, 72% (95% CI, 31-89%) against disease as defined by qRT-PCR with a quantification cycle (C q ) value <27, 73% (95% CI, 32-90%) against disease that was qRT-PCR positive but EIA negative, and 62% (95% CI, -20-88%) against disease defined solely by EIA. Results were similar when restricting to disease resulting in at most an ambulatory clinic or emergency department visit. CONCLUSIONS These results support the effectiveness of rotavirus vaccination in protecting US children from mild to moderate and severe disease. Our findings are also useful to show the effectiveness of rotavirus vaccination against qRT-PCR-defined illness.
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Affiliation(s)
- Rachel M Burke
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Holly C Groom
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Allison L Naleway
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Eric M Katz
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Cherokee Nation Assurance, Contracting Agency to the Division of Viral Diseases, Centers for Disease Control and Prevention, Arlington, Virginia, USA
| | - Bianca Salas
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Claire P Mattison
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Judy Donald
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA
| | | | | | - Michael D Bowen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jacqueline E Tate
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Umesh D Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mark Schmidt
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Aron J Hall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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22
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Wa-1 Equine-Like G3P[8] Rotavirus from a Child with Diarrhea in Colombia. Viruses 2021; 13:v13061075. [PMID: 34199978 PMCID: PMC8226935 DOI: 10.3390/v13061075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
Rotavirus A (RVA) has been considered the main cause of diarrheal disease in children under five years in emergency services in both developed and developing countries. RVA belongs to the Reoviridae family, which comprises 11 segments of double-stranded RNA (dsRNA) as a genomic constellation that encodes for six structural and five to six nonstructural proteins. RVA has been classified in a binary system with Gx[Px] based on the spike protein (VP4) and the major outer capsid glycoprotein (VP7), respectively. The emerging equine-like G3P[8] DS-1-like strains reported worldwide in humans have arisen an important concern. Here, we carry out the complete genome characterization of a previously reported G3P[8] strain in order to recognize the genetic diversity of RVA circulating among infants in Colombia. A near-full genome phylogenetic analysis was done, confirming the presence of the novel equine-like G3P[8] with a Wa-like backbone for the first time in Colombia. This study demonstrated the importance of surveillance of emerging viruses in the Colombian population; furthermore, additional studies must focus on the understanding of the spread and transmission dynamic of this important RVA strain in different areas of the country.
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23
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Prevalence and Genetic Diversity of Group A Rotavirus Genotypes in Moscow (2019-2020). Pathogens 2021; 10:pathogens10060674. [PMID: 34070814 PMCID: PMC8228337 DOI: 10.3390/pathogens10060674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022] Open
Abstract
Group A rotavirus (RVA) infection is the leading cause of hospitalization of children under 5 years old, presenting with symptoms of acute gastroenteritis. The aim of our study was to explore the genetic diversity of RVA among patients admitted to Moscow Infectious Disease Clinical Hospital No. 1 with symptoms of acute gastroenteritis. A total of 653 samples were collected from May 2019 through March 2020. Out of them, 135 (20.67%) fecal samples were found to be positive for rotavirus antigen by ELISA. RT-PCR detected rotavirus RNA in 80 samples. Seven G-genotypes (G1, G2, G3, G4, G8, G9, and G12) and three P-genotypes (P[8], P[4], and P[6]) formed 9 different combinations. The most common combination was G9P[8]. However, for the first time in Moscow, the combination G3P[8] took second place. Moreover, all detected viruses of this combination belonged to Equine-like G3P[8] viruses that had never been detected in Russia before. The genotype G8P[8] and G9P[4] rotaviruses were also detected in Moscow for the first time. Among the studied rotaviruses, there were equal proportions of Wa and DS-1-like strains; previous studies showed that Wa-like strains accounted for the largest proportion of rotaviruses in Russia.
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24
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Tsugawa T, Akane Y, Honjo S, Kondo K, Kawasaki Y. Rotavirus vaccination in Japan: Efficacy and safety of vaccines, changes in genotype, and surveillance efforts. J Infect Chemother 2021; 27:940-948. [PMID: 33867267 DOI: 10.1016/j.jiac.2021.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/25/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
In Japan, a monovalent rotavirus vaccine (RV1) and a pentavalent rotavirus vaccine (RV5) were launched as voluntary vaccinations in November 2011 and July 2012, respectively. Rotavirus (RV) vaccine coverage in Japan increased from 30.0% in 2012 to 78.4% in 2019. The number of RV gastroenteritis hospitalizations decreased after 2014 in Japan, and is expected to decrease further following the introduction of RV vaccines into the national immunization program in October 2020. The incidence rates of intussusception (IS) among children aged <1 year were 102.8 and 94.0 per 100,000 person-years in the pre-vaccine (2007-2011) and post-vaccine (2012-September 2014) eras, respectively. IS incidence did not increase following RV vaccine introduction in Japan. The efficacy and safety of RV vaccination were both documented in Japan. To reduce the risk of IS following RV vaccination, it is important that children receive a first dose of RV vaccine at age <15 weeks, preferably at age 2 months. Some strains that have emerged since RV vaccine introduction, such as DS-1-like G1P[8], eG3, and G8P[8], have spread nationwide. These three emerging genotypes did not affect the severity of the RV infection. Continuous city-level surveillance, using analysis of all 11 RV genome segments, is necessary to elucidate the genetic characteristics of prevalent RV strains. These efforts would also clarify the influence of vaccination on genetic changes of RV strains and the emergence of new genotypes.
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Affiliation(s)
- Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan.
| | - Yusuke Akane
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
| | - Saho Honjo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sunagawa City Hospital, Sunagawa, 073-0196, Japan
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
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25
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Esona MD, Ward ML, Wikswo ME, Rustempasic SM, Gautam R, Perkins C, Selvarangan R, Harrison CJ, Boom JA, Englund JA, Klein EJ, Staat MA, McNeal MM, Halasa N, Chappell J, Weinberg GA, Payne DC, Parashar UD, Bowen MD. Rotavirus Genotype Trends and Gastrointestinal Pathogen Detection in the United States, 2014-16: Results from the New Vaccine Surveillance Network. J Infect Dis 2021; 224:1539-1549. [PMID: 33822119 DOI: 10.1093/infdis/jiab177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/30/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Following the implementation of rotavirus vaccination in 2006, severe acute gastroenteritis (AGE) due to group A rotavirus (RVA) has substantially declined in USA (US) children. We report the RVA genotype prevalence as well as co-infection data from seven US New Vaccine Surveillance Network (NVSN) sites during three consecutive RVA seasons, 2014-2016. METHODS A total of 1041 stool samples that tested positive for RVA by Rotaclone enzyme immunoassay (EIA) were submitted to the Centers for Disease Control and Prevention (CDC) for RVA genotyping and multipathogen testing. RESULTS A total of 795 (76%) contained detectable RVA at CDC. Rotavirus disease was highest in children < 3 years of age. Four G types (G1, G2, G9, and G12) accounted for 94.6% of strains while two P types (P[4] and P[8]) accounted 94.7% of the strains. Overall, G12P[8] was the most common genotype detected in all three seasons. Stepwise conditional logistic analysis found year and study site were significant predictors of genotype. Twenty four percent (24%) of RVA-positive specimens contained other AGE pathogens. CONCLUSIONS G12P[8] predominated over three seasons, but strain predominance varied by year and study site. Ongoing surveillance provides continuous tracking and monitoring of US genotypes during the post vaccine era.
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Affiliation(s)
- Mathew D Esona
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - M Leanne Ward
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Mary E Wikswo
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | | | - Rashi Gautam
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Charity Perkins
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Rangaraj Selvarangan
- Kansas City Children's Mercy Hospitals and Clinics, Kansas City, Kansas, United States
| | | | - Julie A Boom
- Texas Children's Hospital, Houston, Texas, United States
| | - Janet A Englund
- Seattle Children's Hospital, Seattle, Washington, United States
| | - Eileen J Klein
- Seattle Children's Hospital, Seattle, Washington, United States
| | - Mary Allen Staat
- Department of Pediatrics, University of Cincinnati, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| | - Monica M McNeal
- Department of Pediatrics, University of Cincinnati, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| | - Natasha Halasa
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - James Chappell
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Geoffrey A Weinberg
- University of Rochester School of Medicine and Dentistry, Rochester, New York, United States
| | - Daniel C Payne
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Umesh D Parashar
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Michael D Bowen
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States
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26
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Akane Y, Tsugawa T, Fujii Y, Honjo S, Kondo K, Nakata S, Fujibayashi S, Ohara T, Mori T, Higashidate Y, Nagai K, Kikuchi M, Sato T, Kato S, Tahara Y, Kubo N, Katayama K, Kimura H, Tsutsumi H, Kawasaki Y. Molecular and clinical characterization of the equine-like G3 rotavirus that caused the first outbreak in Japan, 2016. J Gen Virol 2021; 102. [PMID: 33587029 DOI: 10.1099/jgv.0.001548] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Since 2013, equine-like G3 rotavirus (eG3) strains have been detected throughout the world, including in Japan, and the strains were found to be dominant in some countries. In 2016, the first eG3 outbreak in Japan occurred in Tomakomai, Hokkaido prefecture, and the strains became dominant in other Hokkaido areas the following year. There were no significant differences in the clinical characteristics of eG3 and non-eG3 rotavirus infections. The eG3 strains detected in Hokkaido across 2 years from 2016 to 2017 had DS-1-like constellations (i.e. G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2), and the genes were highly conserved (97.5-100 %). One strain, designated as To16-12 was selected as the representative strain for these strains, and all 11 genes of this strain (To16-12) exhibited the closest identity to one foreign eG3 strain (STM050) seen in Indonesia in 2015 and two eG3 strains (IS1090 and MI1125) in another Japanese prefecture in 2016, suggesting that this strain might be introduced into Japan from Indonesia. Sequence analyses of VP7 genes from animal and human G3 strains found worldwide did not identify any with close identity (>92 %) to eG3 strains, including equine RV Erv105. Analysis of another ten genes indicated that the eG3 strain had low similarity to G2P[4] strains, which are considered traditional DS-1-like strains, but high similarity to DS-1-like G1P[8] strains, which first appeared in Asia in 2012. These data suggest that eG3 strains were recently generated in Asia as mono-reassortant strain between DS-1-like G1P[8] strains and unspecified animal G3 strains. Our results indicate that rotavirus surveillance in the postvaccine era requires whole-genome analyses.
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Affiliation(s)
- Yusuke Akane
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Saho Honjo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sunagawa City Hospital, Sunagawa, Japan
| | - Shuji Nakata
- Department of Pediatrics, Nakata Pediatric Clinic, Sapporo, Japan
| | | | - Toshio Ohara
- Department of Pediatrics, Tomakomai City Hospital, Tomakomai, Japan
| | - Toshihiko Mori
- Department of Pediatrics, NTT East Sapporo Hospital, Sapporo, Japan
| | - Yoshihito Higashidate
- Department of Pediatrics, Japan Community Health Care Organization (JCHO) Sapporo Hokushin Hospital, Sapporo, Japan
| | - Kazushige Nagai
- Department of Pediatrics, Takikawa Municipal Hospital, Takikawa, Japan
| | | | - Toshiya Sato
- Department of Pediatrics, Iwamizawa Municipal General Hospital, Iwamizawa, Japan
| | - Shinsuke Kato
- Department of Pediatrics, Rumoi City Hospital, Rumoi, Japan
| | - Yasuo Tahara
- Department of Pediatrics, Steel Memorial Muroran Hospital, Muroran, Japan
| | - Noriaki Kubo
- Department of Pediatrics, Japanese Red Cross Urakawa Hospital, Urakawa, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Graduate School of Health Science, Gunma Paz University, Gunma, Japan.,Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroyuki Tsutsumi
- Present address: Midorinosato, Saiseikai Otaru Hospital, Otaru, Japan.,Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
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27
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Burke RM, Mattison CP, Marsh Z, Shioda K, Donald J, Salas SB, Naleway AL, Biggs C, Schmidt MA, Hall AJ. Norovirus and Other Viral Causes of Medically Attended Acute Gastroenteritis Across the Age Spectrum: Results from the Medically Attended Acute Gastroenteritis Study in the United States. Clin Infect Dis 2021; 73:e913-e920. [PMID: 34398953 DOI: 10.1093/cid/ciab033] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Acute gastroenteritis (AGE) causes a substantial burden in the United States, but its etiology frequently remains undetermined. Active surveillance within an integrated healthcare delivery system was used to estimate the prevalence and incidence of medically attended norovirus, rotavirus, sapovirus, and astrovirus. METHODS Active surveillance was conducted among all enrolled members of Kaiser Permanente Northwest during July 2014-June 2016. An age-stratified, representative sample of AGE-associated medical encounters were recruited to provide a stool specimen to be tested for norovirus, rotavirus, sapovirus, and astrovirus. Medically attended AGE (MAAGE) encounters for a patient occurring within 30 days were grouped into 1 episode, and all-cause MAAGE incidence was calculated. Pathogen- and healthcare setting-specific incidence estimates were calculated using age-stratified bootstrapping. RESULTS The overall incidence of MAAGE was 40.6 episodes per 1000 person-years (PY), with most episodes requiring no more than outpatient care. Norovirus was the most frequently detected pathogen, with an incidence of 5.5 medically attended episodes per 1000 PY. Incidence of norovirus MAAGE was highest among children aged < 5 years (20.4 episodes per 1000 PY), followed by adults aged ≥ 65 years (4.5 episodes per 1000 PY). Other study pathogens showed similar patterns by age, but lower overall incidence (sapovirus: 2.4 per 1000 PY; astrovirus: 1.3 per 1000 PY; rotavirus: 0.5 per 1000 PY). CONCLUSIONS Viral enteropathogens, particularly norovirus, are important contributors to MAAGE, especially among children < 5 years of age. The present findings underline the importance of judicious antibiotics use for pediatric AGE and suggest that an effective norovirus vaccine could substantially reduce MAAGE.
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Affiliation(s)
- Rachel M Burke
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA
| | - Claire P Mattison
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee,USA
| | - Zachary Marsh
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee,USA
| | - Kayoko Shioda
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee,USA
| | - Judy Donald
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - S Bianca Salas
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - Allison L Naleway
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - Christianne Biggs
- Public Health Division of the Oregon Health Authority, Portland, Oregon,USA
| | - Mark A Schmidt
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - Aron J Hall
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA
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Reverse Genetics Approach for Developing Rotavirus Vaccine Candidates Carrying VP4 and VP7 Genes Cloned from Clinical Isolates of Human Rotavirus. J Virol 2020; 95:JVI.01374-20. [PMID: 33087468 DOI: 10.1128/jvi.01374-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
Species A rotaviruses (RVs) are a leading cause of severe acute gastroenteritis in infants and children younger than 5 years. Currently available RV vaccines were adapted from wild-type RV strains by serial passage of cultured cells or by reassortment between human and animal RV strains. These traditional methods require large-scale screening and genotyping to obtain vaccine candidates. Reverse genetics is a tractable, rapid, and reproducible approach to generating recombinant RV vaccine candidates carrying any VP4 and VP7 genes that provide selected antigenicity. Here, we developed a vaccine platform by generating recombinant RVs carrying VP4 (P[4] and P[8]), VP7 (G1, G2, G3, G8, and G9), and/or VP6 genes cloned from human RV clinical samples using the simian RV SA11 strain (G3P[2]) as a backbone. Neutralization assays using monoclonal antibodies and murine antisera revealed that recombinant VP4 and VP7 monoreassortant viruses exhibited altered antigenicity. However, replication of VP4 monoreassortant viruses was severely impaired. Generation of recombinant RVs harboring a chimeric VP4 protein for SA11 and human RV gene components revealed that the VP8* fragment was responsible for efficient infectivity of recombinant RVs. Although this system must be improved because the yield of vaccine viruses directly affects vaccine manufacturing costs, reverse genetics requires less time than traditional methods and enables rapid production of safe and effective vaccine candidates.IMPORTANCE Although vaccines have reduced global RV-associated hospitalization and mortality over the past decade, the multisegmented genome of RVs allows reassortment of VP4 and VP7 genes from different RV species and strains. The evolutionary dynamics of novel RV genotypes and their constellations have led to great genomic and antigenic diversity. The reverse genetics system is a powerful tool for manipulating RV genes, thereby controlling viral antigenicity, growth capacity, and pathogenicity. Here, we generated recombinant simian RVs (strain SA11) carrying heterologous VP4 and VP7 genes cloned from clinical isolates and showed that VP4- or VP7-substituted chimeric viruses can be used for antigenic characterization of RV outer capsid proteins and as improved seed viruses for vaccine production.
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29
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Mwanga MJ, Verani JR, Omore R, Tate JE, Parashar UD, Murunga N, Gicheru E, Breiman RF, Nokes DJ, Agoti CN. Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Kilifi, Coastal Kenya, 4 Years after Nationwide Vaccine Introduction. Pathogens 2020; 9:pathogens9120981. [PMID: 33255256 PMCID: PMC7761311 DOI: 10.3390/pathogens9120981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 01/22/2023] Open
Abstract
Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in more than 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged less than 13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected RVA in 55 samples (22.2%). Of these, VP7 (G) and VP4 (P) segments were successfully sequenced in 48 (87.3%) and phylogenetic analysis based on the VP7 sequences identified seven genetic clusters with six different GP combinations: G3P[8], G1P[8], G2P[4], G2P[8], G9P[8] and G12P[8]. The G3P[8] strains predominated the season (n = 37, 67.2%) and comprised three distinct G3 genetic clusters that fell within Lineage I and IX (the latter also known as equine-like G3 Lineage). Both the two G3 lineages have been recently detected in several countries. Our study is the first to document African children infected with G3 Lineage IX. These data highlight the global nature of RVA transmission and the importance of increasing global rotavirus vaccine coverage.
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Affiliation(s)
- Mike J. Mwanga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Jennifer R. Verani
- Centers for Disease Control and Prevention (CDC), KEMRI Complex, off Mbagathi Way, Village Market, Nairobi 00621, Kenya;
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Richard Omore
- KEMRI, Center for Global Health Research (KEMRI-CGHR), Kisumu 00202, Kenya;
| | - Jacqueline E. Tate
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Umesh D. Parashar
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Nickson Murunga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Elijah Gicheru
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Robert F. Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
| | - D. James Nokes
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
- School of Life Sciences and Zeeman Institute (SBIDER), The University of Warwick, Coventry CV4 7AL, UK
| | - Charles N. Agoti
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
- School of Health and Human Sciences, Pwani University, Kilifi 80108, Kenya
- Correspondence:
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30
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Taylor AR, Echeverry DF, Anderson TJC, Neafsey DE, Buckee CO. Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast. PLoS Genet 2020; 16:e1009101. [PMID: 33196661 PMCID: PMC7704048 DOI: 10.1371/journal.pgen.1009101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 11/30/2020] [Accepted: 09/08/2020] [Indexed: 01/09/2023] Open
Abstract
Characterising connectivity between geographically separated biological populations is a common goal in many fields. Recent approaches to understanding connectivity between malaria parasite populations, with implications for disease control efforts, have used estimates of relatedness based on identity-by-descent (IBD). However, uncertainty around estimated relatedness has not been accounted for. IBD-based relatedness estimates with uncertainty were computed for pairs of monoclonal Plasmodium falciparum samples collected from five cities on the Colombian-Pacific coast where long-term clonal propagation of P. falciparum is frequent. The cities include two official ports, Buenaventura and Tumaco, that are separated geographically but connected by frequent marine traffic. Fractions of highly-related sample pairs (whose classification using a threshold accounts for uncertainty) were greater within cities versus between. However, based on both highly-related fractions and on a threshold-free approach (Wasserstein distances between parasite populations) connectivity between Buenaventura and Tumaco was disproportionally high. Buenaventura-Tumaco connectivity was consistent with transmission events involving parasites from five clonal components (groups of statistically indistinguishable parasites identified under a graph theoretic framework). To conclude, P. falciparum population connectivity on the Colombian-Pacific coast abides by accessibility not isolation-by-distance, potentially implicating marine traffic in malaria transmission with opportunities for targeted intervention. Further investigations are required to test this hypothesis. For the first time in malaria epidemiology (and to our knowledge in ecological and epidemiological studies more generally), we account for uncertainty around estimated relatedness (an important consideration for studies that plan to use genotype versus whole genome sequence data to estimate IBD-based relatedness); we also use threshold-free methods to compare parasite populations and identify clonal components. Threshold-free methods are especially important in analyses of malaria parasites and other recombining organisms with mixed mating systems where thresholds do not have clear interpretation (e.g. due to clonal propagation) and thus undermine the cross-comparison of studies.
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Affiliation(s)
- Aimee R. Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad Icesi, Calle 18 No. 122-135, Cali, Colombia
- Departamento de Microbiologia, Facultad de Salud, Universidad del Valle, Cali, Colombia
| | - Timothy J. C. Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Daniel E. Neafsey
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Caroline O. Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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31
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Chansaenroj J, Chuchaona W, Lestari FB, Pasittungkul S, Klinfueng S, Wanlapakorn N, Vongpunsawad S, Chirathaworn C, Poovorawan Y. High prevalence of DS-1-like rotavirus infection in Thai adults between 2016 and 2019. PLoS One 2020; 15:e0235280. [PMID: 32584905 PMCID: PMC7316273 DOI: 10.1371/journal.pone.0235280] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/11/2020] [Indexed: 01/07/2023] Open
Abstract
Rotavirus infection is the most common cause of viral diarrhea in infants and young children but uncommon and usually asymptomatic in adults. In the winter of 2017–2018, a large-scale outbreak of rotavirus in both children and adults was reported in Thailand. The current study focused on the prevalence, genotyping, and molecular characterization of rotavirus infections in Thai adults from July 2016 to December 2019. In 2,598 stool samples collected from adult residents of Bangkok (aged #x2265; 15 years) with acute gastroenteritis, rotavirus was detected via real-time RT-PCR analysis of the VP6 gene. G, P and I genotypes were determined by direct sequencing of VP7, VP4, and VP6 genes, respectively. Our results showed 8.7% (226/2,598) of stool samples were positive for rotavirus. The incidence of rotavirus was high during the winter season of 2017–2018 (17.7%) compared to another studied periods (4.5% between July 2016- October 2017 and 2.8% between March 2018- December 2019). Nucleotide sequencing of VP7 and VP4 revealed G3P[8] as the predominant strain (33.2%,75/226), followed by G9P[8] (17.3%,39/226), and G2P[4] (15.0%,34/226). Uncommon G and P combinations were additionally detected at low frequencies. VP6 sequencing was conducted to discriminate I genotype between the Wa and DS-1 genogroup. The unusual DS-1-like G3P[8] strain was most prevalent amomg rotavirus strains detected in this study (29.6%, 67/226), and the corresponding VP7 sequences showed high nucleotide identity with unusual DS-1-like globally circulating strains. Our study demonstrates that rotavirus outbreaks in adults are attributable not only to high prevalence of RV infection but also the unusual DS-like genogroup. The collective findings reinforce the importance of investigating rotavirus diagnosis in adults suffering from acute gastroenteritis and taking appropriate preventive measures.
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Affiliation(s)
- Jira Chansaenroj
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Watchaporn Chuchaona
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Fajar Budi Lestari
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Siripat Pasittungkul
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sirapa Klinfueng
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chintana Chirathaworn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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32
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Fukuda S, Tacharoenmuang R, Guntapong R, Upachai S, Singchai P, Ide T, Hatazawa R, Sutthiwarakom K, Kongjorn S, Onvimala N, Ruchusatsawast K, Rungnopakun P, Mekmallika J, Kawamura Y, Motomura K, Tatsumi M, Takeda N, Murata T, Yoshikawa T, Uppapong B, Taniguchi K, Komoto S. Full genome characterization of novel DS-1-like G9P[8] rotavirus strains that have emerged in Thailand. PLoS One 2020; 15:e0231099. [PMID: 32320419 PMCID: PMC7176146 DOI: 10.1371/journal.pone.0231099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/16/2020] [Indexed: 01/05/2023] Open
Abstract
The emergence and rapid spread of unusual DS-1-like intergenogroup reassortant rotaviruses having G1/3/8 genotypes have been recently reported from major parts of the world (Africa, Asia, Australia, Europe, and the Americas). During rotavirus surveillance in Thailand, three novel intergenogroup reassortant strains possessing the G9P[8] genotype (DBM2017-016, DBM2017-203, and DBM2018-291) were identified in three stool specimens from diarrheic children. In the present study, we determined and analyzed the full genomes of these three strains. On full-genomic analysis, all three strains were found to share a unique genotype constellation comprising both genogroup 1 and 2 genes: G9-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis demonstrated that each of the 11 genes of the three strains was closely related to that of emerging DS-1-like intergenogroup reassortant, human, and/or locally circulating human strains. Thus, the three strains were suggested to be multiple reassortants that had acquired the G9-VP7 genes from co-circulating Wa-like G9P[8] rotaviruses in the genetic background of DS-1-like intergenogroup reassortant (likely equine-like G3P[8]) strains. To our knowledge, this is the first description of emerging DS-1-like intergenogroup reassortant strains having the G9P[8] genotype. Our observations will add to the growing insights into the dynamic evolution of emerging DS-1-like intergenogroup reassortant rotaviruses through reassortment.
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Affiliation(s)
- Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ratana Tacharoenmuang
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ratigorn Guntapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sompong Upachai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Phakapun Singchai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Center for Research Promotion and Support, Joint Research Support Promotion Facility, Fujita Health University, Toyoake, Aichi, Japan
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Karun Sutthiwarakom
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Santip Kongjorn
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Napa Onvimala
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | | | | | | | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Kazushi Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
- Osaka Institute of Public Health, Osaka, Japan
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Naokazu Takeda
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ballang Uppapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- * E-mail:
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33
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Tacharoenmuang R, Komoto S, Guntapong R, Upachai S, Singchai P, Ide T, Fukuda S, Ruchusatsawast K, Sriwantana B, Tatsumi M, Motomura K, Takeda N, Murata T, Sangkitporn S, Taniguchi K, Yoshikawa T. High prevalence of equine-like G3P[8] rotavirus in children and adults with acute gastroenteritis in Thailand. J Med Virol 2019; 92:174-186. [PMID: 31498444 DOI: 10.1002/jmv.25591] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/02/2019] [Indexed: 12/28/2022]
Abstract
Group A rotavirus (RVA) is a major cause of acute gastroenteritis in infants and young children worldwide. This study aims to clarify the distribution of G/P types and genetic characteristics of RVAs circulating in Thailand. Between January 2014 and September 2016, 1867 stool specimens were collected from children and adults with acute gastroenteritis in six provinces in Thailand. RVAs were detected in 514/1867 (27.5%) stool specimens. G1P[8] (44.7%) was the most predominant genotype, followed by G3P[8] (33.7%), G2P[4] (11.5%), G8P[8] (7.0%), and G9P[8] (1.3%). Unusual G3P[9] (0.8%), G3P[10] (0.4%), G4P[6] (0.4%), and G10P[14] (0.2%) were also detected at low frequencies. The predominant genotype, G1P[8] (64.4%), in 2014 decreased to 6.1% in 2016. In contrast, the frequency of G3P[8] markedly increased from 5.5% in 2014 to 65.3% in 2015 and 89.8% in 2016. On polyacrylamide gel electrophoresis, most (135/140; 96.4%) of the G3P[8] strains exhibited a short RNA profile. Successful determination of the nucleotide sequences of the VP7 genes of 98 G3P[8] strains with a short RNA profile showed that they are all equine-like G3P[8] strains. On phylogenetic analysis of genome segments of two representative Thai equine-like G3P[8] strains, it was noteworthy that they possessed distinct NSP4 genes, one bovine-like and the other human-like. Thus, we found that characteristic equine-like G3P[8] strains with a short RNA electropherotype are becoming highly prevalent in children and adults in Thailand.
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Affiliation(s)
- Ratana Tacharoenmuang
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand.,Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.,Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ratigorn Guntapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sompong Upachai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Phakapun Singchai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.,Center for Research Promotion and Support, Joint Research Support Promotion Facility, Fujita Health University, Toyoake, Aichi, Japan
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | | | - Busarawan Sriwantana
- Department of Medical Sciences, Medical Sciences Technical Office, Nonthaburi, Thailand
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Kazushi Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand.,Osaka Institute of Public Health, Osaka, Japan
| | - Naokazu Takeda
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Somchai Sangkitporn
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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