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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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2
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Moraes MTBD, Silva MFD, Pimenta YC, Cantelli CP, Assis RMSD, Fialho AM, Bueno MG, Olivares AIO, Svensson L, Leite JPG, Nordgren J. G6P[8] Rotavirus a Possessing a Wa-like VP3 Gene from a Child with Acute Gastroenteritis Living in the Northwest Amazon Region. Pathogens 2023; 12:956. [PMID: 37513803 PMCID: PMC10385053 DOI: 10.3390/pathogens12070956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The introduction of rotavirus A (RVA) vaccines has considerably reduced the RVA-associated mortality among children under 5 years of age worldwide. The ability of RVA to reassort gives rise to different combinations of surface proteins G (glycoprotein, VP7) and P (protease sensitive, VP4) RVA types infecting children. During the epidemiological surveillance of RVA in the Northwest Amazon region, an unusual rotavirus genotype G6P[8] was detected in feces of a 2-year-old child with acute gastroenteritis (AGE) that had been vaccinated with one dose of Rotarix® (RV1). The G6P[8] sample had a DS-1-like constellation with a Wa-like VP3 gene mono-reassortment similar to equine-like G3P[8] that has been frequently detected in Brazil previously. The results presented here reinforce the evolutionary dynamics of RVA and the importance of constant molecular surveillance.
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Affiliation(s)
- Marcia Terezinha Baroni de Moraes
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
- Post-Graduate Program in Tropical Medicine, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Mauro França da Silva
- Post-Graduate Program in Tropical Medicine, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
- Technological Coordination, Tetraviral Vaccine, Immunobiological Technology Institute (Biomanguinhos), Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Yan Cardoso Pimenta
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
- Post-Graduate Program in Tropical Medicine, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Carina Pacheco Cantelli
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Rosane Maria Santos de Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Alexandre Madi Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Marina Galvão Bueno
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Alberto Ignácio Olivares Olivares
- Secretaria Estadual de Saúde de Roraima, SESAU/RR, Rua Madrid, 180-Aeroporto, Boa Vista 69310-043, Brazil
- College of Medicine, State University of Roraima, Avenida Helio Campo, s/n-Centro, Caracaraí, Boa Vista 69360-000, Brazil
| | - Lennart Svensson
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Medicine, Kalolinska Institutet, Nobels Väg 6, 171 77 Stockholm, Sweden
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, 4365-Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Johan Nordgren
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
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Zhang T, Li J, Jiang YZ, Xu JQ, Guan XH, Wang LQ, Chen J, Liang Y. Genotype Distribution and Evolutionary Analysis of Rotavirus Associated with Acute Diarrhea Outpatients in Hubei, China, 2013–2016. Virol Sin 2022; 37:503-512. [PMID: 35643410 PMCID: PMC9437618 DOI: 10.1016/j.virs.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/17/2022] [Indexed: 11/23/2022] Open
Abstract
Group A human rotaviruses (RVAs) annually cause the deaths of 215,000 infants and young children. To understand the epidemiological characteristics and genetic evolution of RVAs, we performed sentinel surveillance on RVA prevalence in a rotavirus-surveillance network in Hubei, China. From 2013 to 2016, a total of 2007 fecal samples from hospital outpatients with acute gastroenteritis were collected from four cities of Hubei Province. Of the 2007 samples, 153 (7.62%) were identified positive for RVA by real-time RT-PCR. RVA infection in Hubei mainly occurred in autumn and winter. The highest detection rate of RVA infection was in 1–2 years old of outpatients (16.97%). No significant difference of RVA positive rate was observed between females and males. We performed a phylogenetic analysis of the G/P genotypes based on the partial VP7/VP4 gene sequences of RVAs. G9P[8] was the most predominant strain in all four years but the prevalence of G2P[4] genotype increased rapidly since 2014. We reconstructed the evolutionary time scale of RVAs in Hubei, and found that the evolutionary rates of the G9, G2, P[8], and P[4] genotypes of RVA were 1.069 × 10−3, 1.029 × 10−3, 1.283 × 10−3 and 1.172 × 10−3 nucleotide substitutions/site/year, respectively. Importantly, using a molecular clock model, we showed that most G9, G2, P[8], and P[4] genotype strains dated from the recent ancestor in 2005, 2005, 1993, and 2013, respectively. The finding of the distribution of RVAs in infants and young children in Hubei Province will contribute to the understanding of the epidemiological characteristics and genetic evolution of RVAs in China. A four-year study of sentinel surveillance program of RVAs was performed in Hubei, China. The key population of rotavirus infection is 1–2 years old of outpatients with acute gastroenteritis. G9P[8] was the most predominant strain between 2013 and 2016. The estimating time to the most recent common ancestor for the G9 genotype based on partial VP7 gene was 46 years. RVA distribution in Hubei Province contributes to the understanding of the epidemiological characteristics of RVAs in China.
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Ali S, Khan S, Khan SN, Rauf M, Khan MF, Majid A, Dawar FU, Akbar NU, Ullah R, Bari A, Khan MY. Molecular detection and prevalence of Rotavirus with acute gastroenteritis among the children of rural and urban areas. BRAZ J BIOL 2021; 83:e244365. [PMID: 34932615 DOI: 10.1590/1519-6984.244365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/19/2021] [Indexed: 11/22/2022] Open
Abstract
Rotavirus is the main infective agent of acute gastroenteritis (AGE) in children under the age of five years and causing significant morbidity as well as mortality throughout the world. The study was carried out to detect the prevalence rate, genotypes strain and risk factors of Rotavirus among the children of rural and urban areas of district Bannu Khyber Pakhtunkhwa Pakistan. A total of 180 stool samples were collected from children under the age of 5 years from two major hospitals of Bannu from January to December (2015). The samples were analyzed by Reverse-transcriptase Polymerase Chain Reaction (RT-PCR) for the detection of Rotavirus, positive samples were further processed for genotyping (G and P type) through specific PCR. Of the total, 41 (23%) samples were positive for Rotavirus. The most prevalent G genotypes found were: G3, G8, G9 (each 29%), followed by G10 (15%), and G11 (10%). Whereas the prevalent P genotypes were: P-8 (25%), P-4 and P-10 (each 20%), P-9 (15%), followed by P-6 and P-11 (each 10%). Moreover, Rotavirus infection was more prevalent in summer (23.73%) and winter (22.7%) than spring (20%) and autumn (21.4%). Rotavirus infection exhibited high frequency in June (14%), October (8%) and November (6%). It is concluded that Rotavirus is more prevalent in children and various genotypes (G and P) of Rotavirus are present in the study area. Lack of studies, awareness and rarer testing of Rotavirus are the principal reasons of virus prevalence in district Bannu, Pakistan.
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Affiliation(s)
- S Ali
- Kohat University of Science e Technology Kohat, Department of Zoology, Khyber Pakhtunkhwa, Pakistan
| | - S Khan
- University of Peshawar, Department of Zoology, Khyber Pakhtunkhwa, Pakistan
| | - S N Khan
- Kohat University of Science e Technology Kohat, Department of Zoology, Khyber Pakhtunkhwa, Pakistan
| | - M Rauf
- Kohat University of Science e Technology Kohat, Department of Zoology, Khyber Pakhtunkhwa, Pakistan
| | - M F Khan
- University of Hazara Dhodial, Department of Zoology, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - A Majid
- Kohat University of Science e Technology Kohat, Department of Zoology, Khyber Pakhtunkhwa, Pakistan
| | - F U Dawar
- Kohat University of Science e Technology Kohat, Department of Zoology, Khyber Pakhtunkhwa, Pakistan
| | - N Ul Akbar
- Kohat University of Science e Technology Kohat, Department of Zoology, Khyber Pakhtunkhwa, Pakistan
| | - R Ullah
- College of Pharmacy, Department of Pharmacognosy, King Saud University Riyadh, Riyadh, Saudi Arabia
| | - A Bari
- King Saud University Riyadh, College of Pharmacy, Department of Pharmaceutical Chemistry, Riyadh, Saudi Arabia
| | - M Y Khan
- Lancaster University, Lancaster Environmental Centre, Lancaster, United Kingdon
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5
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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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6
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Olivares AIO, Leitão GAA, Pimenta YC, Cantelli CP, Fumian TM, Fialho AM, da Silva E Mouta S, Delgado IF, Nordgren J, Svensson L, Miagostovich MP, Leite JPG, de Moraes MTB. Epidemiology of enteric virus infections in children living in the Amazon region. Int J Infect Dis 2021; 108:494-502. [PMID: 34052409 DOI: 10.1016/j.ijid.2021.05.060] [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] [Received: 03/14/2021] [Revised: 05/17/2021] [Accepted: 05/21/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES To verify the frequency of viruses causing acute gastroenteritis (AGE) in association with the histo-blood group antigen (HBGA) and Rotarix™ vaccination coverage in children from the Amazon region. DESIGN Fecal and saliva samples were collected from children with AGE (n = 485) and acute respiratory infection (ARI) (n = 249) clinical symptoms. Rotavirus A (RVA), norovirus, human adenovirus (HAdV), and sapovirus (SaV) were verified in feces by molecular detection. Saliva samples were used for HBGA phenotyping/FUT3 genotyping. Blood group types, clinical aspects and Rotarix™ RVA vaccination data were recorded. RESULTS Norovirus remained the most prevalently detected cause of AGE (38%, 184/485 and ARI 21.3%, 53/249). High HAdV frequencies were observed in AGE children (28.6%, 139/485) and ARI children (37.3%, 93/249). RVA was the third most prevalent virus causing AGE (22.7%, 110/485 and ARI 19.3%, 48/249) and a low RV1 coverage (61%, 448/734) was verified. The SaV frequencies were lower (7.2%, 35/485 for AGE and 6.8%, 17/249 for ARI). Secretor children were HBGA susceptible to HAdV infection (OR 1.5, 95% CI 1.0-2.3; P = 0.04) but not to RVA, norovirus or SaV infection. CONCLUSIONS Norovirus could be considered the main etiological agent of AGE. No association was verified for HBGA susceptibility to RVA, norovirus and SaV. Secretor children showed a slight susceptibility to HAdV infection and the Le (a-b-) heterogeneous SNPs on the FUT3 gene.
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Affiliation(s)
- Alberto Ignacio Olivares Olivares
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil; Post-Graduate Program in Parasite Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil
| | - Gabriel Azevedo Alves Leitão
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil; Post-Graduate Program in Sanitary Surveillance, National Institute for Quality Control in Health, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil
| | - Yan Cardoso Pimenta
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil; Post-Graduate Program in Sanitary Surveillance, National Institute for Quality Control in Health, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil
| | - Carina Pacheco Cantelli
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil
| | - Alexandre Madi Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil
| | - Sergio da Silva E Mouta
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil
| | - Isabella Fernandes Delgado
- Post-Graduate Program in Sanitary Surveillance, National Institute for Quality Control in Health, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil
| | - Johan Nordgren
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Lennart Svensson
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil
| | - Marcia Terezinha Baroni de Moraes
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Fiocruz, Avenida Brasil, Rio de Janeiro, RJ, Brazil.
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Silva-Sales M, Leal E, Milagres FADP, Brustulin R, Morais VDS, Marcatti R, Araújo ELL, Witkin SS, Deng X, Sabino EC, Delwart E, Luchs A, Costa ACD. Genomic constellation of human Rotavirus A strains identified in Northern Brazil: a 6-year follow-up (2010-2016). Rev Inst Med Trop Sao Paulo 2020; 62:e98. [PMID: 33331517 PMCID: PMC7748031 DOI: 10.1590/s1678-9946202062098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/27/2020] [Indexed: 02/21/2023] Open
Abstract
Surveillance of Rotavirus A (RVA) throughout the national territory is important
to establish a more complete epidemiological-molecular scenario of this virus
circulation in Brazil. The aim of the present study was to investigate the
genetic diversity of RVA strains circulating in Tocantins State (Northern
Brazil) during six years of post-vaccination follow-up (2010-2016). A total of
248 stool samples were screened by next generation sequencing and 107 (43.1%)
nearly full length RVA genome sequences were obtained; one sample was
co-infected with two RVA strains (G2/G8P[4]). Six G and P genotypes combinations
were detected: G12P[8] strains (78.6%), as well as the G3P[8] (9.3%) and G1P[8]
(0.9%) were associated with a Wa-like genogroup backbone. All G2P[4] (5.6%) and
G8P[4] (2.8%) strains, including the mixed G2/G8P[4] infection (0.9%) showed the
DS-1-like genetic background. The two G12P[4] strains (1.9%) were associated
with distinct genetic backbones: Wa-like and DS-1-like. The phylogenetic
analysis revealed the circulation of lineages G1-I, G2-IV, G3-III, G8-I and
G12-III, and P[4]-V and P[8]-III of the VP7 and VP4 genes, respectively.
Conserved clustering pattern and low genetic diversity were observed regarding
VP1-VP3 and VP6, as well as NSP1-5 segments. We identified the same RVA
circulation pattern reported in other Brazilian regions in the period of
2010-2016, suggesting that rural and low-income areas may not have a different
RVA genotypic distribution compared to other parts of the country. The unique
presentation of whole-genome data of RVA strains detected in the Tocantins State
provides a baseline for monitoring variations in the genetic composition of RVA
in this area.
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Affiliation(s)
- Marcelle Silva-Sales
- Universidade Federal de Goiás, Instituto de Patologia Tropical e Saúde Pública, Laboratório de Virologia e Cultivo Celular, Goiânia, Goiás, Brazil
| | - Elcio Leal
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, Pará, Brazil
| | - Flavio Augusto de Pádua Milagres
- Universidade Federal do Tocantins, Palmas, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Estado de Tocantins, Palmas, Tocantins, Brazil
| | - Rafael Brustulin
- Universidade Federal do Tocantins, Palmas, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Estado de Tocantins, Palmas, Tocantins, Brazil
| | - Vanessa Dos Santos Morais
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Roberta Marcatti
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Emerson Luiz Lima Araújo
- Ministério da Saúde, Secretaria de Vigilância em Saúde, Departamento de Articulação Estratégica de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Brasília, Distrito Federal, Brazil
| | - Steven S Witkin
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil.,Weill Cornell Medicine, Department of Obstetrics and Gynecology, New York, New York, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, California, USA.,University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, USA
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA.,University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, USA
| | - Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
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8
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Gutierrez MB, Fialho AM, Maranhão AG, Malta FC, de Andrade JDSR, de Assis RMS, Mouta SDSE, Miagostovich MP, Leite JPG, Machado Fumian T. Rotavirus A in Brazil: Molecular Epidemiology and Surveillance during 2018-2019. Pathogens 2020; 9:pathogens9070515. [PMID: 32605014 PMCID: PMC7400326 DOI: 10.3390/pathogens9070515] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 02/06/2023] Open
Abstract
Rotavirus A (RVA) vaccines succeeded in lowering the burden of acute gastroenteritis (AGE) worldwide, especially preventing severe disease and mortality. In 2019, Brazil completed 13 years of RVA vaccine implementation (Rotarix™) within the National Immunization Program (NIP), and as reported elsewhere, the use of Rotarix™ in the country has reduced childhood mortality and morbidity due to AGE. Even though both marketed vaccines are widely distributed, the surveillance of RVA causing AGE and the monitoring of circulating genotypes are important tools to keep tracking the epidemiological scenario and vaccines impact. Thus, our study investigated RVA epidemiological features, viral load and G and P genotypes circulation in children and adults presenting AGE symptoms in eleven states from three out of five regions in Brazil. By using TaqMan®-based one-step RT-qPCR, we investigated a total of 1536 stool samples collected from symptomatic inpatients, emergency department visits and outpatients from January 2018 to December 2019. G and P genotypes of RVA-positive samples were genetically characterized by multiplex RT-PCR or by nearly complete fragment sequencing. We detected RVA in 12% of samples, 10.5% in 2018 and 13.7% in 2019. A marked winter/spring seasonality was observed, especially in Southern Brazil. The most affected age group was children aged >24-60 months, with a positivity rate of 18.8% (p < 0.05). Evaluating shedding, we found a statistically lower RVA viral load in stool samples collected from children aged up to six months compared to the other age groups (p < 0.05). The genotype G3P[8] was the most prevalent during the two years (83.7% in 2018 and 65.5% in 2019), and nucleotide sequencing of some strains demonstrated that they belonged to the emergent equine-like G3P[8] genotype. The dominance of an emergent genotype causing AGE reinforces the need for continuous epidemiological surveillance to assess the impact of mass RVA immunization as well as to monitor the emergence of novel genotypes.
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Zaraket R, Salami A, Bahmad M, El Roz A, Khalaf B, Ghssein G, Bahmad HF. Prevalence, risk factors, and clinical characteristics of rotavirus and adenovirus among Lebanese hospitalized children with acute gastroenteritis. Heliyon 2020; 6:e04248. [PMID: 32613122 PMCID: PMC7322251 DOI: 10.1016/j.heliyon.2020.e04248] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/16/2020] [Accepted: 06/15/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Acute gastroenteritis is a very common infectious disease facing all age groups worldwide, especially the pediatric population. Viruses, bacteria, and parasites are all possible causes of infectious gastroenteritis; however, viruses have become more frequently identified with the advances in the ability to diagnose viral infections, particularly rotavirus and adenovirus. We aimed in our study to compare between the prevalence, risk factors, and clinical characteristics of rotavirus and adenovirus among children with viral gastroenteritis in Lebanon. MATERIALS AND METHODS A 12-months retrospective study was performed between January 1st and December 31st, 2018 including 308 children aged 1 month to 12 years, who were admitted to three tertiary healthcare centers in South Lebanon. Medical data were retrieved from patients' files, including clinical and laboratory information. RESULTS Rotavirus was found in stool of 204 patients (66.23 %), followed by adenovirus in 78 cases (25.32 %), and mixed group (rotavirus and adenovirus) in 26 cases (8.44%). The highest prevalence of rotavirus in our present study was seen among children between 12 and 23 months old, whereas patients infected with adenovirus were mainly aged between 24-35 months or 4-11 months. Majority of patients in the adenovirus and mixed groups had high-grade fever compared to the rotavirus group. Laboratory findings presented significantly higher average of white blood cells (WBCs), absolute neutrophil count (ANC), and C-reactive protein (CRP) in the mixed group compared to the two other groups. Monthly distribution of rotavirus and adenovirus infection revealed a biennial pattern of rotavirus incidence during January and July-August while frequency of adenovirus infection was highest during July-August. CONCLUSION Due to the high prevalence of viral diarrhea among the pediatric age group in our region, particularly rotavirus and adenovirus, along with the associated non-specific signs and symptoms, we highly recommend that medical laboratories be equipped for virus detection. Also, vaccination against rotavirus should be considered as a prevention strategy.
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Affiliation(s)
- Rasha Zaraket
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
| | - Ali Salami
- Rammal Hassan Rammal Research Laboratory, Physio-toxicity (PhyTox) Research Group, Lebanese University, Faculty of Sciences (V), Nabatieh, Lebanon
| | - Marwan Bahmad
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
| | - Ali El Roz
- Rammal Hassan Rammal Research Laboratory, Physio-toxicity (PhyTox) Research Group, Lebanese University, Faculty of Sciences (V), Nabatieh, Lebanon
| | - Batoul Khalaf
- Rammal Hassan Rammal Research Laboratory, Physio-toxicity (PhyTox) Research Group, Lebanese University, Faculty of Sciences (V), Nabatieh, Lebanon
| | - Ghassan Ghssein
- Rammal Hassan Rammal Research Laboratory, Physio-toxicity (PhyTox) Research Group, Lebanese University, Faculty of Sciences (V), Nabatieh, Lebanon
- Department of Laboratory Sciences, Faculty of Nursing and Health Sciences, Islamic University of Lebanon, Khalde, Lebanon
| | - Hisham F. Bahmad
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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Full genome characterization of human G3P[6] and G3P[9] rotavirus strains in Lebanon. INFECTION GENETICS AND EVOLUTION 2019; 78:104133. [PMID: 31812761 DOI: 10.1016/j.meegid.2019.104133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/04/2019] [Accepted: 12/02/2019] [Indexed: 11/24/2022]
Abstract
Rotaviruses are the most common infectious agents causing severe diarrheal diseases in young children globally. Three rare human rotavirus strains, two G3P[9] and one G3P[6], were detected in stool samples of children under 5 years of age hospitalized for gastroenteritis in Lebanon during the course of a surveillance study. Complete genomes of these strains were sequenced using VirCapSeq-VERT, a capture based high-throughput sequencing method. Genomic sequences were further characterized by using phylogenetic analyses with global RVA G3P[6]/P[9] strains, other vaccine and reference strains. Genetic analysis revealed that the G3P[6] strain emerged as a DS-1/Wa-like mono-reassortant strain with a potential Ethiopian origin. The two G3P[9] strains possessed a mixed DS-1/Wa/AU-1-like origin indicating that these may have evolved via multiple reassortment events involving feline, human and bovine rotaviruses. Furthermore, analysis of these strains revealed high antigenic variability compared to the vaccine strains. Additional studies are essential to fully understand the evolutionary dynamics of G3P[6]/P[9] strains spreading worldwide and their implications on vaccine effectiveness.
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11
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Degiuseppe JI, Stupka JA. Genotype distribution of Group A rotavirus in children before and after massive vaccination in Latin America and the Caribbean: Systematic review. Vaccine 2019; 38:733-740. [PMID: 31771863 DOI: 10.1016/j.vaccine.2019.11.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 10/10/2019] [Accepted: 11/08/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND During the last decade, most of Latin American and the Caribbean (LAC) countries have implemented oral live rotavirus vaccines in their national vaccination programs with remarkable results. However, it has been suggested that massive vaccination could lead to the replacement of circulating genotypes or the emergence of new variants or neutralizing antibodies escape mutants, which may reduce the effectiveness of the vaccine. The objective was to analyze the genetic diversity of Group A rotavirus before and after the introduction of universal vaccination in LAC. METHODS We conducted a systematic review of studies published in PubMed, Scielo and LILACS. There were considered only LAC countries with rotavirus massive vaccination strategy which had described circulating genotypes data in children under 5 years of age, either for surveillance or vaccine effectiveness purposes, from 2001 to 2017. Systematic review stages were carried out following the recommendations of PRISMA. RESULTS Of the 18 countries that included any of the two licensed rotavirus vaccines in their national schedules since 2006, only 7 (~39%) presented studies of RVA genetic diversity before and after implementation, and met the inclusion criteria. Four of them (Argentina, Brazil, Colombia and Nicaragua) experienced a rapid switch from Wa-like to DS-1-like strains. Also, G1P[8] association, considered the most predominant worldwide in the pre-vaccination era, decreased significantly and was only frequently detected in Venezuela and Nicaragua. No defined pattern of emergence at high frequencies of unusual associations was observed in the post vaccination period, except for some evidence of G9P[4] in Colombia, G3P[6] and G1P[4] in Nicaragua. CONCLUSIONS Even though the evidence shows a DS-1-like change trend, data from studies conducted in Latin America and the Caribbean are diverse and still not sufficient to assess the impact of vaccines on viral ecology or if genetic diversity is influenced by natural mechanisms of fluctuation.
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Affiliation(s)
- Juan Ignacio Degiuseppe
- Laboratory of Viral Gastroenteritis, INEI-ANLIS "Dr. Carlos G. Malbrán", Avenida Vélez Sársfield 563, Buenos Aires, Argentina.
| | - Juan Andrés Stupka
- Laboratory of Viral Gastroenteritis, INEI-ANLIS "Dr. Carlos G. Malbrán", Avenida Vélez Sársfield 563, Buenos Aires, Argentina
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Castro LRP, Calvet FC, Sousa KL, Silva VP, Lobo PS, Penha ET, Guerra SFS, Bezerra DAM, Mascarenhas JDP, Pinheiro HHC, Costa IB, Resque HR, Soares LS. Prevalence of rotavirus and human bocavirus in immunosuppressed individuals after renal transplantation in the Northern Region of Brazil. J Med Virol 2019; 91:2125-2133. [PMID: 31429939 DOI: 10.1002/jmv.25569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/05/2019] [Indexed: 12/16/2022]
Abstract
Immunosuppressive therapy causes severe impairment of host defense and diarrhea is a frequent complication in renal transplant recipients. This study aimed to describe the occurrence of Rotavirus A (RVA) and Human Bocavirus (HBoV) in fecal samples of immunosuppressed patients submitted to renal transplantation during posttransplant follow-up. A longitudinal study was carried out involving a 25-patient cohort, selected for kidney transplantation. A total of 126 fecal samples were collected between May 2014 and May 2016. Molecular techniques were used to detect and characterize circulating RVA and HBoV genotypes and statistical analysis were applied to verify the association between epidemiological and clinical characteristics. The prevalence of RVA and HBoV was 24% (6/25) and 40% (10/25), respectively. Among RVA and HBoV positive cases, the majority was female; did not conduct water treatment nor had adequate sewage facilities. The most detected genotypes were RVA G3 (62.5%) and HBoV-3 (95%). Phylogenetic analysis of HBoV strains indicated that studied samples were similar to those found in Asian and American countries. The present study point out the circulation of these viral agents among immunosuppressed individuals and these findings will enable the construction of new knowledge and care perspectives on the cause of diarrhea in this population.
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Affiliation(s)
- Luanda R P Castro
- Postgraduate Program in Epidemiology and Surveillance in Health, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Flávio C Calvet
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Karoline L Sousa
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Victor P Silva
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Patrícia S Lobo
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Edvaldo T Penha
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Sylvia F S Guerra
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Delana A M Bezerra
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Joana D P Mascarenhas
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Helder H C Pinheiro
- Center for Tropical Medicine, Federal University of Pará, Belém, Pará, Brazil
| | - Igor B Costa
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Hugo R Resque
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Luana S Soares
- Laboratory of Rotavirus, Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
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Emergence of G12P[6] rotavirus strains among hospitalised children with acute gastroenteritis in Belém, Northern Brazil, following introduction of a rotavirus vaccine. Arch Virol 2019; 164:2107-2117. [PMID: 31144039 DOI: 10.1007/s00705-019-04295-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 04/29/2019] [Indexed: 10/26/2022]
Abstract
Species A rotavirus still remains a major cause of acute gastroenteritis in infants and young children. Globally, six genotypes (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]) account for >90% of circulating strains; however, genotype G12 in combination with P[6] or P[9] has been detected at increasing rates. We sought to broaden our knowledge about the rotavirus strains circulating during the early post-vaccine-introduction period. Stool samples were obtained from children hospitalised for acute gastroenteritis in Belém, Northern Brazil, from May 2008 to May 2011 and examined by reverse transcription polymerase chain reaction and nucleotide sequencing. A total of 122 out of the original 1076 rotavirus strains were judged to be non-typeable in the first analysis and were therefore re-examined. G2P[4] was the most prevalent genotype (58.0%), followed by G1P[8] (16.9%), and G12P[6] (7.5%). G12P[6] strains were identified at similar rates during the first (2.5%) and second (3.9%) years, and the rate jumped to 15.6% in the third year. Analysis of VP7 sequences of the G12P[6] strains showed that they belonged to lineage III. In addition, co-circulating G12P[6] strains displaying long and short RNA patterns were found to belong to the Wa-like and DS-1-like constellation, respectively. Additional unusual circulating strains G12P[9] and G3P[9] were also identified. This hospital-based study showed a high prevalence of G12P[6] strains in the third year of surveillance. Our results highlight the need for continuous longitudinal monitoring of circulating rotavirus strains after introduction of rotavirus vaccines in Brazil and elsewhere.
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Carvalho-Costa FA, de Assis RMS, Fialho AM, Araújo IT, Silva MF, Gómez MM, Andrade JS, Rose TL, Fumian TM, Volotão EM, Miagostovich MP, Leite JPG. The evolving epidemiology of rotavirus A infection in Brazil a decade after the introduction of universal vaccination with Rotarix®. BMC Pediatr 2019; 19:42. [PMID: 30704518 PMCID: PMC6354375 DOI: 10.1186/s12887-019-1415-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 01/22/2019] [Indexed: 01/15/2023] Open
Abstract
Background Brazil introduced the monovalent rotavirus vaccine (Rotarix®) in 2006. This study aimed to assess the epidemiology and genotype distribution of species-A rotavirus (RVA) in Brazil, comparing the pre- and post-vaccination periods. Methods Laboratory-based RVA surveillance included 866 municipalities in 22 Brazilian states, over a 21-year period. A total of 16,185 children with diarrheal diseases (DD) aged up to 12 years between 1996 and 2005 (pre-vaccination period, n = 7030) and from 2006 to 2017 (post-vaccination period, n = 9155) were enrolled. RVA was detected using ELISA immune assay and/or polyacrylamide gel electrophoresis and genotyped using nested PCR and/or nucleotide sequencing. RVA-positivity and genotypes detection rates were compared in distinct periods and age groups and Rotarix vaccination status. Results RVA-positivity in pre- and post-vaccination periods was, respectively: 4–11 months bracket, 33.3% (668/2006) and 16.3% (415/2547) (p < 0.001); 12–24 months, 28.2% (607/2154) and 22.2% (680/3068) (p < 0.001); 25–48 months, 17.4% (215/1235) and 29.4% (505/1720) (p < 0.001). Genotypes distribution in the pre- and post-vaccination periods was, respectively: G1P [8]/G1P[Not Typed], 417/855 (48.8%) and 118/1835 (6.4%) (p < 0.001); G2P [4]/G2P[NT], 47/855 (5.5%) and 838/1835 (45.7%) (p < 0.001); G3P [8]/G3P[NT], 55/855 (6.4%) and 253/1835 (13.8%) (p < 0.001); G9P [8]/G9P[NT], 238/855 (27.8%) and 152/1835 (8.3%) (p < 0.001); G12P [8]/G129P[NT], 0/871 (0%) and 249/1835(13.6%) (p < 0.001). Concerning infants aged 4–11 months, RVA frequency in fully vaccinated and non-vaccinated individuals was 11.9% (125/1052) and 24.5% (58/237) (p < 0.001), respectively. In children aged 12–24 months, RVA detection rate was 18.1% (253/1395) and 29.6% (77/260) (p < 0.001), for the vaccinated and non-vaccinated individuals, respectively (p < 0.001). Conclusions RVA infection was significantly less frequent in children aged ≤2 years with DD after implementing vaccination, mainly among vaccinated children. It was also observed a decrease of P [8] circulation and emergence of G2P[4] in 2005, and afterwards in the post-vaccine era, with spreading of G12P[8] in 2014–2015 and of G3P[8] in 2017. Continuous RVA surveillance must be carried out in this scenario.
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Affiliation(s)
- Filipe A Carvalho-Costa
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil. .,Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Leonidas Deane, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil. .,Regional Office Fiocruz Piauí. Rua Magalhães Filho, n° 519, Centro/Norte, Teresina, Piauí, Brazil.
| | - Rosane M S de Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre M Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Irene T Araújo
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelle F Silva
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariela M Gómez
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana S Andrade
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tatiana L Rose
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tulio M Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eduardo M Volotão
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marize P Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Paulo G Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
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Pratte-Santos R, Miagostovich MP, Fumian TM, Maciel EL, Martins SA, Cassini ST, Keller R. High prevalence of enteric viruses associated with acute gastroenteritis in pediatric patients in a low-income area in Vitória, Southeastern Brazil. J Med Virol 2019; 91:744-750. [PMID: 30614007 DOI: 10.1002/jmv.25392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/26/2018] [Indexed: 12/28/2022]
Abstract
Acute gastroenteritis (AGE) is a significant cause of child mortality worldwide. In Brazil, despite the reduction in infant mortality achieved in recent years, many children still die because of undiagnosed AGE. The prevalence, viral load, and circulating genotypes of rotavirus A (RVA), human adenovirus (HAdV), and norovirus GII (NoV GII) were investigated in children with AGE during 12 months in Vitoria, Espírito Santo, Southeastern Brazil. Enteric viruses were detected in stool samples, quantified by quantitative polymerase chain reaction, sequenced, and compared phylogenetically. The overall prevalence was 93.3% (125/134). Cases of single infection (41.8%) and mixed infection (51.5%) were observed; in 21.6% of cases, all the three viruses were detected. RVA had the highest number of copies in all infections. Phylogenetic analysis revealed predominantly the presence of RVA genotype G3, followed by G2 and G9. HAdV clustered within subgroup C, but some samples harbored subgroups A, D, or F. All sequenced NoV-positive samples clustered within the prevalent genotype GII.4. The high prevalence of RVA, HAdV, and NoV in diarrheal feces clarifies the etiology of AGE in this population, and the presence of RVA in vaccinated children reinforces the importance of monitoring programs to identify the causes of gastroenteritis and contribute to the reliability of diagnosis.
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Affiliation(s)
- Rodrigo Pratte-Santos
- Laboratório de Saneamento, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Marize Pereira Miagostovich
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Túlio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ethel Leonor Maciel
- Laboratório de Epidemiologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Sara Angelino Martins
- Laboratório de Saneamento, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Sérvio Túlio Cassini
- Laboratório de Saneamento, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Regina Keller
- Laboratório de Saneamento, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
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Wandera EA, Komoto S, Mohammad S, Ide T, Bundi M, Nyangao J, Kathiiko C, Odoyo E, Galata A, Miring'u G, Fukuda S, Hatazawa R, Murata T, Taniguchi K, Ichinose Y. Genomic characterization of uncommon human G3P[6] rotavirus strains that have emerged in Kenya after rotavirus vaccine introduction, and pre-vaccine human G8P[4] rotavirus strains. INFECTION GENETICS AND EVOLUTION 2018; 68:231-248. [PMID: 30543939 DOI: 10.1016/j.meegid.2018.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 10/27/2022]
Abstract
A monovalent rotavirus vaccine (RV1) was introduced to the national immunization program in Kenya in July 2014. There was increased detection of uncommon G3P[6] strains that coincided temporally with the timing of this vaccine introduction. Here, we sequenced and characterized the full genomes of two post-vaccine G3P[6] strains, RVA/Human-wt/KEN/KDH1951/2014/G3P[6] and RVA/Human-wt/KEN/KDH1968/2014/G3P[6], as representatives of these uncommon strains. On full-genomic analysis, both strains exhibited a DS-1-like genotype constellation: G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that all 11 genes of strains KDH1951 and KDH1968 were very closely related to those of human G3P[6] strains isolated in Uganda in 2012-2013, indicating the derivation of these G3P[6] strains from a common ancestor. Because the uncommon G3P[6] strains that emerged in Kenya are fully heterotypic as to the introduced vaccine strain regarding the genotype constellation, vaccine effectiveness against these G3P[6] strains needs to be closely monitored.
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Affiliation(s)
- Ernest Apondi Wandera
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan.
| | - Shah Mohammad
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Martin Bundi
- National Biosafety Authority, Nairobi 00100, Kenya
| | - James Nyangao
- Center for Virus Research, KEMRI, Nairobi 54840-00200, Kenya
| | - Cyrus Kathiiko
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Erick Odoyo
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Amina Galata
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Gabriel Miring'u
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Yoshio Ichinose
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
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Monitoring Shedding of Five Genotypes of RotaTeq Vaccine Viruses by Genotype-Specific Real-Time Reverse Transcription-PCR Assays. J Clin Microbiol 2018; 56:JCM.00035-18. [PMID: 29563200 DOI: 10.1128/jcm.00035-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/14/2018] [Indexed: 11/20/2022] Open
Abstract
RotaTeq (RV5) is a widely used live attenuated pentavalent rotavirus (RV) vaccine. Although fecal shedding of RV vaccine strains persists for long time periods, it is unclear how each vaccine strain replicates in intestinal tissue and is excreted in stool. To examine this issue, we established RV5 genotype-specific real-time reverse transcription-PCR (RT-PCR) assays. Five real-time RT-PCR assays were designed for the VP7 gene in genotypes G1, G2, G3, G4, and G6. All assays exhibited excellent linearity, and the detection limit was 1 infectious unit (IU)/reaction for G2, G4, and G6 and 10 IUs/reaction for G1 and G3. No cross-reactivity was observed among G genotypes. The inter- and intra-assay coefficients of variation were less than 3%. The assays were used to examine 129 stool samples collected from eight infants who received RV5. In cases 1 and 2, who received three rounds of vaccination, RV shedding decreased gradually with the number of vaccinations. G1 and G6 shedding appeared to be predominant in comparison to shedding of the other genotypes. Patterns of fecal shedding of the five genotypes of vaccine viruses differed between the eight vaccine recipients. RV5 genotype-specific real-time RT-PCR assays will be useful to study the molecular biology of RV5 replication in infants and experimental animals.
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Durmaz R, Bakkaloglu Z, Unaldi O, Karagoz A, Korukluoglu G, Kalaycioglu AT, Acar S, Kilic S. Prevalence and diversity of rotavirus A genotypes cirulating in Turkey during a 2-year sentinel surveillance period, 2014-2016. J Med Virol 2017; 90:229-238. [PMID: 28892173 DOI: 10.1002/jmv.24945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/01/2017] [Indexed: 12/29/2022]
Abstract
Human rotavirus A (RVA) is the main etiological agent of watery diarrhea among children under 5 years of age worldwide. The aims of this study were to investigate the prevalence and diversity of RVA genotypes circulating in Turkey during a 2-year sentinel surveillance study. A total of 1639 rotavirus antigen-positive stool samples were obtained from children younger than 5 years of age hospitalized with acute gastroenteritis. Rotavirus G and P genotypes were determined by reverse transcription polymerase chain reaction (RT-PCR) with consensus primers for the VP7 and VP4 genes, followed by semi-nested type-specific multiplex PCR. Rotavirus RNA was detected in 1396 (85.3%) of the samples tested. The highest detection rate (38.2%) was obtained among children in the 0-12 months age group, followed by children in the 13-24 months age group (36.2%). The most prevalent genotype was G1P[8] (24.6%) followed by G3P[8] (19.6%), G9P[8] (12.2%), G2P[4] (9.5%), G2P[8] (6.5%), and G4P[8] (4.8%). The proportions of uncommon and mixed genotypes were 21.5% and 1.14%, respectively. The large number of genotypes observed, including common, uncommon, and mixed types, indicates a high heterogeneity of RVA strains circulating in Turkey. The current study also exhibited dramatic fluctuations on the prevalences of the common genotypes, with increases in G3 and G1 and decreases in G9 and G2 from 2014-2016.
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Affiliation(s)
- Riza Durmaz
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey.,Department of Medical Microbiology, Faculty of Medicine Yildirim Beyazit University, Ankara, Turkey
| | - Zekiye Bakkaloglu
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Ozlem Unaldi
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Alper Karagoz
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Gulay Korukluoglu
- Virology Reference Central Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Atila T Kalaycioglu
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey.,Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Karadeniz Technical University, Trabzon, Turkey
| | - Sumeyra Acar
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Selcuk Kilic
- Microbiology Reference Laboratories, Public Health Agency of Turkey, Ankara, Turkey
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Umair M, Abbasi BH, Nisar N, Alam MM, Sharif S, Shaukat S, Rana MS, Khurshid A, Mujtaba G, Aamir UB, Zaidi SSZ. Molecular analysis of group A rotaviruses detected in hospitalized children from Rawalpindi, Pakistan during 2014. INFECTION GENETICS AND EVOLUTION 2017; 53:160-166. [DOI: 10.1016/j.meegid.2017.05.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/26/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
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Rotavirus vaccine and health-care utilization for rotavirus gastroenteritis in Tsu City, Japan. Western Pac Surveill Response J 2016; 7:28-36. [PMID: 28246579 PMCID: PMC5330216 DOI: 10.5365/wpsar.2016.7.3.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Rotavirus vaccines were introduced in Japan in November 2011. We evaluated the subsequent reduction of the health-care burden of rotavirus gastroenteritis. Methods We conducted active surveillance for rotavirus gastroenteritis among children under 5 years old before and after the vaccine introduction. We surveyed hospitalization rates for rotavirus gastroenteritis in children in Tsu City, Mie Prefecture, Japan, from 2007 to 2015 and surveyed the number of outpatient visits at a Tsu City clinic from 2010 to 2015. Stool samples were obtained for rotavirus testing and genotype investigation. We assessed rotavirus vaccine coverage for infants living in Tsu City. Results In the pre-vaccine years (2007–2011), hospitalization rates for rotavirus gastroenteritis in children under 5 years old were 5.5, 4.3, 3.1 and 3.9 cases per 1000 person-years, respectively. In the post-vaccine years (2011–2015), the rates were 3.0, 3.5, 0.8 and 0.6 cases per 1000 person-years, respectively. The hospitalization rate decreased significantly in the 2013–2014 and 2014–2015 seasons compared to the average of the seasons before vaccine introduction (P < 0.0001). In one pre-vaccine year (2010–2011), the number of outpatient visits due to the rotavirus infection was 66. In the post-vaccine years (2011–2015), the numbers for each season was 23, 23, 7 and 5, respectively. The most dominant rotavirus genotype shifted from G3P[8] to G1P[8] and to G2P[4]. The coverage of one dose of rotavirus vaccine in Tsu City was 56.5% in 2014. Conclusion After the vaccine introduction, the hospitalization rates and outpatient visits for rotavirus gastroenteritis greatly decreased.
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Jain S, Thakur N, Vashistt J, Grover N, Krishnan T, Changotra H. Predominance of unusual rotavirus G1P[6] strain in North India: An evidence from hospitalized children and adult diarrheal patients. INFECTION GENETICS AND EVOLUTION 2016; 46:65-70. [PMID: 27806915 DOI: 10.1016/j.meegid.2016.10.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 10/09/2016] [Accepted: 10/25/2016] [Indexed: 12/16/2022]
Abstract
Group A Rotavirus remains the leading cause of gastroenteritis in children and accounts for 0.2 million fatalities each year; out of which, approximately 47,100 deaths occur in India. In adults also, rotavirus is reported to be responsible for diarrhea severe enough to require hospitalizations. India has recently introduced rotavirus vaccine in the Universal Immunization Programme and Himachal Pradesh became the first Indian state to implement this project. This study is an attempt to provide the pre-vaccination data on rotavirus gastroenteritis burden and circulating genotypes in Himachal Pradesh, India. A total of 607 faecal specimens (247 children ≤5years, 50 older children and 310 adults) from hospitalized diarrheal patients from Himachal Pradesh, India were screened for rotavirus using ELISA and RT-PCR. The positive samples were further G/P genotyped using semi-nested PCR. Rotavirus was detected in 25.2% and 28.3% of samples with ELISA and RT-PCR, respectively. In children, rotavirus frequency was significantly high with positivity in 49.0% cases whereas 14.0% adult samples have rotavirus in them. Genotyping of the positive samples revealed predominance of G1 (66.0%) and P[6] (66.7%) genotypes. The most common G and P combination was G1P[6] (62.8%) followed by G1P[8] (16.5%), G9P[6] (7.4%) and G12P[6] (5.0%). Molecular analysis reveals the belonging of P[6] strains in Lineage 1a. This pre-vaccination data on rotavirus prevalence and diversity would be helpful for assessing the affect of vaccination on the disease burden and its comparison with post-vaccination data of circulating genotypes would help in studying the effect on diversity of rotavirus strains possibly due to vaccine selection pressure.
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Affiliation(s)
- Swapnil Jain
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173234, Himachal Pradesh, India
| | - Nutan Thakur
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173234, Himachal Pradesh, India
| | - Jitendraa Vashistt
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173234, Himachal Pradesh, India
| | - Neelam Grover
- Department of Pediatrics, Indira Gandhi Medical College, Shimla 171001, Himachal Pradesh, India
| | - Triveni Krishnan
- Division of Virology, National Institute of Cholera and Enteric Diseases (NICED), P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700 010, West Bengal, India
| | - Harish Changotra
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173234, Himachal Pradesh, India.
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Guerra SFS, Soares LS, Lobo PS, Penha Júnior ET, Sousa Júnior EC, Bezerra DAM, Vaz LR, Linhares AC, Mascarenhas JDP. Detection of a novel equine-like G3 rotavirus associated with acute gastroenteritis in Brazil. J Gen Virol 2016; 97:3131-3138. [PMID: 27902376 DOI: 10.1099/jgv.0.000626] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genotype G3P[8] of rotavirus A (RVA) is detected worldwide, usually associated with Wa-like constellation and exhibiting a long RNA migration pattern. More recently, a novel inter-genogroup, G3P[8] reassortant variant with a short electropherotype, has emerged in Asia, Oceania and Europe, denoting an overall potential of unusual rotavirus strains. During a RVA surveillance in Brazil, G3P[8] strains were found displaying a short electropherotype pattern, which had not been detected before in this region. This study aims to characterize the complete genome of 10 G3P[8] strains detected in the northern region of Brazil. All G3P[8] samples were subjected to partial sequencing, and the whole-genome phylogenetic analysis demonstrated that all strains possessed I2-R2-C2-M2-A2-N1-T2-E2-H2 genotype background, representing reassortants with an equine-like G3 VP7 and amino acid changes in VP4 and VP7 antigenic regions as compared to vaccine strains. Phylogenetic analysis demonstrated high nucleotide identity in almost all RNA segments of G3P[8] DS-1 samples detected in Asia, Oceania and Europe as well as G3P[4] strains in Japan. This study reports a novel, equine-like G3P[8] strain circulating in Brazil and isolated from children hospitalized for severe gastroenteritis, and highlights the complex dynamics of RVA molecular epidemiology. Our findings point to a novel RVA strain emerging in this region, and studies should be done to detect whether this may represent a challenge to current vaccine strategies.
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Affiliation(s)
| | - Luana Silva Soares
- Evandro Chagas Institute, Health Surveillance Secretariat, Belém, Brazil
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Changing distribution of age, clinical severity, and genotypes of rotavirus gastroenteritis in hospitalized children after the introduction of vaccination: a single center study in Seoul between 2011 and 2014. BMC Infect Dis 2016; 16:287. [PMID: 27296987 PMCID: PMC4906974 DOI: 10.1186/s12879-016-1623-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/04/2016] [Indexed: 01/07/2023] Open
Abstract
Background This study aimed to explore changes in clinical epidemiology and genotype distribution and their association among hospitalized children with rotavirus gastroenteritis after the introduction of vaccines. Methods Between November 2010 and October 2014, hospitalized children with acute gastroenteritis were enrolled. Rotavirus genotypes were confirmed through reverse transcription-polymerase chain reaction (RT-PCR), semi-nested PCR, and sequencing. Clinical information including vaccination status and the modified Vesikari scores were collected. Results Among 179 children with rotavirus infection, nineteen (10.6 %) were completely vaccinated. During the study period, the number of children between three and 23 months of age decreased significantly compared to the number of children older than 24 months of age (P = 0.010), who showed lower diarrhea severity (duration, P = 0.042; frequency, P = 0.021) but higher vomiting severity (P = 0.007, 0.036) compared to the former. Vaccination status was also significantly associated with lower vomiting severity after adjustment for age (frequency only, P = 0.018). The predominant genotypes were G2P[4] (18.4 %), G1P[8] (14.5 %), and G1P[4]P[8] (12.8 %), and the prevalence of genotypes with uncommon and mixed combinations was more than 50 %. Children infected with G2P[4] strains tended to be older (P = 0.005) and had more severe vomiting (P = 0.018, 0.006) than those with G1P[8]. Conclusions Increase in age of infected, hospitalized children was accompanied by change in clinical severity during 2011–2014 after the introduction of vaccines in Seoul. Clinical severity was also associated with vaccination status and genotype. Long-term large scale studies are needed to document the significance of the increase in genotypes of uncommon and mixed combinations. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1623-y) contains supplementary material, which is available to authorized users.
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Unusual rotavirus genotypes in humans and animals with acute diarrhoea in Northeast India. Epidemiol Infect 2016; 144:2780-9. [PMID: 27113208 DOI: 10.1017/s0950268816000807] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Rotavirus (RV) infection causes acute infantile diarrhoea in humans and animals and remains a major concern for vaccine development. The close proximity of humans to animals may foster cross-species infection resulting in the emergence of novel/unusual strains by genetic reassortment. In this study, we characterized 500 diarrhoeal samples for group A rotaviruses (RVA) from children (n = 290), piglets (n = 95) and calves (n = 115) in Northeast India during 2012-2013. The data showed that 142/500 (28·4%) faecal samples were positive for RVA with the highest level of infection detected in piglets (57/142, 40·1%) followed by children (51/142, 35·9%) and calves (34/142, 23·9%). Sequence-based G- and P-typing showed G1P[8] (25%) and G1P[7] (35%) were the prevailing genotypes in both humans and animals. Single cases of unusual genotypes, i.e. G9P[8], G5P[8] in humans and G1P[13], G1P[23] and G3P[7] in animals were also identified. Cluster analyses of the sequences showed regional strains were genetically closer to their homologous strains. However, human G5P[8] and porcine G1P[8] strains showed homology to heterologous hosts of their prototype strains. The subsequent global spread of unusual RV strains may result in their establishment over time, presenting challenges to future vaccine evaluation programmes. More studies on emerging genotypes are required to elucidate how RVA strains evolve post-vaccination. This study supports the need for continuous surveillance of RVA infections after detecting from diverse hosts in a common setting.
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25
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Vieira CB, de Abreu Corrêa A, de Jesus MS, Luz SLB, Wyn-Jones P, Kay D, Vargha M, Miagostovich MP. Viruses Surveillance Under Different Season Scenarios of the Negro River Basin, Amazonia, Brazil. FOOD AND ENVIRONMENTAL VIROLOGY 2016; 8:57-69. [PMID: 26783031 DOI: 10.1007/s12560-016-9226-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/07/2016] [Indexed: 06/05/2023]
Abstract
The Negro River is located in the Amazon basin, the largest hydrological catchment in the world. Its water is used for drinking, domestic activities, recreation and transportation and water quality is significantly affected by anthropogenic impacts. The goals of this study were to determine the presence and concentrations of the main viral etiological agents of acute gastroenteritis, such as group A rotavirus (RVA) and genogroup II norovirus (NoV GII), and to assess the use of human adenovirus (HAdV) and JC polyomavirus (JCPyV) as viral indicators of human faecal contamination in the aquatic environment of Manaus under different hydrological scenarios. Water samples were collected along Negro River and in small streams known as igarapés. Viruses were concentrated by an organic flocculation method and detected by quantitative PCR. From 272 samples analysed, HAdV was detected in 91.9%, followed by JCPyV (69.5%), RVA (23.9%) and NoV GII (7.4%). Viral concentrations ranged from 10(2) to 10(6) GC L(-1) and viruses were more likely to be detected during the flood season, with the exception of NoV GII, which was detected only during the dry season. Statistically significant differences on virus concentrations between dry and flood seasons were observed only for RVA. The HAdV data provides a useful complement to faecal indicator bacteria in the monitoring of aquatic environments. Overall results demonstrated that the hydrological cycle of the Negro River in the Amazon Basin affects the dynamics of viruses in aquatic environments and, consequently, the exposure of citizens to these waterborne pathogens.
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Affiliation(s)
- Carmen Baur Vieira
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Pavilhão Helio e Peggy Pereira, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 21040-360, Brazil.
| | - Adriana de Abreu Corrêa
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Pavilhão Helio e Peggy Pereira, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Michele Silva de Jesus
- Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane (ILMD), Fundação Oswaldo Cruz (FIOCRUZ), Rua Terezina, 476, Adrianópolis, Manaus, AM, 69057-070, Brazil
| | - Sérgio Luiz Bessa Luz
- Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane (ILMD), Fundação Oswaldo Cruz (FIOCRUZ), Rua Terezina, 476, Adrianópolis, Manaus, AM, 69057-070, Brazil
| | - Peter Wyn-Jones
- Department of Geography and Earth Sciences (DGES), Aberystwyth University, Penglais Campus, Aberystwyth, Ceredigion, SY23 3DB, UK
| | - David Kay
- Department of Geography and Earth Sciences (DGES), Aberystwyth University, Penglais Campus, Aberystwyth, Ceredigion, SY23 3DB, UK
| | - Marta Vargha
- Department of Water Hygiene, National Institute for Environmental Health, Gyáli út 2-6, Budapest, 1097, Hungary
| | - Marize Pereira Miagostovich
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Pavilhão Helio e Peggy Pereira, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 21040-360, Brazil
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Neves MAO, Pinheiro HHC, Silva RSU, Linhares AC, Silva LD, Gabbay YB, Silva MCM, Loureiro ECB, Soares LS, Mascarenhas JDP. High prevalence of G12P[8] rotavirus strains in Rio Branco, Acre, Western Amazon, in the post-rotavirus vaccine introduction period. J Med Virol 2015; 88:782-9. [PMID: 26466923 DOI: 10.1002/jmv.24404] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2015] [Indexed: 12/11/2022]
Abstract
The present study aimed to provide a molecular characterization of circulating rotavirus (RVA) strains in Rio Branco, Acre, in the post-rotavirus vaccination period, particularly with regard to the emerging, increasingly prevalent G12P[8] genotype. A total of 488 fecal specimens from diarrheic and non-diarrheic children were obtained between January and December 2012. RVA detection was initially performed using enzyme-linked immunosorbent assay (ELISA) method, followed by reverse-transcription polymerase chain reaction (RT-PCR) using specific primers. RVA was detected in 18.3% (44/241) of the children with acute diarrhea and in 1.2% (3/247) of the non-diarrheic children (P < 0.001), with overall RVA-positivity of 9.6% (47/488). The most common genotype was G2P[4] with 43.2% (19/44) of the diarrheic cases, followed by G12P[8] (27.3%, 12/44), G3P[6] (18.2%, 8/44), G3P[8] (4.5%, 2/44), and G12P[6] (2.3%, 1/44). G12 samples belonged to lineage III and were from children aged 4-52 months. All of these children had acute diarrhea associated with fever (83.3%, 10/12) and vomiting (66.7%, 8/12). Most of the cases occurred in August (58.3%, 7/12), 75% (9/12) of which having received the full vaccination scheme with Rotarix™. For the first time G12 was reported at relative high prevalence in Brazil. Our findings warrant further monitoring studies on the molecular characterization of circulating RVA strains after rotavirus vaccine introduction in Brazil and elsewhere, since the occurrence of either unusual our emerging genotypes may pose a challenge to vaccination strategies.
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Affiliation(s)
- Mayara A O Neves
- Center for Biological and Health Sciences, University of State of Pará, Pará, Brazil
| | | | - Rita S U Silva
- Municipality Secretary of Health of Rio Branco, Acre, Brazil
| | - Alexandre C Linhares
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
| | - Luciana D Silva
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
| | - Yvone B Gabbay
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
| | - Mônica C M Silva
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
| | - Edvaldo C B Loureiro
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
| | - Luana S Soares
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
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Mayindou G, Ngokana B, Sidibé A, Moundélé V, Koukouikila-Koussounda F, Christevy Vouvoungui J, Kwedi Nolna S, Velavan TP, Ntoumi F. Molecular epidemiology and surveillance of circulating rotavirus and adenovirus in Congolese children with gastroenteritis. J Med Virol 2015; 88:596-605. [DOI: 10.1002/jmv.24382] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Gontran Mayindou
- Fondation Congolaise pour la Recherche Médicale; Brazzaville Republic of Congo
- Faculty of Health Sciences; Marien Ngouabi University; Brazzaville Republic of Congo
| | - Berge Ngokana
- Fondation Congolaise pour la Recherche Médicale; Brazzaville Republic of Congo
- Faculty of Health Sciences; Marien Ngouabi University; Brazzaville Republic of Congo
| | - Anissa Sidibé
- Fondation Congolaise pour la Recherche Médicale; Brazzaville Republic of Congo
- Faculty of Health Sciences; Marien Ngouabi University; Brazzaville Republic of Congo
| | - Victoire Moundélé
- Fondation Congolaise pour la Recherche Médicale; Brazzaville Republic of Congo
- Faculty of Health Sciences; Marien Ngouabi University; Brazzaville Republic of Congo
| | - Felix Koukouikila-Koussounda
- Fondation Congolaise pour la Recherche Médicale; Brazzaville Republic of Congo
- Faculty of Health Sciences; Marien Ngouabi University; Brazzaville Republic of Congo
| | - Jeannhey Christevy Vouvoungui
- Fondation Congolaise pour la Recherche Médicale; Brazzaville Republic of Congo
- Faculty of Health Sciences; Marien Ngouabi University; Brazzaville Republic of Congo
| | - Sylvie Kwedi Nolna
- Fondation Congolaise pour la Recherche Médicale; Brazzaville Republic of Congo
- Capacity for Leadership Excellence and Research; Yaoundé Cameroon
| | - Thirumalaisamy P. Velavan
- Fondation Congolaise pour la Recherche Médicale; Brazzaville Republic of Congo
- Institute for Tropical Medicine; University of Tübingen; Tübingen Germany
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale; Brazzaville Republic of Congo
- Faculty of Health Sciences; Marien Ngouabi University; Brazzaville Republic of Congo
- Institute for Tropical Medicine; University of Tübingen; Tübingen Germany
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Luchs A, Cilli A, Morillo SG, Ribeiro CD, Carmona RDCC, Timenetsky MDCST. Rotavirus genotypes and the indigenous children of Brazilian midwest in the vaccine era, 2008-2012: Footprints of animal genome. J Med Virol 2015; 87:1881-9. [PMID: 25963945 DOI: 10.1002/jmv.24241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2015] [Indexed: 01/28/2023]
Abstract
World group A rotavirus (RVA) surveillance data provides useful estimates of the disease burden, however, indigenous population might require special consideration. The aim of this study was to describe the results of G- and P-types from Brazilian native children ≤ 3 years. Furthermore, selected strains have been analyzed for the VP7, VP6, VP4, and NSP4 encoding genes in order to gain insight into genetic variability of Brazilian strains. A total of 149 samples, collected during 2008-2012, were tested for RVA using ELISA and PAGE, following by RT-PCR and sequencing. RVA infection was detected in 8.7% of samples (13/149). Genotype G2P[4] was detected in 2008 and 2010, G8P[6] in 2009, and G3P[8] in 2011. The phylogenetic analysis of the VP7 and VP4 genes grouped the Brazilian G2P[4] and G3P[8] strains within the lineages currently circulating in humans worldwide. However, the phylogenetic analysis of the VP6 and NSP4 from the Brazilian G2P[4] strains, and the VP7 and NSP4 from the Brazilian G3P[8] strains suggest a distant common ancestor with different animal strains (bovine, caprine, and porcine). The epidemiological and genetic information obtained in the present study is expected to provide an updated understanding of RVA genotypes circulating in the native infant population, and to formulate policies for the use of RVA vaccines in indigenous Brazilian people. Moreover, these results highlight the great diversity of human RVA strains circulating in Brazil, and an in-depth surveillance of human and animal RVA will lead to a better understanding of the complex dynamics of RVA evolution.
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Affiliation(s)
- Adriana Luchs
- Enteric Disease Laboratory, Adolfo Lutz Institute, São Paulo, Brazil
| | - Audrey Cilli
- Enteric Disease Laboratory, Adolfo Lutz Institute, São Paulo, Brazil
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Aly M, Al Khairy A, Al Johani S, Balkhy H. Unusual rotavirus genotypes among children with acute diarrhea in Saudi Arabia. BMC Infect Dis 2015; 15:192. [PMID: 25884670 PMCID: PMC4407833 DOI: 10.1186/s12879-015-0923-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 04/01/2015] [Indexed: 02/08/2023] Open
Abstract
Background Human rotavirus A (human RV-A) is the most common cause of viral gastroenteritis in infants. The objective of the study was to characterize the G and P genotypes among clinical rotavirus isolates from children with acute diarrhea admitted to a tertiary care hospital in Riyadh, Saudi Arabia. Methods From 2011 to 2012, 541 pediatric patients with acute diarrhea were tested for rotavirus infection. RNA extractions from the fecal specimens were done by commercial kit. RT-PCR and sequencing techniques were used to detect the prevalent genotypes. Phylogenetic analysis by Maximum Likelihood method was used to study the clustering of the circulating genotypes. Results The data showed that 171/541 (31.6%) faecal samples were positive for human RVA and majority were children aged below 2 years. From the G and P [types] detected it was seen that (a) 171 minus 43 ie. 128 rotavirus positives were G typed successfully (b) 171 minus 20 ie. 151 rotavirus positives were P typed successfully; (c) overall G [P] nature was determined for 113 rotavirus positives out of 171. VP4 genotyping showed that majority of the positives 146/151 (96.7%) were P [8]; 4/151 (2.6%) were P [4]; 1/151 (0.66%) was P [6]. The dominant strains included G1P [8] 70/113 (61.9%); G9P [8] 19/113 (16.8%); G12P [8] 7/113 (6.2%) and G3P [8] 5/113 (4.4%) while the uncommon strains detected from Saudi Arabia during the study were G1P [4] 1/113 (0.88%) and G12P [6] 1/113 (0.88%). Phylogenetic tree, based on VP4/VP7 sequence analysis, revealed that G1P [8] was distinctly related to homologous strains included in human RV-A vaccine strains. Nevertheless, the uncommon genotypes G1P [4] and G12P [6] were clustered with isolates from other countries such as Bangladesh, China, Japan, Thailand and Philippines. Conclusions More studies will be required to further focus on newly emerging genotypes in our region together with the seasonality of rotavirus infection in the region, especially after January 2013 when the rotavirus vaccination has become part of routine childhood immunizations.
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Affiliation(s)
- Mahmoud Aly
- King Abdullah International Medical Research Centre, P.O. Box 22490, Riyadh, 11426, Kingdom of Saudi Arabia. .,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
| | - Aisha Al Khairy
- King Abdullah International Medical Research Centre, P.O. Box 22490, Riyadh, 11426, Kingdom of Saudi Arabia.
| | - Sameera Al Johani
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia. .,Department of Microbiology, King Abdulaziz Medical City, Riyadh, Saudi Arabia.
| | - Hanan Balkhy
- King Abdullah International Medical Research Centre, P.O. Box 22490, Riyadh, 11426, Kingdom of Saudi Arabia. .,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia. .,Department of Infection Prevention and Control, King Abdulaziz Medical City, Riyadh, Saudi Arabia.
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Zeller M, Heylen E, Damanka S, Pietsch C, Donato C, Tamura T, Kulkarni R, Arora R, Cunliffe N, Maunula L, Potgieter C, Tamim S, Coster SD, Zhirakovskaya E, Bdour S, O'Shea H, Kirkwood CD, Seheri M, Nyaga MM, Mphahlele J, Chitambar SD, Dagan R, Armah G, Tikunova N, Van Ranst M, Matthijnssens J. Emerging OP354-Like P[8] Rotaviruses Have Rapidly Dispersed from Asia to Other Continents. Mol Biol Evol 2015; 32:2060-71. [PMID: 25858434 DOI: 10.1093/molbev/msv088] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The majority of human group A rotaviruses possess the P[8] VP4 genotype. Recently, a genetically distinct subtype of the P[8] genotype, also known as OP354-like P[8] or lineage P[8]-4, emerged in several countries. However, it is unclear for how long the OP354-like P[8] gene has been circulating in humans and how it has spread. In a global collaborative effort 98 (near-)complete OP354-like P[8] VP4 sequences were obtained and used for phylogeographic analysis to determine the viral migration patterns. During the sampling period, 1988-2012, we found that South and East Asia acted as a source from which strains with the OP354-like P[8] gene were seeded to Africa, Europe, and North America. The time to the most recent common ancestor (TMRCA) of all OP354-like P[8] genes was estimated at 1987. However, most OP354-like P[8] strains were found in three main clusters with TMRCAs estimated between 1996 and 2001. The VP7 gene segment of OP354-like P[8] strains showed evidence of frequent reassortment, even in localized epidemics, suggesting that OP354-like P[8] genes behave in a similar manner on the evolutionary level as other P[8] subtypes. The results of this study suggest that OP354-like P[8] strains have been able to disperse globally in a relatively short time period. This, in combination with a relatively large genetic distance to other P[8] subtypes, might result in a lower vaccine effectiveness, underscoring the need for a continued surveillance of OP354-like P[8] strains, especially in countries where rotavirus vaccination programs are in place.
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Affiliation(s)
- Mark Zeller
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Elisabeth Heylen
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Susan Damanka
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | | | - Celeste Donato
- Enteric Virus Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Tsutomu Tamura
- Department of Virology, Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata, Japan
| | - Ruta Kulkarni
- Enteric Viruses Group, National Institute of Virology, Pune, Maharashtra, India
| | - Ritu Arora
- Enteric Viruses Group, National Institute of Virology, Pune, Maharashtra, India
| | - Nigel Cunliffe
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Leena Maunula
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Christiaan Potgieter
- Department of Biochemistry, Centre for Human Metabonomics, North-West University, Potchefstroom, South Africa Deltamune (Pty) Ltd, Lyttelton, Centurion, South Africa
| | - Sana Tamim
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sarah De Coster
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Elena Zhirakovskaya
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Salwa Bdour
- Department of Biological Sciences, Faculty of Science, The University of Jordan, Amman, Jordan
| | - Helen O'Shea
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - Carl D Kirkwood
- Enteric Virus Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Mapaseka Seheri
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Martin Monene Nyaga
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Jeffrey Mphahlele
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Shobha D Chitambar
- Enteric Viruses Group, National Institute of Virology, Pune, Maharashtra, India
| | - Ron Dagan
- Soroka University Medical Center and the Faculty of Health Sciences, Ben-Gurion University of Negev, Beer Sheva, Israel
| | - George Armah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Nina Tikunova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Marc Van Ranst
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
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Silva FDF, Espinoza LRL, Tonietti PO, Barbosa BRP, Gregori F. Whole-genomic analysis of 12 porcine group A rotaviruses isolated from symptomatic piglets in Brazil during the years of 2012-2013. INFECTION GENETICS AND EVOLUTION 2015; 32:239-54. [PMID: 25796358 DOI: 10.1016/j.meegid.2015.03.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 11/18/2022]
Abstract
Group A rotaviruses (RVAs) are leading causes of viral diarrhea in children and in the young of many animal species, particularly swine. In the current study, porcine RVAs were found in fecal specimens from symptomatic piglets on 4 farms in Brazil during the years of 2012-2013. Using RT-PCR, Sanger nucleotide sequencing, and phylogenetic analyses, the whole genomes of 12 Brazilian porcine RVA strains were analyzed. Specifically, the full-length open reading frame (ORF) sequences were determined for the NSP2-, NSP3-, and VP6-coding genes, and partial ORF sequences were determined for the VP1-, VP2-, VP3-, VP4-, VP7-, NSP1-, NSP4-, and NSP5/6-coding genes. The results indicate that all 12 strains had an overall porcine-RVA-like backbone with most segments being designated as genotype 1, with the exception of the VP6- and NSP1-coding genes, which were genotypes I5 and A8, respectively. These results add to our growing understanding of porcine RVA genetic diversity and will provide a platform for monitoring the role of animals as genetic reservoirs of emerging human RVAs strains.
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Affiliation(s)
- Fernanda D F Silva
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, 05508-270 São Paulo, SP, Brazil.
| | - Luis R L Espinoza
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, 05508-270 São Paulo, SP, Brazil.
| | - Paloma O Tonietti
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, 05508-270 São Paulo, SP, Brazil.
| | - Bruna R P Barbosa
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, 05508-270 São Paulo, SP, Brazil.
| | - Fabio Gregori
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, 05508-270 São Paulo, SP, Brazil.
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Durmaz R, Kalaycioglu AT, Acar S, Bakkaloglu Z, Karagoz A, Korukluoglu G, Ertek M, Torunoglu MA. Prevalence of rotavirus genotypes in children younger than 5 years of age before the introduction of a universal rotavirus vaccination program: report of rotavirus surveillance in Turkey. PLoS One 2014; 9:e113674. [PMID: 25437502 PMCID: PMC4249891 DOI: 10.1371/journal.pone.0113674] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/29/2014] [Indexed: 02/01/2023] Open
Abstract
Background Group A rotaviruses are the most common causative agent of acute gastroenteritis among children less than 5 years of age throughout the world. This sentinel surveillance study was aimed to obtain baseline data on the rotavirus G and P genotypes across Turkey before the introduction of a universal rotavirus vaccination program. Methods Rotavirus antigen-positive samples were collected from 2102 children less than 5 years of age who attended hospitals participating in the Turkish Rotavirus Surveillance Network. Rotavirus antigen was detected in the laboratories of participating hospitals by commercial serological tests such as latex agglutination, immunochromatographic test or enzyme immunoassay. Rotavirus G and P genotypes were determined by reverse transcription polymerase chain reaction (RT-PCR) using consensus primers detecting the VP7 and VP4 genes, followed by semi-nested type-specific multiplex PCR. Results RT-PCR found rotavirus RNA in 1644 (78.2%) of the samples tested. The highest rate of rotavirus positivity (38.7%) was observed among children in the 13 to 24 month age group, followed by children in the age group of 25 to 36 months (28.3%). A total of eight different G types, six different P types, and 42 different G–P combinations were obtained. Four common G types (G1, G2, G3, and G9) and two common P types (P[8] and P[4]) accounted for 95.1% and 98.8% of the strains, respectively. G9P[8] was the most common G/P combination found in 40.5% of the strains followed by G1P[8] (21.6%), G2P[8] (9.3%), G2P[4] (6.5%), G3P[8] (3.5%), and finally, G4P[8] (3.4%). These six common genotypes included 83.7% of the strains tested in this study. The rate of uncommon genotypes was 14%. Conclusion The majority of the strains analyzed belonged to the G1–G4 and G9 genotypes, suggesting high coverage of current rotavirus vaccines. This study also demonstrates a dramatic increase in G9 genotype across the country.
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Affiliation(s)
- Riza Durmaz
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
- Department of Medical Microbiology, Faculty of Medicine Yıldırım Beyazıt University, Ankara, Turkey
- * E-mail:
| | - Atila Taner Kalaycioglu
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Sumeyra Acar
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Zekiye Bakkaloglu
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Alper Karagoz
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Gulay Korukluoglu
- Virology Reference Central Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Mustafa Ertek
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Mehmet Ali Torunoglu
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
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Gómez MM, Carvalho-Costa FA, de Mello Volotão E, Rose TL, da Silva MFM, Fialho AM, Assis RMS, da Silva Ribeiro de Andrade J, Sá ACC, Zeller M, Heylen E, Matthijnssens J, Leite JPG. Prevalence and genomic characterization of G2P[4] group A rotavirus strains during monovalent vaccine introduction in Brazil. INFECTION GENETICS AND EVOLUTION 2014; 28:486-94. [DOI: 10.1016/j.meegid.2014.09.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 11/15/2022]
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Degiuseppe JI, Parra GI, Stupka JA. Genetic diversity of G3 rotavirus strains circulating in Argentina during 1998-2012 assessed by full genome analyses. PLoS One 2014; 9:e110341. [PMID: 25337915 PMCID: PMC4206407 DOI: 10.1371/journal.pone.0110341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 09/19/2014] [Indexed: 12/28/2022] Open
Abstract
Seasonal shifts in the predominant strains and the periodic emergence of new strains are epidemiological features of human rotaviruses. After the sporadic detection in two samples in 1998, G3P[8] strains reemerged as the predominant rotavirus during 2008-2009 in Argentina. Notably, in 2011 6.3% (37/587) of samples presented the G3P[6] genotypes, which coincided with the recent detection of G3P[6] and G2P[6] strains in South America and Europe. Analyses of the 11 gene segments of four G3P[8] and two G3P[6] strains revealed that G3P[8] strains detected a decade apart (1998 and 2009) presented minor differences, while the G3P[6] strains presented a complete different genomic constellation albeit showing a similar VP7 gene. This study provides insights in the dynamics and evolution of one of the genotypes with the wider range of hosts and inter-species transmission potential.
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Affiliation(s)
- Juan Ignacio Degiuseppe
- Laboratorio de Gastroenteritis Virales, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Gabriel Ignacio Parra
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Juan Andrés Stupka
- Laboratorio de Gastroenteritis Virales, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
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Kim JS, Kim HS, Hyun J, Kim HS, Song W, Lee KM, Shin SH. Analysis of rotavirus genotypes in Korea during 2013: an increase in the G2P[4] genotype after the introduction of rotavirus vaccines. Vaccine 2014; 32:6396-402. [PMID: 25312273 DOI: 10.1016/j.vaccine.2014.09.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 09/18/2014] [Accepted: 09/29/2014] [Indexed: 01/15/2023]
Abstract
BACKGROUND Group A rotavirus is the leading cause of acute gastroenteritis in children worldwide. We investigated G and P genotypes of group A rotavirus strains isolated from patients during 2013 and investigated which genotypes were identified from vaccinated patients. METHODS From January to December 2013, 2235 fecal specimens were tested for rotavirus antigen, of which 374 specimens (16.7%) showed positive results. Strains from 288 rotavirus-positive specimens were genotyped using PCR and sequencing, and individual patients' corresponding vaccine histories were investigated through the Korean Center for Disease Control website. RESULTS G2 (22.6%) and P[4] (24.0%) were the most frequently identified G and P genotypes, respectively; accordingly, G2P[4] (19.8%) was the most prevalent G/P genotype observed in this period. G4P[6] (10.1%) was the second most prevalent G/P genotype and was mostly detected in neonates. Other genotypes, G1P[8], G9P[8], G1P[6], and G3P[6], were also detected. Of 288 rotavirus-positive specimens, 48 specimens were obtained from previously vaccinated patients. G2P[4] was also the genotype most frequently isolated from vaccinated patients. VP7 epitope analysis of G1P[8] and G2P[4] strains showed at least one amino acid differences in comparison with Rotarix and RotaTeq vaccine strains. The genotypic distribution of rotavirus strains in Korea has been shown temporal and geographical differences. CONCLUSION This study showed that G2P[4] was the genotype most frequently isolated from both vaccinated and unvaccinated patients in Korea during 2013. However, it is unclear whether the change of predominant genotype is due to the effect of vaccination or due to natural variation.
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Affiliation(s)
- Jae-Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea.
| | - Jungwon Hyun
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea
| | - Han-Sung Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea
| | - Kyu Man Lee
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea
| | - Seon-Hee Shin
- Department of Pediatrics, Hallym University College of Medicine, Republic of Korea
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Review of global rotavirus strain prevalence data from six years post vaccine licensure surveillance: is there evidence of strain selection from vaccine pressure? INFECTION GENETICS AND EVOLUTION 2014; 28:446-61. [PMID: 25224179 DOI: 10.1016/j.meegid.2014.08.017] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 11/23/2022]
Abstract
Comprehensive reviews of pre licensure rotavirus strain prevalence data indicated the global importance of six rotavirus genotypes, G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]. Since 2006, two vaccines, the monovalent Rotarix (RV1) and the pentavalent RotaTeq (RV5) have been available in over 100 countries worldwide. Of these, 60 countries have already introduced either RV1 or RV5 in their national immunization programs. Post licensure vaccine effectiveness is closely monitored worldwide. This review aimed at describing the global changes in rotavirus strain prevalence over time. The genotype distribution of the nearly 47,000 strains that were characterized during 2007-2012 showed similar picture to that seen in the preceding period. An intriguing finding was the transient predominance of heterotypic strains, mainly in countries using RV1. Unusual and novel antigen combinations continue to emerge, including some causing local outbreaks, even in vaccinated populations. In addition, vaccine strains have been found in both vaccinated infants and their contacts and there is evidence for genetic interaction between vaccine and wild-type strains. In conclusion, the post-vaccine introduction strain prevalence data do not show any consistent pattern indicative of selection pressure resulting from vaccine use, although the increased detection rate of heterotypic G2P[4] strains in some countries following RV1 vaccination is unusual and this issue requires further monitoring.
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Victoria M, Tort LFL, García M, Lizasoain A, Maya L, Leite JPG, Miagostovich MP, Cristina J, Colina R. Assessment of gastroenteric viruses from wastewater directly discharged into Uruguay River, Uruguay. FOOD AND ENVIRONMENTAL VIROLOGY 2014; 6:116-24. [PMID: 24777819 DOI: 10.1007/s12560-014-9143-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 03/24/2014] [Indexed: 05/02/2023]
Abstract
The aim of this study was to assess the viral contamination of group A rotavirus (RVA), norovirus (NoV), and human astrovirus (HAstV) in sewage directly discharged into Uruguay River and to characterize RVA genotypes circulating in Uruguay. For this purpose, sewage samples (n = 96) were collected biweekly from March 2011 to February 2012 in four Uruguayan cities: Bella Unión, Salto, Paysandú, and Fray Bentos. Each sample was concentrated by ultracentrifugation method. Qualitative and quantitative RT-PCR for RVA, NoV, and HAstV were performed. A wide dissemination of gastroenteric viruses was observed in the sewage samples analyzed with 80% of positivity, being NoV (51%) the most frequently detected followed by RVA with a frequency of 49% and HAstV with 45%. Genotypes of RVA were typed using multiplex semi-nested RT-PCR as follows: P[8] (n = 15), P[4] (n = 8), P[10] (n = 1), P[11] (n = 1), G2 (n = 29), and G3 (n = 2). The viral load ranged from 10(3) to 10(7) genomic copies/liter, and they were detected roughly with the same frequency in all participant cities. A peak of RVA and HAstV detection was observed in colder months (June to September), whereas no seasonality was observed for NoV. This study demonstrates for the first time, the high degree of gastroenteric viral contamination in the country; highlighting the importance of developing these analyses as a tool to determine the viral contamination in this hydrographic boundary region used by the local populations for recreation and consumption, establishing an elevated risk of gastroenteric diseases for human health.
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Affiliation(s)
- M Victoria
- Laboratorio de Virología Molecular - Regional Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
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