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Fujii Y, Tsugawa T, Fukuda Y, Adachi S, Honjo S, Akane Y, Kondo K, Sakai Y, Tanaka T, Sato T, Higasidate Y, Kubo N, Mori T, Kato S, Hamada R, Kikuchi M, Tahara Y, Nagai K, Ohara T, Yoshida M, Nakata S, Noguchi A, Kikuchi W, Hamada H, Tokutake-Hirose S, Fujimori M, Muramatsu M. Molecular evolutionary analysis of novel NSP4 mono-reassortant G1P[8]-E2 rotavirus strains that caused a discontinuous epidemic in Japan in 2015 and 2018. Front Microbiol 2024; 15:1430557. [PMID: 39050631 PMCID: PMC11266183 DOI: 10.3389/fmicb.2024.1430557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/17/2024] [Indexed: 07/27/2024] Open
Abstract
In the 2010s, several unusual rotavirus strains emerged, causing epidemics worldwide. This study reports a comprehensive molecular epidemiological study of rotaviruses in Japan based on full-genome analysis. From 2014 to 2019, a total of 489 rotavirus-positive stool specimens were identified, and the associated viral genomes were analyzed by next-generation sequencing. The genotype constellations of those strains were classified into nine patterns (G1P[8] (Wa), G1P[8]-E2, G1P[8] (DS-1), G2P[4] (DS-1), G3P[8] (Wa), G3P[8] (DS-1), G8P[8] (DS-1), G9P[8] (Wa), and G9P[8]-E2). The major prevalent genotype differed by year, comprising G8P[8] (DS-1) (37% of that year's isolates) in 2014, G1P[8] (DS-1) (65%) in 2015, G9P[8] (Wa) (72%) in 2016, G3P[8] (DS-1) (66%) in 2017, G1P[8]-E2 (53%) in 2018, and G9P[8] (Wa) (26%) in 2019. The G1P[8]-E2 strains (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1) isolated from a total of 42 specimens in discontinuous years (2015 and 2018), which were the newly-emerged NSP4 mono-reassortant strains. Based on the results of the Bayesian evolutionary analyses, G1P[8]-E2 and G9P[8]-E2 were hypothesized to have been generated from distinct independent inter-genogroup reassortment events. The G1 strains detected in this study were classified into multiple clusters, depending on the year of detection. A comparison of the predicted amino acid sequences of the VP7 epitopes revealed that the G1 strains detected in different years encoded VP7 epitopes harboring distinct mutations. These mutations may be responsible for immune escape and annual changes in the prevalent strains.
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Affiliation(s)
- Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Yuya Fukuda
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Shuhei Adachi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Saho Honjo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Yusuke Akane
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Yoshiyuki Sakai
- Department of Pediatrics, Hakodate Municipal Hospital, Hokkaido, Japan
| | - Toju Tanaka
- Department of Pediatrics, National Hospital Organization Hokkaido Medical Center, Hokkaido, Japan
| | - Toshiya Sato
- Department of Pediatrics, Iwamizawa Municipal General Hospital, Hokkaido, Japan
| | - Yoshihito Higasidate
- Department of Pediatrics, Japan Community Health Care Organization Sapporo Hokushin Hospital, Hokkaido, Japan
| | - Noriaki Kubo
- Department of Pediatrics, Japan Red Cross Urakawa Hospital, Hokkaido, Japan
| | - Toshihiko Mori
- Department of Pediatrics, NTT Medical Center Sapporo, Hokkaido, Japan
| | - Shinsuke Kato
- Department of Pediatrics, Rumoi City Hospital, Hokkaido, Japan
| | - Ryo Hamada
- Department of Pediatrics, Rumoi City Hospital, Hokkaido, Japan
| | - Masayoshi Kikuchi
- Department of Pediatrics, Sunagawa City Medical Center, Hokkaido, Japan
| | - Yasuo Tahara
- Department of Pediatrics, Steel Memorial Muroran Hospital, Hokkaido, Japan
| | - Kazushige Nagai
- Department of Pediatrics, Takikawa Municipal Hospital, Hokkaido, Japan
| | - Toshio Ohara
- Department of Pediatrics, Tomakomai City Hospital, Hokkaido, Japan
| | - Masaki Yoshida
- Department of Pediatrics, Yakumo General Hospital, Hokkaido, Japan
| | | | - Atsuko Noguchi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, Japan
| | - Wakako Kikuchi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiromichi Hamada
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, Japan
| | - Shoko Tokutake-Hirose
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, Japan
| | - Makoto Fujimori
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Infectious Disease Research, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Hyogo, Japan
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Amin AB, Cates JE, Liu Z, Wu J, Ali I, Rodriguez A, Panjwani J, Tate JE, Lopman BA, Parashar UD. Rotavirus Genotypes in the Postvaccine Era: A Systematic Review and Meta-analysis of Global, Regional, and Temporal Trends by Rotavirus Vaccine Introduction. J Infect Dis 2024; 229:1460-1469. [PMID: 37738554 PMCID: PMC11095550 DOI: 10.1093/infdis/jiad403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Even moderate differences in rotavirus vaccine effectiveness against nonvaccine genotypes may exert selective pressures on circulating rotaviruses. Whether this vaccine effect or natural temporal fluctuations underlie observed changes in genotype distributions is unclear. METHODS We systematically reviewed studies reporting rotavirus genotypes from children <5 years of age globally between 2005 and 2023. We compared rotavirus genotypes between vaccine-introducing and nonintroducing settings globally and by World Health Organization (WHO) region, calendar time, and time since vaccine introduction. RESULTS Crude pooling of genotype data from 361 studies indicated higher G2P[4], a nonvaccine genotype, prevalence in vaccine-introducing settings, both globally and by WHO region. This difference did not emerge when examining genotypes over time in the Americas, the only region with robust longitudinal data. Relative to nonintroducing settings, G2P[4] detections were more likely in settings with recent introduction (eg, 1-2 years postintroduction adjusted odds ratio [aOR], 4.39; 95% confidence interval [CI], 2.87-6.72) but were similarly likely in settings with more time elapsed since introduction, (eg, 7 or more years aOR, 1.62; 95% CI, .49-5.37). CONCLUSIONS When accounting for both regional and temporal trends, there was no substantial evidence of long-term vaccine-related selective pressures on circulating genotypes. Increased prevalence of G2P[4] may be transient after rotavirus vaccine introduction.
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Affiliation(s)
- Avnika B Amin
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Jordan E Cates
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Zihao Liu
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Joanne Wu
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Iman Ali
- Centers for Disease Control and Prevention Foundation, Atlanta, Georgia, USA
| | - Alexia Rodriguez
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Junaid Panjwani
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jacqueline E Tate
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Benjamin A Lopman
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Umesh D Parashar
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Gutierrez MB, Arantes I, Bello G, Berto LH, Dutra LH, Kato RB, Fumian TM. Emergence and dissemination of equine-like G3P[8] rotavirus A in Brazil between 2015 and 2021. Microbiol Spectr 2024; 12:e0370923. [PMID: 38451227 PMCID: PMC10986506 DOI: 10.1128/spectrum.03709-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/22/2024] [Indexed: 03/08/2024] Open
Abstract
Rotavirus A (RVA) is a major cause of acute gastroenteritis globally that is classically genotyped by its two immunodominant outer capsid proteins, VP7 (G-) and VP4 (P-). Recent evidence suggests that the reassortant equine-like G3P[8] strain played a substantial role in RVA transmission in Brazil since 2015. To understand its global emergence and dissemination in Brazilian territory, stool samples collected from 11 Brazilian states (n = 919) were genotyped by RT-qPCR and proceeded to sequence the VP7 gene (n = 102, 79 being newly generated) of the G3P[8] samples with pronounced viral loads. Our phylogenetic genotyping showed that G3P[8] became the dominant strain in Brazil between 2017 and 2020, with equine-like variants representing 75%-100% of VP7 samples in this period. A Bayesian discrete phylogeographic analysis strongly suggests that the equine-like G3P[8] strain originated in Asia during the early 2010s and subsequently spread to Europe, the Caribbean, and South America. Multiple introductions were detected in Brazil between 2014 and 2017, resulting in five national clusters. The reconstruction of the effective population size of the largest Brazilian cluster showed an expansion until 2017, followed by a plateau phase until 2019 and subsequent contraction. Our study also supports that most mutations fixed during equine-like G3P[8] evolution were synonymous, suggesting that adaptive evolution was not an important driving force during viral dissemination in humans, potentially increasing its susceptibility to acquired immunity. This research emphasizes the need for comprehensive rotavirus genomic surveillance that allows close monitoring of its ever-shifting composition and informs more effective public health policies.IMPORTANCEOur original article demonstrated the origin and spread in a short time of equine-like G3P[8] in Brazil and the world. Due to its segmented genome, it allows numerous mechanisms including genetic drift and reassortment contribute substantially to the genetic diversity of rotavirus. Although the effectiveness and increasing implementation of vaccination have not been questioned, a matter of concern is its impact on the emergence of escape mutants or even the spread of unusual strains of zoonotic transmission that could drive epidemic patterns worldwide. This research emphasizes the need for comprehensive rotavirus genomic surveillance, which could facilitate the formulation of public policies aimed at preventing and mitigating its transmission.
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Affiliation(s)
| | - Ighor Arantes
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Lúcia Helena Berto
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Leonardo Hermes Dutra
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Rodrigo Bentes Kato
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
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Fukuda Y, Kusuhara H, Takai-Todaka R, Haga K, Katayama K, Tsugawa T. Human transmission and outbreaks of feline-like G6 rotavirus revealed with whole-genome analysis of G6P[9] feline rotavirus. J Med Virol 2024; 96:e29565. [PMID: 38558056 DOI: 10.1002/jmv.29565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/01/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
Group A rotaviruses (RVAs) are generally highly species-specific; however, some strains infect across species. Feline RVAs sporadically infect humans, causing gastroenteritis. In 2012 and 2013, rectal swab samples were collected from 61 asymptomatic shelter cats at a public health center in Mie Prefecture, Japan, to investigate the presence of RVA and any association with human infections. The analysis identified G6P[9] strains in three cats and G3P[9] strains in two cats, although no feline RVA sequence data were available for the former. A whole-genome analysis of these G6P[9] strains identified the genotype constellation G6-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3. The nucleotide identity among these G6P[9] strains exceeded 99.5% across all 11 gene segments, indicating the circulation of this G6P[9] strain among cats. Notably, strain RVA/Human-wt/JPN/KF17/2010/G6P[9], previously detected in a 3-year-old child with gastroenteritis, shares high nucleotide identity (>98%) with Mie20120017f, the representative G6P[9] strain in this study, across all 11 gene segments, confirming feline RVA infection and symptomatic presentation in this child. The VP7 gene of strain Mie20120017f also shares high nucleotide identity with other sporadically reported G6 RVA strains in humans. This suggests that feline-origin G6 strains as the probable source of these sporadic G6 RVA strains causing gastroenteritis in humans globally. Moreover, a feline-like human G6P[8] strain circulating in Brazil in 2022 was identified, emphasizing the importance of ongoing surveillance to monitor potential global human outbreaks of RVA.
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Affiliation(s)
- Yuya Fukuda
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Hajime Kusuhara
- Mie Prefecture Health and Environment Research Institute, Mie, Japan
| | - Reiko Takai-Todaka
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kei Haga
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
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Weldegebriel GG, Okot C, Majingo N, Oumer NJ, Mokomane M, Monyatsi NJ, Phologolo TM, Visagie L, Moakofh K, Seobakeng M, Masresha BG, Seheri M, Mihigo R, Mwenda JM. Resurgent rotavirus diarrhoea outbreak five years after introduction of rotavirus vaccine in Botswana, 2018. Vaccine 2024; 42:1534-1541. [PMID: 38331661 PMCID: PMC10953700 DOI: 10.1016/j.vaccine.2024.01.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/20/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024]
Abstract
INTRODUCTION Botswana had a resurgent diarrhea outbreak in 2018, mainly affecting children under five years old. Botswana introduced rotavirus vaccine (RotarixTM) into the national immunization programme in July 2012. Official rotavirus vaccine coverage estimates averaged 77.2% over the five years following introduction. MATERIALS AND METHODS The outbreak was investigated using multiple data sources, including stool laboratory testing, immunization data review, water assessment, and vaccine storage assessment. We reviewed official reports of the routine immunization data from 2013 to 2017 and compared district-level rotavirus vaccine coverage with district-level attack rates during the outbreak. RESULTS During the outbreak, a total of 228 stool samples were tested at the national health laboratory and 152 (67%) of the specimens were positive for rotavirus. A portion of adequate samples (80) were selected for referral to the Regional Reference Lab. The laboratory testing of 80 samples at the Regional Reference Laboratory in South Africa showed that 91% of the stool samples were positive for rotavirus, and the dominant strain 47/80 (58.7%) was G3P[8]. The immunization data showed that rotavirus vaccine coverage varied widely among districts, and there was no correlation between districts with high attack rates and those with low immunization coverage. Water assessment showed that some water sources were contaminated with E Coli. There was no problem with vaccine storage. CONCLUSION The outbreak was caused by rotavirus G3P[8], a strain that was not common in the country prior to the outbreak. Despite the significant pressure and anxiety that outbreaks cause, the number of diarrhea cases and deaths were less compared to pre-vaccine era due to the impact of vaccination. This highlights the need for continuous implementation of high impact child survival interventions.
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Affiliation(s)
- Goitom G Weldegebriel
- World Health Organization, Intercountry Support Team, East and Southern Africa, Harare, Zimbabwe.
| | - Charles Okot
- World Health Organization African Regional Office, Brazzaville, Congo
| | | | | | | | | | | | | | | | | | - Balcha G Masresha
- World Health Organization African Regional Office, Brazzaville, Congo
| | - Mapaseka Seheri
- Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Richard Mihigo
- World Health Organization African Regional Office, Brazzaville, Congo
| | - Jason M Mwenda
- World Health Organization African Regional Office, Brazzaville, Congo
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Li Q, Wang Z, Jiang J, He B, He S, Tu C, Guo Y, Gong W. Outbreak of piglet diarrhea associated with a new reassortant porcine rotavirus B. Vet Microbiol 2024; 288:109947. [PMID: 38101077 DOI: 10.1016/j.vetmic.2023.109947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
Rotavirus B (RVB) is a causative agent leading to acute viral gastroenteritis diarrhea in both children and young animals, and has been commonly detected in piglets. In order to determine the causative agent of diarrheal outbreak occurring in December 2022 in piglets from a pig herd in Luoyang, Henan province of China, four common viral pathogens causing piglet diarrhea-three coronaviruses and rotavirus A (RVA) were first tested and found negative, therefore metagenomic sequencing was performed to explore other potential pathogens in the diarrheal samples. Unexpectedly, the most abundant viral reads mapped to RVB, and were de novo assembled to complete 11 viral gene segments. Sequence comparisons revealed that 5 gene segments encoding VP1, VP2, VP3, NSP3 and NSP4 of RVB strain designated as HNLY-2022 are most closely related to RVB strains derived from herbivores with low nucleotide similarities of 65.7-75.3%, and the remaining segments were relatively close to porcine RVB strains with the VP4 gene segment showing very low nucleotide identity (65.0%) with reference strains, indicating HNLY-2022 is a new reassortant RVB strain. Based on the previously proposed genotype classification criterion, the genotype constellation of RVB strain HNLY-2022 is G6-P[6]-I4-R6-C6-M6-A7-N5-T7-E5-H4 with more than half of the genotypes (P[6], R6, C6, M6, T7 and E5) newly reported. Therefore, the new reassortant RVB strain is the likely causative agent for the diarrheal outbreak of piglets occurred in China and more epidemiological studies should be conducted to monitor the spread of this newly identified porcine RVB strain.
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Affiliation(s)
- Qingxian Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Zunbao Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jianfeng Jiang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Biao He
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Sun He
- TECON Biopharmaceutical Co., Ltd., Urumqi 830000, China
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yidi Guo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Wenjie Gong
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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Morozova OV, Sashina TA, Epifanova NV, Velikzhanina EI, Novikova NA. Phylodynamic characteristics of reassortant DS-1-like G3P[8]-strains of rotavirus type A isolated in Nizhny Novgorod (Russia). Braz J Microbiol 2023; 54:2867-2877. [PMID: 37897627 PMCID: PMC10689624 DOI: 10.1007/s42770-023-01155-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Since 2013, there has been an increase in reports of the spread of a double intergroup reassortant strain of rotavirus type A (RVA) with the genotype G3P[8] and other genes belonging to the second genogroup I2-R2-C2-M2-A2-N2-T2-E2-H2. In our study, we provide a molecular genetic characterization of rotaviruses with genotype G3P[8]-I2 isolated in Nizhny Novgorod. In our study, we used RT-PCR, Sanger sequencing, RNA-PAGE methods. Phylogenetic and phylodynamic analysis were performed using the Bayesian approach. According to our study, there was a significant increase in the proportion of G3P[8] from 15% during the period of 2020-2021 to 53% during the period of 2021-2022 in Nizhny Novgorod, Russia. Phylogenetic analysis based on the VP4 gene revealed that DS-1-like RVAs isolated in Nizhny Novgorod belong to different clusters of the P[8]-3.1 lineage, with a level of variation ranging from 1.1% to 1.3%. Based on the VP6 gene, the equine-like RVAs identified by us carry genetic variants belonging to three distinct clusters of the lineage I2-V, with a variation level ranging from 2.0% to 4.5%. These data indicate the genotypic diversity of circulating DS-1-like G3 RVAs. Phylogenetic analysis of the VP7 gene allowed us to assign the isolates identified in our study to the G3-1 lineage. We estimated that the circulation of the most recent common ancestor of the spreading strains dates back to 2002. Additionally, we determined the typical level of mutations in the VP7 gene, which amounted to 2.14*10-3 substitutions/per site/per year.
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Affiliation(s)
- Olga V Morozova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia.
| | - T A Sashina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N V Epifanova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - E I Velikzhanina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N A Novikova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
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Cao M, Yuan F, Ma X, Ma J, Ma X, Chen H, Zhang W, Zhao J, Kuai W. Surveillance of human Group A rotavirus in Ningxia, China (2015-2021): Emergence and prevalence of G9P[8]-E2 and G3P[8]-E2 genotypes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105469. [PMID: 37331499 DOI: 10.1016/j.meegid.2023.105469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
BACKGROUND Group A rotaviruses (RVA) are the primary pathogens of acute gastroenteritis. Currently, two live attenuated RVA vaccines, LLR and RotaTeq, have been introduced into mainland China but are not included in the national immunization program. Because of the unknown genetic evolution of group A rotavirus in an all-age population in Ningxia, China, we monitored the epidemiological characteristics and circulating genotypes of RVA as a reference for developing vaccine strategies. METHODS We conducted seven years of consecutive surveillance of RVA based on stool samples from patients with acute gastroenteritis in sentinel hospitals in Ningxia, China, from 2015 to 2021. Reverse transcription quantitative polymerase chain reaction(RT-qPCR) was used to detect RVA in stool samples. Genotyping and phylogenetic analysis of VP7, VP4 and NSP4 genes were performed by reverse transcription-polymerase chain reaction(RT-PCR) and nucleotide sequence determination. RESULTS RVA was detected in 16.58% (1436/8662) of 8662 stool samples. The positive rates were 7.17% (201/2805) and 21.09% (1235/5857) in adults and children, respectively. The most affected age group was infants and children aged 12-23 months, with a positive rate of 29.53% (p < 0.05). A significant winter/spring seasonality was observed. 23.29% positive rate in 2020 was the highest in 7 years (p < 0.05). The region with the highest positive rate in the adult group was Yinchuan, and the children's group was Guyuan. A total of 9 genotype combinations were found to be distributed in Ningxia. The dominant genotype combinations in this region gradually changed from G9P[8]-E1, G3P[8]-E1, G1P[8]-E1 to G9P[8]-E1, G9P[8]-E2, and G3P[8]-E2 during these seven years. Rare strains (e.g., G9P[4]-E1, G3P[9]-E3 and G1P[8]-E2) were occasionally detected during the study. CONCLUSIONS During the study period, changes in the significant RVA circulating genotype combinations and the emergence of reassortment strains were observed, particularly the emergence and prevalence of G9P[8]-E2, G3P[8]-E2 reassortants in the region. These results indicate the importance of continuous monitoring of the molecular evolution and recombination characteristics of RVA, and should not be limited to G/P genotyping but should consider multi-gene fragment co-analysis and whole genome sequencing.
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Affiliation(s)
- Min Cao
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Fang Yuan
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Xueping Ma
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Jiangtao Ma
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Xuemin Ma
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Hui Chen
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Wei Zhang
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Jianhua Zhao
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Wenhe Kuai
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China.
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9
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Sashina TA, Velikzhanina EI, Morozova OV, Epifanova NV, Novikova NA. Detection and full-genotype determination of rare and reassortant rotavirus A strains in Nizhny Novgorod in the European part of Russia. Arch Virol 2023; 168:215. [PMID: 37524885 DOI: 10.1007/s00705-023-05838-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
Reassortant DS-1-like rotavirus A strains have been shown to circulate widely in many countries around the world. In Russia, the prevalence of such strains remains unclear due to the preferred use of the traditional binary classification system. In this work, we obtained partial sequence data from all 11 genome segments and determined the full-genotype constellations of rare and reassortant rotaviruses circulating in Nizhny Novgorod in 2016-2019. DS-1-like G3P[8] and G8P[8] strains were found, reflecting the global trend. Most likely, these strains were introduced into the territory of Russia from other countries but subsequently underwent further evolutionary changes locally. G3P[8], G9P[8], and G12P[8] Wa-like strains of subgenotypic lineages that are unusual for the territory of Russia were also identified. Reassortant G2P[8], G4P[4], and G9P[4] strains with one Wa-like gene (VP4 or VP7) on a DS-1-like backbone were found, and these apparently had a local origin. Feline-like G3P[9] and G6P[9] strains were found to be phylogenetically close to BA222 isolated from a cat in Italy but carried some traces of reassortment with human strains from Russia and other countries. Thus, full-genotype determination of rotavirus A strains in Nizhny Novgorod has clarified some questions related to their origin and evolution.
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Affiliation(s)
- Tatiana A Sashina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation.
| | - E I Velikzhanina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - O V Morozova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N V Epifanova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N A Novikova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
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10
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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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11
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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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12
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Mhango C, Banda A, Chinyama E, Mandolo JJ, Kumwenda O, Malamba-Banda C, Barnes KG, Kumwenda B, Jambo KC, Donato CM, Esona MD, Mwangi PN, Steele AD, Iturriza-Gomara M, Cunliffe NA, Ndze VN, Kamng’ona AW, Dennis FE, Nyaga MM, Chaguza C, Jere KC. Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi. Virus Evol 2023; 9:vead030. [PMID: 37305707 PMCID: PMC10256189 DOI: 10.1093/ve/vead030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/12/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
G3 rotaviruses rank among the most common rotavirus strains worldwide in humans and animals. However, despite a robust long-term rotavirus surveillance system from 1997 at Queen Elizabeth Central Hospital in Blantyre, Malawi, these strains were only detected from 1997 to 1999 and then disappeared and re-emerged in 2017, 5 years after the introduction of the Rotarix rotavirus vaccine. Here, we analysed representative twenty-seven whole genome sequences (G3P[4], n = 20; G3P[6], n = 1; and G3P[8], n = 6) randomly selected each month between November 2017 and August 2019 to understand how G3 strains re-emerged in Malawi. We found four genotype constellations that were associated with the emergent G3 strains and co-circulated in Malawi post-Rotarix vaccine introduction: G3P[4] and G3P[6] strains with the DS-1-like genetic backbone genes (G3-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2), G3P[8] strains with the Wa-like genetic backbone genes (G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1), and reassortant G3P[4] strains consisting of the DS-1-like genetic backbone genes and a Wa-like NSP2 (N1) gene (G3-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2). Time-resolved phylogenetic trees demonstrated that the most recent common ancestor for each ribonucleic acid (RNA) segment of the emergent G3 strains was between 1996 and 2012, possibly through introductions from outside the country due to the limited genetic similarity with G3 strains which circulated before their disappearance in the late 1990s. Further genomic analysis revealed that the reassortant DS-1-like G3P[4] strains acquired a Wa-like NSP2 genome segment (N1 genotype) through intergenogroup reassortment; an artiodactyl-like VP3 through intergenogroup interspecies reassortment; and VP6, NSP1, and NSP4 segments through intragenogroup reassortment likely before importation into Malawi. Additionally, the emergent G3 strains contain amino acid substitutions within the antigenic regions of the VP4 proteins which could potentially impact the binding of rotavirus vaccine-induced antibodies. Altogether, our findings show that multiple strains with either Wa-like or DS-1-like genotype constellations have driven the re-emergence of G3 strains. The findings also highlight the role of human mobility and genome reassortment events in the cross-border dissemination and evolution of rotavirus strains in Malawi necessitating the need for long-term genomic surveillance of rotavirus in high disease-burden settings to inform disease prevention and control.
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Affiliation(s)
- Chimwemwe Mhango
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Akuzike Banda
- Department of Computer Science, Faculty of Science, University of Malawi, Zomba 305205, Malawi
| | - End Chinyama
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Jonathan J Mandolo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Orpha Kumwenda
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Chikondi Malamba-Banda
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
- Department of Biological Sciences, Academy of Medical Sciences, Malawi University of Science and Technology, Thyolo 310105, Malawi
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Kayla G Barnes
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Benjamin Kumwenda
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Kondwani C Jambo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Celeste M Donato
- Enteric Diseases Group, Murdoch Children’s Research Institute, 50 Flemington Road, Parkville, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mathew D Esona
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa
| | - Peter N Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of Free State, Bloemfontein 9300, South Africa
| | - A Duncan Steele
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa
| | - Miren Iturriza-Gomara
- Centre for Vaccine Innovation and Access, Program for Appropriate Technology in Health (PATH), Geneva 1218, Switzerland
| | - Nigel A Cunliffe
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool L69 7BE, UK
| | - Valentine N Ndze
- Faculty of Health Sciences, University of Buea, PO Box 63, Buea, Cameroon
| | - Arox W Kamng’ona
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Francis E Dennis
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, P. O. Box LG 581, Legon, Ghana
| | | | - Chrispin Chaguza
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut 06510, USA
- NIHR Mucosal Pathogens Research Unit, Division of Infection and Immunity, University College London, London WC1E 6BT, UK
- Yale Institute for Global Health, Yale University, New Haven, Connecticut 06510, USA
| | - Khuzwayo C Jere
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool L69 7BE, UK
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of Free State, Bloemfontein 9300, South Africa
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13
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Gutierrez MB, de Assis RMS, Arantes I, Fumian TM. Full genotype constellations analysis of unusual DS-1-like G12P[6] and G6P[8] rotavirus strains detected in Brazil, 2019. Virology 2022; 577:74-83. [PMID: 36323046 DOI: 10.1016/j.virol.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022]
Abstract
Rotavirus A (RVA) is a major cause of acute gastroenteritis (AGE) in children worldwide. We report unusual RVA G12P[6] and G6P[8] strains isolated from fecal samples from Brazilian children hospitalized for AGE. The characterized RVA have genome segments backbone: G12-P[6]/ G6-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 of DS-1-like genogroup. Our study describes the first identification of G6P[8], a DS-1-like genogroup strain. Nucleotide analysis of VP7 and VP4 genes revealed that all G12 Brazilian strains clustered into the sub-lineages IIIB, mostly associated with P[6] lineage I. Additionally, our G6 lineage I strains were closely related to German G6 genotypes, bound with P[8] lineage III, differing from both vaccine strains. The comparative sequence analysis of our strains with vaccine strains revealed amino acid substitutions located in immunodominant regions of VP7 and VP4 proteins. Continuous monitoring of RVA genotypes is essential to evaluate the impact of vaccination on the dynamic nature of RVA evolution.
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Affiliation(s)
- Meylin Bautista Gutierrez
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Av. Brasil, 4365, Rio de Janeiro, RJ 21040-360, Brazil
| | - Rosane Maria Santos de Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Av. Brasil, 4365, Rio de Janeiro, RJ 21040-360, Brazil
| | - Ighor Arantes
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Av. Brasil, 4365, Rio de Janeiro, RJ 21040-360, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Av. Brasil, 4365, Rio de Janeiro, RJ 21040-360, Brazil.
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14
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Brnić D, Čolić D, Kunić V, Maltar-Strmečki N, Krešić N, Konjević D, Bujanić M, Bačani I, Hižman D, Jemeršić L. Rotavirus A in Domestic Pigs and Wild Boars: High Genetic Diversity and Interspecies Transmission. Viruses 2022; 14:v14092028. [PMID: 36146832 PMCID: PMC9503859 DOI: 10.3390/v14092028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/05/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Rotavirus A (RVA) is an important pathogen for porcine health. In comparison to humans, RVA in domestic animals and especially in wildlife is under researched. Therefore, the aim of the present study was to investigate the prevalence, genetic diversity, molecular epidemiology and interspecies transmission of RVA in domestic pigs and wild boars. During the three consecutive RVA seasons (2018–2021) we collected 445 and 441 samples from domestic pigs and wild boars, respectively. Samples were tested by real-time RT-PCR, and RVA-positive samples were genotyped in VP7 and VP4 segments. Our results report an RVA prevalence of 49.9% in domestic pigs and 9.3% in wild boars. Outstanding RVA genetic diversity was observed in VP7 and VP4 segments, especially in domestic pigs exhibiting a striking 23 different RVA combinations (G5P[13] and G9P[23] prevailed). Interspecies transmission events were numerous between domestic pigs and wild boars, sharing G3, G5, G6, G9, G11 and P[13] genotypes. Furthermore, our data indicate that such transmission events involved even bovines (G6, P[11]) and, intriguingly, humans (G1P[8]). This study contributes to the basic knowledge that may be considered important for vaccine development and introduction, as a valuable and currently missing tool for efficient pig health management in the EU.
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Affiliation(s)
- Dragan Brnić
- Virology Department, Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-6123-674
| | - Daniel Čolić
- Virology Department, Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Valentina Kunić
- Virology Department, Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Nadica Maltar-Strmečki
- Laboratory for Electron Spin Spectroscopy, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Nina Krešić
- Virology Department, Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Dean Konjević
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Miljenko Bujanić
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Ivica Bačani
- Animal Feed Factory Ltd., Dr. Ivana Novaka 11, 40000 Čakovec, Croatia
| | - Dražen Hižman
- Belje Agro-Vet plus Ltd., Kokingrad 4, Mece, 31326 Darda, Croatia
- Rusagro, LLC “Tambovsky bacon”, Bazarnaya 104, 392036 Tambov, Russia
| | - Lorena Jemeršić
- Virology Department, Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
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15
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Were FN, Jere KC, Armah GE, Mphahlele MJ, Mwenda JM, Steele AD. Maintaining Momentum for Rotavirus Immunization in Africa during the COVID-19 Era: Report of the 13th African Rotavirus Symposium. Vaccines (Basel) 2022; 10:vaccines10091463. [PMID: 36146541 PMCID: PMC9503285 DOI: 10.3390/vaccines10091463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
The 13th African Rotavirus Symposium was held as a virtual event hosted by the University of Nairobi, Kenya and The Kenya Paediatric Association on 3rd and 4th November 2021. This biennial event organized under the auspices of the African Rotavirus Network shapes the agenda for rotavirus research and prevention on the continent, attracting key international and regional opinion leaders, researchers, and public health scientists. The African Rotavirus Network is a regional network of institutions initially established in 1999, and now encompassing much of the diarrheal disease and rotavirus related research in Africa, in collaboration with the World Health Organization African Regional Office (WHO-AFRO), Ministries of Health, and other partners. Surges in SARS-CoV2 variants and concomitant travel restrictions limited the meeting to a webinar platform with invited scientific presentations and scientific presentations from selected abstracts. The scientific program covered updates on burden of diarrheal diseases including rotavirus, the genomic characterization of rotavirus strains pre- and post-rotavirus vaccine introduction, and data from clinical evaluation of new rotavirus vaccines in Africa. Finally, 42 of the 54 African countries have fully introduced rotavirus vaccination at the time of the meeting, including the two recently WHO pre-qualified vaccines from India. Nonetheless, the full benefit of rotavirus vaccination is yet to be realized in Africa where approximately 80% of the global burden of rotavirus mortality exists.
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Affiliation(s)
- Frederick N. Were
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi 00625, Kenya
- Kenya Paediatric Association, Nairobi 00100, Kenya
| | - Khuzwayo C. Jere
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
| | - George E. Armah
- Noguchi Memorial Institute of Medical Research, University of Ghana, Legon, Accra LG 581, Ghana
| | | | - Jason M. Mwenda
- WHO Regional Office for Africa, Brazzaville P.O. Box 2465, Congo
| | - A. Duncan Steele
- Department of Virology, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
- Correspondence: ; Tel.: +1-(206)-915-3677
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16
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Lestari FB, Vongpunsawad S, Poovorawan Y. Diverse human and bat-like rotavirus G3 strains circulating in suburban Bangkok. PLoS One 2022; 17:e0268465. [PMID: 35609031 PMCID: PMC9129036 DOI: 10.1371/journal.pone.0268465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/29/2022] [Indexed: 11/18/2022] Open
Abstract
Although rotavirus vaccines are available in many parts of the world and are effective in reducing the overall incidence of rotavirus infection, it remains a major cause of diarrhea in less-developed countries. Among various rotavirus group A (RVA) strains, the increasingly common genotype G3 (defined by the VP7 gene) has been identified in both humans and animals. Our previous epidemiological surveillance in Bangkok found several unusual non-vaccine-like G3 strains in patients with diarrhea. In this study, we sequenced and characterized the genomes of seven of these G3 strains, which formed combinations with genotypes P[4], P[6], P[9], and P[10] (defined by the VP4 gene). Interestingly, we identified a bat-like RVA strain with the genome constellation G3-P[10]-I3-R3-C3-M3-A9-N3-T3-E3-H6, which has not been previously reported in the literature. The amino acid residues deduced from the nucleotide sequences of our G3 strains differed at the antigenic epitopes to those of the VP7 capsid protein of the G3 strain in RotaTeq vaccine. Although it is not unusual for the segmented genomes of RVA to reassort and give rise to emerging novel strains, the atypical G3 strains identified in this study suggest possible animal-to-human RVA zoonotic spillover even in urban areas.
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Affiliation(s)
- Fajar Budi Lestari
- Interdisciplinary Program of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Bioresources Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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17
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Portal TM, Vanmechelen B, Van Espen L, Jansen D, Teixeira DM, de Sousa ESA, da Silva VP, de Lima JS, Reymão TKA, Sequeira CG, da Silva Ventura AMR, da Silva LD, Resque HR, Matthijnssens J, Gabbay YB. Molecular characterization of the gastrointestinal eukaryotic virome in elderly people in Belem, Para, Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105241. [PMID: 35150892 DOI: 10.1016/j.meegid.2022.105241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Acute gastroenteritis is one of the main causes of mortality and morbidity worldwide, affecting mainly children, the immunocompromised and elderly people. Enteric viruses, especially rotavirus A, are considered important etiological agents, while long-term care facilities are considered favorable environments for the occurrence of sporadic cases and outbreaks of acute gastroenteritis. Therefore, it is important to monitor the viral agents present in nursing homes, especially because studies involving the elderly population in Brazil are scarce, resulting in a lack of available virological data. As a result, the causative agent remains unidentified in a large number of reported acute gastroenteritis cases. However, the advent of next-generation sequencing provides new opportunities for viral detection and discovery. The aim of this study was to identify the viruses that circulate among elderly people with and without acute gastroenteritis, living in residential care homes in Belém, Pará, Brazil, between 2017 and 2019. Ninety-three samples were collected and screened by immunochromatography and qPCR. After, the samples were analyzed individually or in pools by next generation sequencing to identify the viruses circulating in this population. In 26 sequenced samples, members of 13 eukaryotic virus families were identified. The most abundantly present virus families were Parvoviridae, Genomoviridae and Smacoviridae. Contigs displaying similarity to pegiviruses were also detected. Furthermore, a near-complete rotavirus A genome was obtained and could be classified as G3P[8] genotype with the equine DS-1-like genetic background. Complete sequences of the VP4 and VP7 genes of a rotavirus C were also detected, belonging to G4P[2]. This study demonstrates the first characterization of the gastrointestinal virome in elderly in Northern Brazil. A diversity of viruses was found to be present in patients with and without diarrhea, reinforcing the need to monitor elderly people residing in long-term care facilities, especially in cases of acute gastroenteritis.
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Affiliation(s)
- Thayara Morais Portal
- Postgraduate Program in Virology, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil.
| | - Bert Vanmechelen
- KU Leuven-University of Leuven, Rega Institute Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Lore Van Espen
- KU Leuven-University of Leuven, Rega Institute Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Daan Jansen
- KU Leuven-University of Leuven, Rega Institute Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Dielle Monteiro Teixeira
- Postgraduate Program in Virology, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Emanuella Sarmento Alho de Sousa
- Scientific Initiation with CNPq and FAPESPA scholarships from Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Victor Pereira da Silva
- Scientific Initiation with CNPq and FAPESPA scholarships from Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Juliana Silva de Lima
- Scientific Initiation with CNPq and FAPESPA scholarships from Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Tammy Katlhyn Amaral Reymão
- Federal University of Pará, Institute of Biological Sciences, Biology of Infectious and Parasitic Agents Graduate Program, Belém, Pará, Brazil
| | | | | | - Luciana Damascena da Silva
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Hugo Reis Resque
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Jelle Matthijnssens
- KU Leuven-University of Leuven, Rega Institute Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Yvone Benchimol Gabbay
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
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18
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Development of a Real-Time Reverse Transcription-PCR Assay To Detect and Quantify Group A Rotavirus Equine-Like G3 Strains. J Clin Microbiol 2021; 59:e0260220. [PMID: 34432486 DOI: 10.1128/jcm.02602-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Since 2013, group A rotavirus strains characterized as novel DS-1-like intergenogroup reassortant "equine-like G3" strains have emerged and spread across 5 continents among human populations in at least 14 countries. Here, we report a novel one-step TaqMan quantitative real-time reverse transcription-PCR assay developed to genotype and quantify the viral load for samples containing rotavirus equine-like G3 strains. Using a universal G forward primer and a newly designed reverse primer and TaqMan probe, we developed and validated an assay with a linear dynamic range of 227 to 2.3 × 109 copies per reaction and a limit of detection of 227 copies. The percent positive agreement, percent negative agreement, and precision of our assay were 100.00%, 99.63%, and 100.00%, respectively. This assay can simultaneously detect and quantify the viral load for samples containing DS-1-like intergenogroup reassortant equine-like G3 strains with high sensitivity and specificity, faster turnaround time, and decreased cost. It will be valuable for high-throughput screening of stool samples collected to monitor equine-like G3 strain prevalence and circulation among human populations throughout the world.
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19
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Uprety T, Sreenivasan CC, Hause BM, Li G, Odemuyiwa SO, Locke S, Morgan J, Zeng L, Gilsenan WF, Slovis N, Metcalfe L, Carter CN, Timoney P, Horohov D, Wang D, Erol E, Adam E, Li F. Identification of a Ruminant Origin Group B Rotavirus Associated with Diarrhea Outbreaks in Foals. Viruses 2021; 13:1330. [PMID: 34372536 PMCID: PMC8310321 DOI: 10.3390/v13071330] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 12/16/2022] Open
Abstract
Equine rotavirus group A (ERVA) is one of the most common causes of foal diarrhea. Starting in February 2021, there was an increase in the frequency of severe watery to hemorrhagic diarrhea cases in neonatal foals in Central Kentucky. Diagnostic investigation of fecal samples failed to detect evidence of diarrhea-causing pathogens including ERVA. Based on Illumina-based metagenomic sequencing, we identified a novel equine rotavirus group B (ERVB) in fecal specimens from the affected foals in the absence of any other known enteric pathogens. Interestingly, the protein sequence of all 11 segments had greater than 96% identity with group B rotaviruses previously found in ruminants. Furthermore, phylogenetic analysis demonstrated clustering of the ERVB with group B rotaviruses of caprine and bovine strains from the USA. Subsequent analysis of 33 foal diarrheic samples by RT-qPCR identified 23 rotavirus B-positive cases (69.69%). These observations suggest that the ERVB originated from ruminants and was associated with outbreaks of neonatal foal diarrhea in the 2021 foaling season in Kentucky. Emergence of the ruminant-like group B rotavirus in foals clearly warrants further investigation due to the significant impact of the disease in neonatal foals and its economic impact on the equine industry.
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Affiliation(s)
- Tirth Uprety
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - Chithra C. Sreenivasan
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - Ben M. Hause
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA;
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA;
| | - Solomon O. Odemuyiwa
- Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, MO 65212, USA;
| | - Stephan Locke
- Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40512, USA; (S.L.); (J.M.); (L.Z.); (C.N.C.)
| | - Jocelynn Morgan
- Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40512, USA; (S.L.); (J.M.); (L.Z.); (C.N.C.)
| | - Li Zeng
- Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40512, USA; (S.L.); (J.M.); (L.Z.); (C.N.C.)
| | | | - Nathan Slovis
- Hagyard Equine Medical Institute, Lexington, KY 40511, USA;
| | - Laurie Metcalfe
- Rood and Riddle Equine Hospital, Lexington, KY 40511, USA; (W.F.G.); (L.M.)
| | - Craig N. Carter
- Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40512, USA; (S.L.); (J.M.); (L.Z.); (C.N.C.)
| | - Peter Timoney
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - David Horohov
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - Dan Wang
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - Erdal Erol
- Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40512, USA; (S.L.); (J.M.); (L.Z.); (C.N.C.)
| | - Emma Adam
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - Feng Li
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
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20
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Wa-1 Equine-Like G3P[8] Rotavirus from a Child with Diarrhea in Colombia. Viruses 2021; 13:v13061075. [PMID: 34199978 PMCID: PMC8226935 DOI: 10.3390/v13061075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
Rotavirus A (RVA) has been considered the main cause of diarrheal disease in children under five years in emergency services in both developed and developing countries. RVA belongs to the Reoviridae family, which comprises 11 segments of double-stranded RNA (dsRNA) as a genomic constellation that encodes for six structural and five to six nonstructural proteins. RVA has been classified in a binary system with Gx[Px] based on the spike protein (VP4) and the major outer capsid glycoprotein (VP7), respectively. The emerging equine-like G3P[8] DS-1-like strains reported worldwide in humans have arisen an important concern. Here, we carry out the complete genome characterization of a previously reported G3P[8] strain in order to recognize the genetic diversity of RVA circulating among infants in Colombia. A near-full genome phylogenetic analysis was done, confirming the presence of the novel equine-like G3P[8] with a Wa-like backbone for the first time in Colombia. This study demonstrated the importance of surveillance of emerging viruses in the Colombian population; furthermore, additional studies must focus on the understanding of the spread and transmission dynamic of this important RVA strain in different areas of the country.
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21
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Wahyuni RM, Utsumi T, Dinana Z, Yamani LN, Juniastuti, Wuwuti IS, Fitriana E, Gunawan E, Liang Y, Ramadhan F, Soetjipto, Lusida MI, Shoji I. Prevalence and Distribution of Rotavirus Genotypes Among Children With Acute Gastroenteritis in Areas Other Than Java Island, Indonesia, 2016-2018. Front Microbiol 2021; 12:672837. [PMID: 34025628 PMCID: PMC8137317 DOI: 10.3389/fmicb.2021.672837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/12/2021] [Indexed: 11/23/2022] Open
Abstract
Group A rotaviruses (RVAs) are the leading cause of acute gastroenteritis, which is often associated with severe symptoms in children under 5 years old. Genetic reassortments and interspecies transmission commonly occur, resulting in a great diversity of RVA circulating in the world. The aim of this study is to determine the prevalence and distribution of RVA genotypes among children in Indonesia over the years 2016–2018 across representative areas of the country. Stool samples were collected from 202 pediatric patients with acute gastroenteritis in three regions of Indonesia (West Nusa Tenggara, South Sumatra, and West Papua) in 2016–2018. Rotavirus G and P genotypes were determined by reverse transcription PCR (RT-PCR) and direct sequencing analysis. The prevalences of RVA in South Sumatra (55.4%) and West Papua (54.0%) were significantly higher than that in East Java (31.7%) as determined in our previous study. The prevalence in West Nusa Tenggara (42.6%) was the lowest among three regions, but higher than that in East Java. Interestingly, equine-like G3 rotavirus strains were found as predominant strains in South Sumatra in 2016 and in West Papua in 2017–2018. Moreover, the equine-like G3 strains in South Sumatra detected in 2016 were completely replaced by human G1 and G2 in 2018. In conclusion, RVA infection in South Sumatra and West Papua was highly endemic. Equine-like G3 strains were also spread to South Sumatra (West Indonesia) and West Papua (East Indonesia), as well as Java Island. Dynamic change in rotavirus genotypes from equine-like G3 to human genotypes was also observed. Continuous monitoring may be warranted in isolated areas in Indonesia.
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Affiliation(s)
- Rury Mega Wahyuni
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Takako Utsumi
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia.,Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Zayyin Dinana
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Laura Navika Yamani
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia.,Department of Epidemiology, Faculty of Public Health, Campus C, Airlangga University, Surabaya, Indonesia
| | - Juniastuti
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | | | - Elsa Fitriana
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Emily Gunawan
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Yujiao Liang
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - Soetjipto
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Maria Inge Lusida
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Ikuo Shoji
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
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22
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Unexpected Role of Rotavirus G3P[8] Infection in Causing Severe Diarrhea in a Major Tertiary Referral Hospital in the Prevaccine Era. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2021. [DOI: 10.5812/archcid.105501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: Rotavirus A species is associated with severe gastroenteritis in children. Rotavirus G1P[8] was the most prevalent genotype found in Kuwait in a study conducted between 2005 and 2006. The RotaTeq vaccine was included in the Kuwait national immunization program at the end of 2017. Objectives: Since there is no available data on the rotavirus genotypes circulating before the introduction of the vaccine, we conducted a study to investigate the role of rotaviruses in causing severe diarrhea in children hospitalized in a major tertiary referral hospital in Kuwait during the year 2016. Methods: Viral RNA was isolated from the stool samples of 101 children under five years of age, hospitalized for acute gastroenteritis. Rotavirus VP4 and VP7 dsRNA were detected by RT-PCR, and their partial sequences were analyzed by phylogenic analysis. Results: Rotavirus dsRNA was detected in 24.7% of children with median age of 1 year. The genotype G3P[8] accounted for 47% of cases, followed by G1P[8] (26%), G9P[8] (10.5%), G4P[8] (10.5%), and G9P[4] (5%). Only VP7 nucleotide sequences of rotavirus G3 or G4 type clustered in the same lineage as RotaTeq vaccine, while most VP4 nucleotide sequences of rotavirus P[8] type clustered in a different lineage compared to Rotarix and RotaTeq vaccines. Conclusions: Our findings highlight the role of rotavirus G3P[8] in causing severe diarrhea and invites future investigations to know whether the recent introduction of RotaTeq vaccine in Kuwait selects certain genotypes and subgenomic lineages.
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Bonura F, Bányai K, Mangiaracina L, Bonura C, Martella V, Giammanco GM, De Grazia S. Emergence in 2017-2019 of novel reassortant equine-like G3 rotavirus strains in Palermo, Sicily. Transbound Emerg Dis 2021; 69:813-835. [PMID: 33905178 DOI: 10.1111/tbed.14054] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/18/2021] [Accepted: 03/02/2021] [Indexed: 12/20/2022]
Abstract
Rotavirus A (RVA) is a major etiologic agent of gastroenteritis in children worldwide. Hospital-based surveillance of viral gastroenteritis in paediatric population in Palermo (Italy) from 2017 onwards revealed a sharp increase in G3P[8] RVAs, accounting for 71% of all the RVAs detected in 2019. This pattern had not been observed before in Italy, with G3 RVA usually being detected at rates lower than 3%. In order to investigate this unique epidemiological pattern, the genetic diversity of G3 RVAs identified during a 16-year long surveillance (2004-2019) was explored by systematic sequencing of the VP7 and VP4 genes and by whole genome sequencing of selected G3 strains, representative of the various RVA seasons. Sequence and phylogenetic analyses of the VP7 and VP4 genes revealed the emergence, in 2017 of reassortant equine-like G3P[8], which gradually replaced former G3P[8] strains. The G3P[8] circulating before 2017 showed a Wa-like constellation of genome segments while the G3P[8] that emerged in 2017 had a DS-1-like backbone. On direct inspection of the VP7 and VP4 antigenic epitopes, the equine-like G3P[8] strains possessed several amino acid variations in neutralizing regions compared with vaccine strains. The equine-like G3P[8] RVAs are a further example of the zoonotic impact of animal viruses on human health.
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Affiliation(s)
- Floriana Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro" (PROSAMI), Università di Palermo, Via del Vespro 133, Palermo, Italy
| | - Kristián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Leonardo Mangiaracina
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro" (PROSAMI), Università di Palermo, Via del Vespro 133, Palermo, Italy
| | - Celestino Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro" (PROSAMI), Università di Palermo, Via del Vespro 133, Palermo, Italy
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italia
| | - Giovanni M Giammanco
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro" (PROSAMI), Università di Palermo, Via del Vespro 133, Palermo, Italy
| | - Simona De Grazia
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro" (PROSAMI), Università di Palermo, Via del Vespro 133, Palermo, Italy
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24
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Tsugawa T, Akane Y, Honjo S, Kondo K, Kawasaki Y. Rotavirus vaccination in Japan: Efficacy and safety of vaccines, changes in genotype, and surveillance efforts. J Infect Chemother 2021; 27:940-948. [PMID: 33867267 DOI: 10.1016/j.jiac.2021.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/25/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
In Japan, a monovalent rotavirus vaccine (RV1) and a pentavalent rotavirus vaccine (RV5) were launched as voluntary vaccinations in November 2011 and July 2012, respectively. Rotavirus (RV) vaccine coverage in Japan increased from 30.0% in 2012 to 78.4% in 2019. The number of RV gastroenteritis hospitalizations decreased after 2014 in Japan, and is expected to decrease further following the introduction of RV vaccines into the national immunization program in October 2020. The incidence rates of intussusception (IS) among children aged <1 year were 102.8 and 94.0 per 100,000 person-years in the pre-vaccine (2007-2011) and post-vaccine (2012-September 2014) eras, respectively. IS incidence did not increase following RV vaccine introduction in Japan. The efficacy and safety of RV vaccination were both documented in Japan. To reduce the risk of IS following RV vaccination, it is important that children receive a first dose of RV vaccine at age <15 weeks, preferably at age 2 months. Some strains that have emerged since RV vaccine introduction, such as DS-1-like G1P[8], eG3, and G8P[8], have spread nationwide. These three emerging genotypes did not affect the severity of the RV infection. Continuous city-level surveillance, using analysis of all 11 RV genome segments, is necessary to elucidate the genetic characteristics of prevalent RV strains. These efforts would also clarify the influence of vaccination on genetic changes of RV strains and the emergence of new genotypes.
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Affiliation(s)
- Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan.
| | - Yusuke Akane
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
| | - Saho Honjo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sunagawa City Hospital, Sunagawa, 073-0196, Japan
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
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25
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Pasittungkul S, Lestari FB, Puenpa J, Chuchaona W, Posuwan N, Chansaenroj J, Mauleekoonphairoj J, Sudhinaraset N, Wanlapakorn N, Poovorawan Y. High prevalence of circulating DS-1-like human rotavirus A and genotype diversity in children with acute gastroenteritis in Thailand from 2016 to 2019. PeerJ 2021; 9:e10954. [PMID: 33680579 PMCID: PMC7919534 DOI: 10.7717/peerj.10954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
Background Human rotavirus A (RVA) infection is the primary cause of acute gastroenteritis (AGE) in infants and young children worldwide, especially in children under 5 years of age and is a major public health problem causing severe diarrhea in children in Thailand. This study aimed to investigate the prevalence, genotype diversity, and molecular characterization of rotavirus infection circulating in children under 15 years of age diagnosed with AGE in Thailand from January 2016 to December 2019. Methods A total of 2,001 stool samples were collected from children with gastroenteritis (neonates to children <15 years of age) and tested for RVA by real-time polymerase chain reaction (RT-PCR). Amplified products were sequenced and submitted to an online genotyping tool for analysis. Results Overall, 301 (15.0%) stool samples were positive for RVA. RVA occurred most frequently among children aged 0-24 months. The seasonal incidence of rotavirus infection occurred typically in Thailand during the winter months (December-March). The G3P[8] genotype was identified as the most prevalent genotype (33.2%, 100/301), followed by G8P[8] (10.6%, 32/301), G9P[8] (6.3%, 19/301), G2P[4] (6.0%, 18/301), and G1P[6] (5.3%, 16/301). Uncommon G and P combinations such as G9P[4], G2P[8], G3P[4] and G3P[9] were also detected at low frequencies. In terms of genetic backbone, the unusual DS-1-like G3P[8] was the most frequently detected (28.2%, 85/301), and the phylogenetic analysis demonstrated high nucleotide identity with unusual DS-1-like G3P[8] detected in Thailand and several countries. Conclusions A genetic association between RVA isolates from Thailand and other countries ought to be investigated given the local and global dissemination of rotavirus as it is crucial for controlling viral gastroenteritis, and implications for the national vaccination programs.
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Affiliation(s)
- Siripat Pasittungkul
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Fajar Budi Lestari
- Department of Bioresources Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Faculty of Graduate School, Chulalongkorn University, Inter-Department of Biomedical Sciences, Bangkok, Bangkok, Thailand
| | - Jiratchaya Puenpa
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Watchaporn Chuchaona
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Nawarat Posuwan
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Jira Chansaenroj
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - John Mauleekoonphairoj
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Natthinee Sudhinaraset
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Nasamon Wanlapakorn
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand.,Faculty of Medicine, Chulalongkorn University, Division of Academic Affairs, Bangkok, Bangkok, Thailand
| | - Yong Poovorawan
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
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26
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Akane Y, Tsugawa T, Fujii Y, Honjo S, Kondo K, Nakata S, Fujibayashi S, Ohara T, Mori T, Higashidate Y, Nagai K, Kikuchi M, Sato T, Kato S, Tahara Y, Kubo N, Katayama K, Kimura H, Tsutsumi H, Kawasaki Y. Molecular and clinical characterization of the equine-like G3 rotavirus that caused the first outbreak in Japan, 2016. J Gen Virol 2021; 102. [PMID: 33587029 DOI: 10.1099/jgv.0.001548] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Since 2013, equine-like G3 rotavirus (eG3) strains have been detected throughout the world, including in Japan, and the strains were found to be dominant in some countries. In 2016, the first eG3 outbreak in Japan occurred in Tomakomai, Hokkaido prefecture, and the strains became dominant in other Hokkaido areas the following year. There were no significant differences in the clinical characteristics of eG3 and non-eG3 rotavirus infections. The eG3 strains detected in Hokkaido across 2 years from 2016 to 2017 had DS-1-like constellations (i.e. G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2), and the genes were highly conserved (97.5-100 %). One strain, designated as To16-12 was selected as the representative strain for these strains, and all 11 genes of this strain (To16-12) exhibited the closest identity to one foreign eG3 strain (STM050) seen in Indonesia in 2015 and two eG3 strains (IS1090 and MI1125) in another Japanese prefecture in 2016, suggesting that this strain might be introduced into Japan from Indonesia. Sequence analyses of VP7 genes from animal and human G3 strains found worldwide did not identify any with close identity (>92 %) to eG3 strains, including equine RV Erv105. Analysis of another ten genes indicated that the eG3 strain had low similarity to G2P[4] strains, which are considered traditional DS-1-like strains, but high similarity to DS-1-like G1P[8] strains, which first appeared in Asia in 2012. These data suggest that eG3 strains were recently generated in Asia as mono-reassortant strain between DS-1-like G1P[8] strains and unspecified animal G3 strains. Our results indicate that rotavirus surveillance in the postvaccine era requires whole-genome analyses.
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Affiliation(s)
- Yusuke Akane
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Saho Honjo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sunagawa City Hospital, Sunagawa, Japan
| | - Shuji Nakata
- Department of Pediatrics, Nakata Pediatric Clinic, Sapporo, Japan
| | | | - Toshio Ohara
- Department of Pediatrics, Tomakomai City Hospital, Tomakomai, Japan
| | - Toshihiko Mori
- Department of Pediatrics, NTT East Sapporo Hospital, Sapporo, Japan
| | - Yoshihito Higashidate
- Department of Pediatrics, Japan Community Health Care Organization (JCHO) Sapporo Hokushin Hospital, Sapporo, Japan
| | - Kazushige Nagai
- Department of Pediatrics, Takikawa Municipal Hospital, Takikawa, Japan
| | | | - Toshiya Sato
- Department of Pediatrics, Iwamizawa Municipal General Hospital, Iwamizawa, Japan
| | - Shinsuke Kato
- Department of Pediatrics, Rumoi City Hospital, Rumoi, Japan
| | - Yasuo Tahara
- Department of Pediatrics, Steel Memorial Muroran Hospital, Muroran, Japan
| | - Noriaki Kubo
- Department of Pediatrics, Japanese Red Cross Urakawa Hospital, Urakawa, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Graduate School of Health Science, Gunma Paz University, Gunma, Japan.,Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroyuki Tsutsumi
- Present address: Midorinosato, Saiseikai Otaru Hospital, Otaru, Japan.,Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
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27
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Epidemiological, molecular, and clinical features of rotavirus infections among pediatrics in Qatar. Eur J Clin Microbiol Infect Dis 2021; 40:1177-1190. [PMID: 33411172 DOI: 10.1007/s10096-020-04108-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
Acute gastroenteritis (AGE) remains a major cause of diarrhea in developing and developed countries. Rotavirus (RV) is a leading cause of severe pediatric diarrhea worldwide. Here we report on the prevalence of circulating genotypes in association with demographics and clinical manifestations outcomes in Qatar. A total of 231 RV-positive fecal samples were collected from children suffering from AGE during 3 years study period between June 2016 and June 2019. The age of the subjects ranged between 2 months and 14 years (median of 16 months). The VP4 and VP7 were amplified and sequenced. Phylogenetic analyses were performed using MEGA7.0. Pearson's chi-squared test was used to determine significant differences for comparisons of general categorical variables. RV infections were most common in children between 1 and 3 years of age (49%), followed by those < 1 year and > 3 years of age (33% and 28%, respectively). RV infections were more frequent in males than females, with a ratio of 1.4:1. RV infections occurred throughout the year, with a noticeable increase in summer (42.8%) and a drop in winter (20.1%). RV genotypes G3P[8] (30.8%), G2P[8] (12.3%), G4P[8] (11.7%), and G1P[8] (10.4%) were the common genotypes during the study period. The G3P[8] strain detected in our study revealed similarities to the equine-like G3P[8] (10.3%; 24/231) (KT988229.1), Wa-like genomic constellation (9%; 21/231) (MF563894.1), and DS-1-like strains (6.4%; 15/231) (LC386081.1). Based on the Vesikari score system, severe clinical illness including diarrhea and vomiting (average frequency: 4 to 5 times/day) was recorded for G3P[8] group, followed by G9P[8], G4P[8], and G1P[8]. Higher incidence for G3P[8], G2P[8], G4P[8], and G1P[8] were reported in Qatari subjects compared to other nationalities. The multinational status of a small country explains the wide diversity of circulating RV genotypes in Qatar. The highest prevalence and severe illnesses were recorded to G3P[8], which is different from other surrounding countries/global levels.
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28
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Esona MD, Gautam R, Katz E, Jaime J, Ward ML, Wikswo ME, Betrapally NS, Rustempasic SM, Selvarangan R, Harrison CJ, Boom JA, Englund J, Klein EJ, Staat MA, McNeal MM, Halasa N, Chappell J, Weinberg GA, Payne DC, Parashar UD, Bowen MD. Comparative genomic analysis of genogroup 1 and genogroup 2 rotaviruses circulating in seven US cities, 2014-2016. Virus Evol 2021; 7:veab023. [PMID: 34522389 PMCID: PMC8432945 DOI: 10.1093/ve/veab023] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
For over a decade, the New Vaccine Surveillance Network (NVSN) has conducted active rotavirus (RVA) strain surveillance in the USA. The evolution of RVA in the post-vaccine introduction era and the possible effects of vaccine pressure on contemporary circulating strains in the USA are still under investigation. Here, we report the whole-gene characterization (eleven ORFs) for 157 RVA strains collected at seven NVSN sites during the 2014 through 2016 seasons. The sequenced strains included 52 G1P[8], 47 G12P[8], 18 G9P[8], 24 G2P[4], 5 G3P[6], as well as 7 vaccine strains, a single mixed strain (G9G12P[8]), and 3 less common strains. The majority of the single and mixed strains possessed a Wa-like backbone with consensus genotype constellation of G1/G3/G9/G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, while the G2P[4], G3P[6], and G2P[8] strains displayed a DS-1-like genetic backbone with consensus constellation of G2/G3-P[4]/P[6]/P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Two intergenogroup reassortant G1P[8] strains were detected that appear to be progenies of reassortment events between Wa-like G1P[8] and DS-1-like G2P[4] strains. Two Rotarix® vaccine (RV1) and two RV5 derived (vd) reassortant strains were detected. Phylogenetic and similarity matrices analysis revealed 2-11 sub-genotypic allelic clusters among the genes of Wa- and DS-1-like strains. Most study strains clustered into previously defined alleles. Amino acid (AA) substitutions occurring in the neutralization epitopes of the VP7 and VP4 proteins characterized in this study were mostly neutral in nature, suggesting that these RVA proteins were possibly under strong negative or purifying selection in order to maintain competent and actual functionality, but fourteen radical (AA changes that occur between groups) AA substitutions were noted that may allow RVA strains to gain a selective advantage through immune escape. The tracking of RVA strains at the sub-genotypic allele constellation level will enhance our understanding of RVA evolution under vaccine pressure, help identify possible mechanisms of immune escape, and provide valuable information for formulation of future RVA vaccines.
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Affiliation(s)
- Mathew D Esona
- Division of Viral Diseases, Centers for Disease Control and Prevention, Viral Gastroenteritis Branch, Atlanta, GA, USA
- Corresponding author: E-mail:
| | - Rashi Gautam
- Division of Viral Diseases, Centers for Disease Control and Prevention, Viral Gastroenteritis Branch, Atlanta, GA, USA
| | - Eric Katz
- Cherokee Nation Assurance, Contracting Agency to the Division of Viral Diseases, Centers for Disease Control and Prevention, Arlington, VA, USA
| | - Jose Jaime
- Division of Viral Diseases, Centers for Disease Control and Prevention, Viral Gastroenteritis Branch, Atlanta, GA, USA
| | - M Leanne Ward
- Division of Viral Diseases, Centers for Disease Control and Prevention, Viral Gastroenteritis Branch, Atlanta, GA, USA
| | - Mary E Wikswo
- Division of Viral Diseases, Centers for Disease Control and Prevention, Viral Gastroenteritis Branch, Atlanta, GA, USA
| | - Naga S Betrapally
- Division of Viral Diseases, Centers for Disease Control and Prevention, Viral Gastroenteritis Branch, Atlanta, GA, USA
| | - Slavica M Rustempasic
- Division of Viral Diseases, Centers for Disease Control and Prevention, Viral Gastroenteritis Branch, Atlanta, GA, USA
| | | | | | | | - Jan Englund
- Seattle Children’s Hospital, Seattle, WA, USA
| | | | - Mary Allen Staat
- Division of Infectious Diseases, Department of Pediatrics, University of Cincinnati, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Monica M McNeal
- Division of Infectious Diseases, Department of Pediatrics, University of Cincinnati, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Natasha Halasa
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - James Chappell
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey A Weinberg
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Daniel C Payne
- Division of Viral Diseases, Centers for Disease Control and Prevention, Viral Gastroenteritis Branch, Atlanta, GA, USA
| | - Umesh D Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Viral Gastroenteritis Branch, Atlanta, GA, USA
| | - Michael D Bowen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Viral Gastroenteritis Branch, Atlanta, GA, USA
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29
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Kanai Y, Onishi M, Kawagishi T, Pannacha P, Nurdin JA, Nouda R, Yamasaki M, Lusiany T, Khamrin P, Okitsu S, Hayakawa S, Ebina H, Ushijima H, Kobayashi T. Reverse Genetics Approach for Developing Rotavirus Vaccine Candidates Carrying VP4 and VP7 Genes Cloned from Clinical Isolates of Human Rotavirus. J Virol 2020; 95:e01374-20. [PMID: 33087468 PMCID: PMC7944460 DOI: 10.1128/jvi.01374-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
Species A rotaviruses (RVs) are a leading cause of severe acute gastroenteritis in infants and children younger than 5 years. Currently available RV vaccines were adapted from wild-type RV strains by serial passage of cultured cells or by reassortment between human and animal RV strains. These traditional methods require large-scale screening and genotyping to obtain vaccine candidates. Reverse genetics is a tractable, rapid, and reproducible approach to generating recombinant RV vaccine candidates carrying any VP4 and VP7 genes that provide selected antigenicity. Here, we developed a vaccine platform by generating recombinant RVs carrying VP4 (P[4] and P[8]), VP7 (G1, G2, G3, G8, and G9), and/or VP6 genes cloned from human RV clinical samples using the simian RV SA11 strain (G3P[2]) as a backbone. Neutralization assays using monoclonal antibodies and murine antisera revealed that recombinant VP4 and VP7 monoreassortant viruses exhibited altered antigenicity. However, replication of VP4 monoreassortant viruses was severely impaired. Generation of recombinant RVs harboring a chimeric VP4 protein for SA11 and human RV gene components revealed that the VP8* fragment was responsible for efficient infectivity of recombinant RVs. Although this system must be improved because the yield of vaccine viruses directly affects vaccine manufacturing costs, reverse genetics requires less time than traditional methods and enables rapid production of safe and effective vaccine candidates.IMPORTANCE Although vaccines have reduced global RV-associated hospitalization and mortality over the past decade, the multisegmented genome of RVs allows reassortment of VP4 and VP7 genes from different RV species and strains. The evolutionary dynamics of novel RV genotypes and their constellations have led to great genomic and antigenic diversity. The reverse genetics system is a powerful tool for manipulating RV genes, thereby controlling viral antigenicity, growth capacity, and pathogenicity. Here, we generated recombinant simian RVs (strain SA11) carrying heterologous VP4 and VP7 genes cloned from clinical isolates and showed that VP4- or VP7-substituted chimeric viruses can be used for antigenic characterization of RV outer capsid proteins and as improved seed viruses for vaccine production.
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Affiliation(s)
- Yuta Kanai
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Misa Onishi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takahiro Kawagishi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Pimfhun Pannacha
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Jeffery A Nurdin
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Ryotaro Nouda
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Moeko Yamasaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tina Lusiany
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Pattara Khamrin
- Department of Microbiology, Chiang Mai University, Faculty of Medicine, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hirotaka Ebina
- Biken Center for Innovative Vaccine Research and Development, The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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30
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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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31
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Mwanga MJ, Verani JR, Omore R, Tate JE, Parashar UD, Murunga N, Gicheru E, Breiman RF, Nokes DJ, Agoti CN. Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Kilifi, Coastal Kenya, 4 Years after Nationwide Vaccine Introduction. Pathogens 2020; 9:pathogens9120981. [PMID: 33255256 PMCID: PMC7761311 DOI: 10.3390/pathogens9120981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 01/22/2023] Open
Abstract
Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in more than 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged less than 13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected RVA in 55 samples (22.2%). Of these, VP7 (G) and VP4 (P) segments were successfully sequenced in 48 (87.3%) and phylogenetic analysis based on the VP7 sequences identified seven genetic clusters with six different GP combinations: G3P[8], G1P[8], G2P[4], G2P[8], G9P[8] and G12P[8]. The G3P[8] strains predominated the season (n = 37, 67.2%) and comprised three distinct G3 genetic clusters that fell within Lineage I and IX (the latter also known as equine-like G3 Lineage). Both the two G3 lineages have been recently detected in several countries. Our study is the first to document African children infected with G3 Lineage IX. These data highlight the global nature of RVA transmission and the importance of increasing global rotavirus vaccine coverage.
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Affiliation(s)
- Mike J. Mwanga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Jennifer R. Verani
- Centers for Disease Control and Prevention (CDC), KEMRI Complex, off Mbagathi Way, Village Market, Nairobi 00621, Kenya;
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Richard Omore
- KEMRI, Center for Global Health Research (KEMRI-CGHR), Kisumu 00202, Kenya;
| | - Jacqueline E. Tate
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Umesh D. Parashar
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Nickson Murunga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Elijah Gicheru
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Robert F. Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
| | - D. James Nokes
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
- School of Life Sciences and Zeeman Institute (SBIDER), The University of Warwick, Coventry CV4 7AL, UK
| | - Charles N. Agoti
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
- School of Health and Human Sciences, Pwani University, Kilifi 80108, Kenya
- Correspondence:
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Huang YC, Wu FT, Huang YC, Liu CC, Chun-Yi-Lee, Lin HC, Chi H, Huang LM, Ho YH, Lee JT, Shih SM, Ching-Yi-Huang, Hsiung CA. Long-term effectiveness of pentavalent and monovalent rotavirus vaccines against hospitalization in Taiwan children. Vaccine 2020; 38:6435-6441. [DOI: 10.1016/j.vaccine.2020.07.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/18/2020] [Accepted: 07/29/2020] [Indexed: 01/05/2023]
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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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Chansaenroj J, Chuchaona W, Lestari FB, Pasittungkul S, Klinfueng S, Wanlapakorn N, Vongpunsawad S, Chirathaworn C, Poovorawan Y. High prevalence of DS-1-like rotavirus infection in Thai adults between 2016 and 2019. PLoS One 2020; 15:e0235280. [PMID: 32584905 PMCID: PMC7316273 DOI: 10.1371/journal.pone.0235280] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/11/2020] [Indexed: 01/07/2023] Open
Abstract
Rotavirus infection is the most common cause of viral diarrhea in infants and young children but uncommon and usually asymptomatic in adults. In the winter of 2017–2018, a large-scale outbreak of rotavirus in both children and adults was reported in Thailand. The current study focused on the prevalence, genotyping, and molecular characterization of rotavirus infections in Thai adults from July 2016 to December 2019. In 2,598 stool samples collected from adult residents of Bangkok (aged #x2265; 15 years) with acute gastroenteritis, rotavirus was detected via real-time RT-PCR analysis of the VP6 gene. G, P and I genotypes were determined by direct sequencing of VP7, VP4, and VP6 genes, respectively. Our results showed 8.7% (226/2,598) of stool samples were positive for rotavirus. The incidence of rotavirus was high during the winter season of 2017–2018 (17.7%) compared to another studied periods (4.5% between July 2016- October 2017 and 2.8% between March 2018- December 2019). Nucleotide sequencing of VP7 and VP4 revealed G3P[8] as the predominant strain (33.2%,75/226), followed by G9P[8] (17.3%,39/226), and G2P[4] (15.0%,34/226). Uncommon G and P combinations were additionally detected at low frequencies. VP6 sequencing was conducted to discriminate I genotype between the Wa and DS-1 genogroup. The unusual DS-1-like G3P[8] strain was most prevalent amomg rotavirus strains detected in this study (29.6%, 67/226), and the corresponding VP7 sequences showed high nucleotide identity with unusual DS-1-like globally circulating strains. Our study demonstrates that rotavirus outbreaks in adults are attributable not only to high prevalence of RV infection but also the unusual DS-like genogroup. The collective findings reinforce the importance of investigating rotavirus diagnosis in adults suffering from acute gastroenteritis and taking appropriate preventive measures.
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Affiliation(s)
- Jira Chansaenroj
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Watchaporn Chuchaona
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Fajar Budi Lestari
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Siripat Pasittungkul
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sirapa Klinfueng
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chintana Chirathaworn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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Nyaga MM, Sabiu S, Ndze VN, Dennis FE, Jere KC. Report of the 1st African Enteric Viruses Genome Initiative (AEVGI) Data and Bioinformatics Workshop on whole-genome analysis of some African rotavirus strains held in Bloemfontein, South Africa. Vaccine 2020; 38:5402-5407. [PMID: 32561119 DOI: 10.1016/j.vaccine.2020.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
Abstract
The University of the Free State - Next Generation Sequencing (NGS) Unit, Bloemfontein, South Africa, hosted a data and bioinformatics workshop from 19 to 22 June 2018. The workshop was coordinated by the African Enteric Viruses Genome Initiative (AEVGI) with support from the Bill & Melinda Gates Foundation. The event introduced technologies in NGS and data analysis with focus on the rotavirus (RV) genome. The workshop fostered interactions and networking between professionals, scientific experts, technicians and students. The courses provided an overview of RV diarrhoea and its burden in Africa, while highlighting the key resources and methodologies in NGS and advanced bioinformatics in deciphering vaccine impact. It was concluded that, despite the reported significant decline in RV associated-diarrhoea mortality and morbidity in Africa due to RV vaccine impact, the need for continuous surveillance and genomic characterization to better understand the ever-changing dynamics of RV strains is imperative.
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Affiliation(s)
- Martin M Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.
| | - Saheed Sabiu
- Biotechnology and Food Technology Department, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Valantine N Ndze
- Faculty of Health Sciences, University of Buea, P.O. Box 63, Buea, Cameroon; USAID-IDDS Project Cameroon, ASLM, Cameroon
| | - Francis E Dennis
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences, University of Ghana, Legon, Ghana
| | - Khuzwayo C Jere
- Centre for Global Vaccine Research, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme/Department of Medical Laboratory Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
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Hoa-Tran TN, Nakagomi T, Vu HM, Nguyen TTT, Takemura T, Hasebe F, Dao ATH, Anh PHQ, Nguyen AT, Dang AD, Nakagomi O. Detection of three independently-generated DS-1-like G9P[8] reassortant rotavirus A strains during the G9P[8] dominance in Vietnam, 2016–2018. INFECTION GENETICS AND EVOLUTION 2020; 80:104194. [DOI: 10.1016/j.meegid.2020.104194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/26/2019] [Accepted: 01/09/2020] [Indexed: 10/25/2022]
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Uncovering the First Atypical DS-1-like G1P[8] Rotavirus Strains That Circulated during Pre-Rotavirus Vaccine Introduction Era in South Africa. Pathogens 2020; 9:pathogens9050391. [PMID: 32443835 PMCID: PMC7281366 DOI: 10.3390/pathogens9050391] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/06/2020] [Accepted: 05/18/2020] [Indexed: 11/21/2022] Open
Abstract
Emergence of DS-1-like G1P[8] group A rotavirus (RVA) strains during post-rotavirus vaccination period has recently been reported in several countries. This study demonstrates, for the first time, rare atypical DS-1-like G1P[8] RVA strains that circulated in 2008 during pre-vaccine era in South Africa. Rotavirus positive samples were subjected to whole-genome sequencing. Two G1P[8] strains (RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1971/2008/G1P[8] and RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1973/2008/G1P[8]) possessed a DS-1-like genome constellation background (I2-R2-C2-M2-A2-N2-T2-E2-H2). The outer VP4 and VP7 capsid genes of the two South African G1P[8] strains had the highest nucleotide (amino acid) nt (aa) identities of 99.6–99.9% (99.1–100%) with the VP4 and the VP7 genes of a locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU1039/2008/G1P[8]. All the internal backbone genes (VP1–VP3, VP6, and NSP1-NSP5) had the highest nt (aa) identities with cognate internal genes of another locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU2344/2008/G2P[6]. The two study strains emerged through reassortment mechanism involving locally circulating South African strains, as they were distinctly unrelated to other reported atypical G1P[8] strains. The identification of these G1P[8] double-gene reassortants during the pre-vaccination period strongly supports natural RVA evolutionary mechanisms of the RVA genome. There is a need to maintain long-term whole-genome surveillance to monitor such atypical strains.
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Kung YH, Chi H, Liu CC, Huang YC, Huang YC, Wu FT, Huang LM. Hospital-based surveillance of severe rotavirus gastroenteritis and rotavirus strains in young Taiwanese children. J Formos Med Assoc 2020; 119:1158-1166. [PMID: 32359880 DOI: 10.1016/j.jfma.2020.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND/PURPOSE Rotavirus remains a leading cause of pediatric gastroenteritis-related hospitalization. Surveillance studies have revealed that several major rotaviral genotypes are responsible for most cases of rotavirus gastroenteritis (RVGE). This study aimed to understand the characteristics of acute gastroenteritis (AGE) caused by rotavirus in young children in Taiwan. METHODS Ten hospitals in Taiwan were subjected to prospective hospital-based AGE surveillance during 2014-2017, and children younger than 5 years old who were hospitalized due to AGE were enrolled in the study. Medical and demographic variables were recorded and analyzed, and stool specimens were collected for rotavirus identification and genotyping via real-time RT-PCR. Non-rotavirus AGE age-matched controls were enrolled. RESULTS Surveillance identified 4747 young children hospitalized with AGE during this study period. The median age of these patients was 2.0 years. Rotavirus was detected in stool samples from 518 patients (10.9%). The prevalent months of RVGE in 2014, 2015, and 2017, wherein the rotavirus positivity rates exceeded 30%. The most common serotypes were G3P[8] (303/518, 58.9%) and G1P[8] (86/518, 16.6%). The percentage of G3P[8] increased from 4.9% in 2014 to 74.3% in 2016 (P < 0.0001), whereas the percentage of G1P[8] decreased from 61.0% in 2014 to 22.5% in 2015 (P < 0.0001). Compared with G3P[8], G1P[8] was associated with a significantly higher C-reactive protein level (P < 0.05). CONCLUSION Rotavirus remains a notable pathogenic etiology of childhood AGE and the G3P[8] serotype was dominant in Taiwan. This study highlighted the importance of rotavirus surveillance to ensure protective effectiveness against the circulating strains.
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Affiliation(s)
- Yen-Hsin Kung
- Department of Pediatrics, Mackay Memorial Hospital and Mackay Children's Hospital, Taipei, Taiwan
| | - Hsin Chi
- Department of Pediatrics, Mackay Memorial Hospital and Mackay Children's Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, New Taipei City, Taiwan.
| | - Ching-Chuan Liu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yhu-Chering Huang
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yi-Chuan Huang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Fang-Tzy Wu
- Department of Health, Research and Diagnostic Center, Centers for Disease Control, Taiwan
| | - Li-Min Huang
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan.
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Fukuda S, Tacharoenmuang R, Guntapong R, Upachai S, Singchai P, Ide T, Hatazawa R, Sutthiwarakom K, Kongjorn S, Onvimala N, Ruchusatsawast K, Rungnopakun P, Mekmallika J, Kawamura Y, Motomura K, Tatsumi M, Takeda N, Murata T, Yoshikawa T, Uppapong B, Taniguchi K, Komoto S. Full genome characterization of novel DS-1-like G9P[8] rotavirus strains that have emerged in Thailand. PLoS One 2020; 15:e0231099. [PMID: 32320419 PMCID: PMC7176146 DOI: 10.1371/journal.pone.0231099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/16/2020] [Indexed: 01/05/2023] Open
Abstract
The emergence and rapid spread of unusual DS-1-like intergenogroup reassortant rotaviruses having G1/3/8 genotypes have been recently reported from major parts of the world (Africa, Asia, Australia, Europe, and the Americas). During rotavirus surveillance in Thailand, three novel intergenogroup reassortant strains possessing the G9P[8] genotype (DBM2017-016, DBM2017-203, and DBM2018-291) were identified in three stool specimens from diarrheic children. In the present study, we determined and analyzed the full genomes of these three strains. On full-genomic analysis, all three strains were found to share a unique genotype constellation comprising both genogroup 1 and 2 genes: G9-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis demonstrated that each of the 11 genes of the three strains was closely related to that of emerging DS-1-like intergenogroup reassortant, human, and/or locally circulating human strains. Thus, the three strains were suggested to be multiple reassortants that had acquired the G9-VP7 genes from co-circulating Wa-like G9P[8] rotaviruses in the genetic background of DS-1-like intergenogroup reassortant (likely equine-like G3P[8]) strains. To our knowledge, this is the first description of emerging DS-1-like intergenogroup reassortant strains having the G9P[8] genotype. Our observations will add to the growing insights into the dynamic evolution of emerging DS-1-like intergenogroup reassortant rotaviruses through reassortment.
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Affiliation(s)
- Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ratana Tacharoenmuang
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ratigorn Guntapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sompong Upachai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Phakapun Singchai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Center for Research Promotion and Support, Joint Research Support Promotion Facility, Fujita Health University, Toyoake, Aichi, Japan
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Karun Sutthiwarakom
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Santip Kongjorn
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Napa Onvimala
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | | | | | | | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Kazushi Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
- Osaka Institute of Public Health, Osaka, Japan
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Naokazu Takeda
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ballang Uppapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- * E-mail:
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Distribution of rotavirus genotypes in Japan from 2015 to 2018: Diversity in genotypes before and after introduction of rotavirus vaccines. Vaccine 2020; 38:3980-3986. [PMID: 32307276 DOI: 10.1016/j.vaccine.2020.03.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/18/2020] [Accepted: 03/05/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Diversity in group A rotavirus (RVA) strains after introduction of RV-vaccines remains an emerging concern worldwide. In this study, we investigated the prevalence and distribution of RVA genotypes in Japanese children with acute gastroenteritis (AGE) from 2015 to 2018. In addition, a comparison of the genotypes in pre-vaccination (2006-2012) and post-vaccination (2012-2018) periods was conducted to understand the impact of these vaccines on genotype distribution. METHODS Fecal samples were collected regularly from outpatient clinics in six localities: Hokkaido, Tokyo, Shizuoka, Osaka, Kyoto, and Saga. RVA were screened and genotyped by RT-PCR and sequence-based genotyping. RESULTS During the period 2015-2018, RVA was detected in 307 (19.7%) samples out of 1557 specimens: 29.9% (95% CI: 25.8% to 34.3%), 17.9% (95% CI: 14.7% to 21.5%), and 13% (95% CI: 10.3% to 16.0%) were detected RVA-positive in 2015-2016, 2016-2017 and 2017-2018, respectively. The average detection of RVA in pre-vaccination (2006-2012) and post-vaccination (2012-2018) era remained almost similar (18%-20%). The G2P[4]I2 (52.1%, 95% CI: 43.5%-60.6%) remained the most common genotype in 2015-2016, whereas G8P[8]I2 (55.9%, 95% CI: 45.2%-66.2%) dominated in 2016-2017. In 2017-2018, G9P[8]I2 (42.0%, 95% CI: 30.5%-53.9%) prevailed, followed by G9P[8]I1 (23.0%, 95% CI: 14.0%-34.2%). The detection rate of some common genotypes of pre-vaccination era like G1P[8] and G3P[8] has been reduced after introduction of RV-vaccine, whereas genotypes that were sporadic before the introduction of vaccines like G2P[4], G2P[8], G9P[8] and G8P[8] were emerged/reemerged in post-vaccination period. CONCLUSIONS Our study presented the diversity in circulating RVA genotypes in Japan before and after introduction of RV-vaccines. Sudden emergence of DS-1-like (I2) unusual strains in post-vaccination era remains alarming. Continuous monitoring of RVA genotypes is therefore indispensable to refine future vaccine strategy.
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Chawla-Sarkar M, Banerjee A, Lo M, Mitra S, Okamoto K, Deb A, Dutta S. A decade-long temporal analyses of human group-A rotavirus among children with gastroenteritis: Prevaccination scenario in West Bengal, eastern India. J Med Virol 2020; 92:1334-1342. [PMID: 32073164 DOI: 10.1002/jmv.25712] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/16/2020] [Indexed: 11/05/2022]
Abstract
Despite the significant reduction in the global infantile death toll due to rotaviral diarrhea, India still contributes substantially to rotavirus-related hospitalization as well as mortality rates. The rotavirus surveillance study conducted from 2008 through 2017 among children (≤5 years) with moderate to severe gastroenteritis seeking healthcare facilities at two hospitals in eastern India, revealed a change in the proportion of rotavirus positivity, seasonality, and age-group specificity along with the cycling of different usual and unusual genotypes in this endemic setting. G1 strains predominated during 2008-2010, while G2 and G9 genotypes eventually upsurged during 2011-2013. G1 strains re-established their lead during 2013-2015, while G3 emerged for the first time in eastern India in 2015 and rooted itself as the cardinal strain 2016 onwards. Evolutionary analyses of all the predominant genotypes (G1, G2, G3, and G9) revealed that they were mostly phylogenetically distant to the rotavirus vaccine strains as depicted in the phylogenetic dendrogram. These decade-long epidemiological studies during the pre-vaccination period in West Bengal (eastern India) underscore the cocirculation of multiple rotavirus genotypes in addition to sporadic occurrence of zoonotic strains like G10P[6] and G11P[25].
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Affiliation(s)
- Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
| | - Anindita Banerjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
| | - Mahadeb Lo
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
| | - Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
| | - Keinosuke Okamoto
- Collaborative Research Center of Okayama University for Infectious Diseases at Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Alok Deb
- Division of Epidemiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
| | - Shanta Dutta
- Regional Virus Research and Diagnostic Laboratory, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
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Sadiq A, Bostan N, Bokhari H, Yinda KC, Matthijnssens J. Whole Genome Analysis of Selected Human Group A Rotavirus Strains Revealed Evolution of DS-1-Like Single- and Double-Gene Reassortant Rotavirus Strains in Pakistan During 2015-2016. Front Microbiol 2019; 10:2641. [PMID: 31798563 PMCID: PMC6868104 DOI: 10.3389/fmicb.2019.02641] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 10/30/2019] [Indexed: 12/20/2022] Open
Abstract
Acute gastroenteritis due to group A rotaviruses (RVAs) is the leading cause of infant and childhood morbidity and mortality particularly in developing countries including Pakistan. In this study we have characterized the whole genomes of five RVA strains (PAK56, PAK419, PAK585, PAK622, and PAK663) using the Illumina HiSeq platform. The strains PAK56 and PAK622 exhibited a typical Wa-like genotype constellation (G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, respectively), whereas PAK419, PAK585, and PAK663 exhibited distinct DS-1-like genotype constellations (G3P[4]-I2-R2-C2-M2-A2-N2-T1-E2-H2, G1P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2, and G3P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2, respectively). Despite their DS-1-like genotype constellation, strain PAK585 possessed the typical Wa-like G1P[8] genotypes, whereas both PAK419 and PAK663 possessed the G3 genotype. In addition, PAK419 also possessed the Wa-like NSP3 genotype T1, suggesting that multiple reassortments have occurred. On Phylogenetic analysis, all of the gene segments of the five strains examined in this study were genetically related to globally circulating human G1, G2, G3, G6, G8, G9, and G12 strains. Interestingly, the NSP2 gene of strain PAK419 showed closest relationship with Indian bovine strain (India/HR/B91), suggesting the occurrence of reassortment between human and bovine RVA strains. Furthermore, strains PAK419, PAK585, and PAK663 were closely related to one another in most of their gene segments, indicating that these strains might have been derived from a common ancestor. To our knowledge this is the first whole genome-based molecular characterization of human rotavirus strains in Pakistan. The results of our study will enhance our existing knowledge on the diversity and evolutionary dynamics of novel RVA strains including DS-1-like intergenogroup reassortant strains spreading in Asian countries including Pakistan, in the pre-vaccine era. Therefore, continuous surveillance is recommended to monitor the evolution, spread and genetic stability of novel reassortant rotavirus strains derived from such events.
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Affiliation(s)
- Asma Sadiq
- Department of Biosciences, COMSATS University (CUI), Islamabad, Pakistan
| | - Nazish Bostan
- Department of Biosciences, COMSATS University (CUI), Islamabad, Pakistan
| | - Habib Bokhari
- Department of Biosciences, COMSATS University (CUI), Islamabad, Pakistan
| | - Kwe Claude Yinda
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven, Leuven, Belgium
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Fujii Y, Oda M, Somura Y, Shinkai T. Molecular Characteristics of Novel Mono-Reassortant G9P[8] Rotavirus A Strains Possessing the NSP4 Gene of the E2 Genotype Detected in Tokyo, Japan. Jpn J Infect Dis 2019; 73:26-35. [PMID: 31564695 DOI: 10.7883/yoken.jjid.2019.211] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rotavirus A (RVA) has been detected in patients with gastroenteritis even after vaccine introduction in Japan. To investigate circulating RVA strains, RVA-positive stool specimens obtained in Tokyo in 2017 and 2018 were analyzed using next-generation sequencing. A total of 50 and 21 RVA samples were obtained in 2017 and 2018, respectively. In 2017, G2P[4] (40.0%) was the most prevalent strain, followed by G3P[8] (DS-1-like) (28.0%), G8P[8] (10.0%), G3P[8] (Wa-like) (8.0%), G9P[8]-E1 (8.0%), and mixed infection (6.0%). In 2018, G3P[8] (DS-1-like) (28.6%) and G9P[8]-E2 (28.6%) were the most prevalent strains, followed by G9P[8]-E1 (19.0%), G2P[4] (9.5%), G8P[8] (9.5%), and mixed infection (4.8%). Six G9P[8]-E2 strains detected in 2018 showed an atypical genotype constellation (G9P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1), which had not been reported previously. Phylogenetic analyses suggested that the RVA virus was generated by inter-genogroup reassortment between commonly circulating G9P[8] and G2P[4] strains in Japan. The G9P[8] strain seemed to be reassorted with only the NSP4 gene of the E2 genotype of the G2P[4] strain. Since this newly-emerged G9P[8]-E2 virus was detected in different locations in Tokyo, the virus appears to have already begun to spread to a wider area.
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Affiliation(s)
- Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases
| | - Mayuko Oda
- Division of Virology, Department of Microbiology, Tokyo Metropolitan Institute of Public Health
| | - Yoshiko Somura
- Division of Virology, Department of Microbiology, Tokyo Metropolitan Institute of Public Health
| | - Takayuki Shinkai
- Division of Virology, Department of Microbiology, Tokyo Metropolitan Institute of Public Health
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Tacharoenmuang R, Komoto S, Guntapong R, Upachai S, Singchai P, Ide T, Fukuda S, Ruchusatsawast K, Sriwantana B, Tatsumi M, Motomura K, Takeda N, Murata T, Sangkitporn S, Taniguchi K, Yoshikawa T. High prevalence of equine-like G3P[8] rotavirus in children and adults with acute gastroenteritis in Thailand. J Med Virol 2019; 92:174-186. [PMID: 31498444 DOI: 10.1002/jmv.25591] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/02/2019] [Indexed: 12/28/2022]
Abstract
Group A rotavirus (RVA) is a major cause of acute gastroenteritis in infants and young children worldwide. This study aims to clarify the distribution of G/P types and genetic characteristics of RVAs circulating in Thailand. Between January 2014 and September 2016, 1867 stool specimens were collected from children and adults with acute gastroenteritis in six provinces in Thailand. RVAs were detected in 514/1867 (27.5%) stool specimens. G1P[8] (44.7%) was the most predominant genotype, followed by G3P[8] (33.7%), G2P[4] (11.5%), G8P[8] (7.0%), and G9P[8] (1.3%). Unusual G3P[9] (0.8%), G3P[10] (0.4%), G4P[6] (0.4%), and G10P[14] (0.2%) were also detected at low frequencies. The predominant genotype, G1P[8] (64.4%), in 2014 decreased to 6.1% in 2016. In contrast, the frequency of G3P[8] markedly increased from 5.5% in 2014 to 65.3% in 2015 and 89.8% in 2016. On polyacrylamide gel electrophoresis, most (135/140; 96.4%) of the G3P[8] strains exhibited a short RNA profile. Successful determination of the nucleotide sequences of the VP7 genes of 98 G3P[8] strains with a short RNA profile showed that they are all equine-like G3P[8] strains. On phylogenetic analysis of genome segments of two representative Thai equine-like G3P[8] strains, it was noteworthy that they possessed distinct NSP4 genes, one bovine-like and the other human-like. Thus, we found that characteristic equine-like G3P[8] strains with a short RNA electropherotype are becoming highly prevalent in children and adults in Thailand.
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Affiliation(s)
- Ratana Tacharoenmuang
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand.,Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.,Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ratigorn Guntapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sompong Upachai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Phakapun Singchai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.,Center for Research Promotion and Support, Joint Research Support Promotion Facility, Fujita Health University, Toyoake, Aichi, Japan
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | | | - Busarawan Sriwantana
- Department of Medical Sciences, Medical Sciences Technical Office, Nonthaburi, Thailand
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Kazushi Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand.,Osaka Institute of Public Health, Osaka, Japan
| | - Naokazu Takeda
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Somchai Sangkitporn
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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45
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Roczo-Farkas S, Kirkwood CD, Cowley D, Barnes GL, Bishop RF, Bogdanovic-Sakran N, Boniface K, Donato CM, Bines JE. The Impact of Rotavirus Vaccines on Genotype Diversity: A Comprehensive Analysis of 2 Decades of Australian Surveillance Data. J Infect Dis 2019; 218:546-554. [PMID: 29790933 DOI: 10.1093/infdis/jiy197] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/03/2018] [Indexed: 12/28/2022] Open
Abstract
Background Introduction of rotavirus vaccines into national immunization programs (NIPs) could result in strain selection due to vaccine-induced selective pressure. This study describes the distribution and diversity of rotavirus genotypes before and after rotavirus vaccine introduction into the Australian NIP. State-based vaccine selection facilitated a unique comparison of diversity in RotaTeq and Rotarix vaccine states. Methods From 1995 to 2015, the Australian Rotavirus Surveillance Program conducted genotypic analysis on 13051 rotavirus-positive samples from children <5 years of age, hospitalized with acute gastroenteritis. Rotavirus G and P genotypes were determined using serological and heminested multiplex reverse-transcription polymerase chain reaction assays. Results G1P[8] was the dominant genotype nationally in the prevaccine era (1995-2006). Following vaccine introduction (2007-2015), greater genotype diversity was observed with fluctuating genotype dominance. Genotype distribution varied based on the vaccine implemented, with G12P[8] dominant in states using RotaTeq, and equine-like G3P[8] and G2P[4] dominant in states and territories using Rotarix. Conclusions The increased diversity and differences in genotype dominance observed in states using RotaTeq (G12P[8]), and in states and territories using Rotarix (equine-like G3P[8] and G2P[4]), suggest that these vaccines exert different immunological pressures that influence the diversity of rotavirus strains circulating in Australia.
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Affiliation(s)
- Susie Roczo-Farkas
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Carl D Kirkwood
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington
| | - Daniel Cowley
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Graeme L Barnes
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Department of Gastroenterology and Clinical Nutrition, Royal Children's Hospital, Parkville
| | - Ruth F Bishop
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Nada Bogdanovic-Sakran
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Karen Boniface
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Celeste M Donato
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Julie E Bines
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington
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46
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Roczo-Farkas S, Cowley D, Bines JE. Australian Rotavirus Surveillance Program: Annual Report, 2017. Commun Dis Intell (2018) 2019. [DOI: 10.33321/cdi.2019.43.28] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This report, from the Australian Rotavirus Surveillance Program and collaborating laboratories Australia-wide, describes the rotavirus genotypes identified in children and adults with acute gastroenteritis during the period 1 January to 31 December 2017. During this period, 2,285 faecal specimens were referred for rotavirus G and P genotype analysis, including 1,103 samples that were confirmed as rotavirus positive. Of these, 1,014/1,103 were wildtype rotavirus strains and 89/1,103 were identified as rotavirus vaccine-like. Genotype analysis of the 1,014 wildtype rotavirus samples from both children and adults demonstrated that G2P[4] was the dominant genotype nationally, identified in 39% of samples, followed by equine-like G3P[8] and G8P[8] (25% and 16% respectively). Multiple outbreaks were recorded across Australia, including G2P[4] (Northern Territory, Western Australia, and South Australia), equine-like G3P[8] (New South Wales), and G8P[8] (New South Wales and Victoria). This year also marks the change in the Australian National Immunisation Program to the use of Rotarix exclusively, on 1 July 2017.
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Affiliation(s)
- Susie Roczo-Farkas
- Enteric Diseases Group, Murdoch Children’s Research Institute, Flemington Road, Parkville, Victoria, 3052
| | - Daniel Cowley
- Enteric Diseases Group, Murdoch Children’s Research Institute, Flemington Road, Parkville, Victoria, 3052
| | - Julie E Bines
- Enteric Diseases Group, Murdoch Children’s Research Institute, Flemington Road, Parkville, Victoria, 3052; Department of Paediatrics, University of Melbourne, Flemington Road, Parkville, Victoria, 3052; Department of Gastroenterology and Clinical Nutrition, Flemington Road, Parkville, Victoria, 3052
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47
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Arana A, Jere KC, Chaguza C, Montes M, Alkorta M, Iturriza-Gomara M, Cilla G. Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010–2018. INFECTION GENETICS AND EVOLUTION 2019; 71:67-75. [DOI: 10.1016/j.meegid.2019.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/31/2019] [Accepted: 03/20/2019] [Indexed: 12/16/2022]
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48
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Damanka SA, Kwofie S, Dennis FE, Lartey BL, Agbemabiese CA, Doan YH, Adiku TK, Katayama K, Enweronu-Laryea CC, Armah GE. Whole genome characterization and evolutionary analysis of OP354-like P[8] Rotavirus A strains isolated from Ghanaian children with diarrhoea. PLoS One 2019; 14:e0218348. [PMID: 31199823 PMCID: PMC6570025 DOI: 10.1371/journal.pone.0218348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/30/2019] [Indexed: 11/22/2022] Open
Abstract
In 2010, the rare OP354-like P[8]b rotavirus subtype was detected in children less than 2 years old in Ghana. In this follow-up study, to provide insight into the evolutionary history of the genome of Ghanaian P[8]b strains RVA/Human-wt/GHA/GHDC949/2010/G9P[8] and RVA/Human-wt/GHA/GHM0094/2010/G9P[8] detected in an infant and a 7-month old child hospitalised for acute gastroenteritis, we sequenced the complete genome using both Sanger sequencing and Illumina MiSeq technology followed by phylogenetic analysis of the near-full length sequences. Both strains possessed the Wa-like/genotype 1 constellation G9P[8]b-I1-R1-C1-M1-A1-N1-T1-E1-H1. Sequence comparison and phylogenetic inference showed that both strains were identical at the lineage level throughout the 11 genome segments. Their VP7 sequences belonged to the major sub-lineage of the G9-lineage III whereas their VP4 sequences belonged to P[8]b cluster I. The VP7 and VP4 genes of the study strains were closely related to a Senegalese G9P[8]b strain detected in 2009. In the remaining nine genome segments, both strains consistently clustered together with Wa-like RVA strains possessing either P[8]a or P[8]b mostly of African RVA origin. The introduction of a P[8]b subtype VP4 gene into the stable Wa-like strain backbone may result in strains that might propagate easily in the human population, with a potential to become an important public health concern, especially because it is not certain if the monovalent rotavirus vaccine (Rotarix) used in Ghana will be efficacious against such strains. Our analysis of the full genomes of GHM0094 and GHDC949 adds to knowledge of the genetic make-up and evolutionary dynamics of P[8]b rotavirus strains.
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Affiliation(s)
- Susan Afua Damanka
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
- * E-mail:
| | - Sabina Kwofie
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
- Department of Microbiology, School of Biomedical and Allied Health Science, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Francis Ekow Dennis
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Belinda Larteley Lartey
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Chantal Ama Agbemabiese
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Theophilus Korku Adiku
- School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo, Japan
| | | | - George Enyimah Armah
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
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49
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Katz EM, Esona MD, Betrapally NS, De La Cruz De Leon LA, Neira YR, Rey GJ, Bowen MD. Whole-gene analysis of inter-genogroup reassortant rotaviruses from the Dominican Republic: Emergence of equine-like G3 strains and evidence of their reassortment with locally-circulating strains. Virology 2019; 534:114-131. [PMID: 31228725 DOI: 10.1016/j.virol.2019.06.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/12/2019] [Accepted: 06/12/2019] [Indexed: 11/26/2022]
Abstract
Inter-genogroup reassortant group A rotavirus (RVA) strains possessing a G3 VP7 gene of putative equine origin (EQL-G3) have been detected in humans since 2013. Here we report detection of EQL-G3P[8] RVA strains from the Dominican Republic collected in 2014-16. Whole-gene analysis of RVA in stool specimens revealed 16 EQL-G3P[8] strains, 3 of which appear to have acquired an N1 NSP1 gene from locally-circulating G9P[8] strains and a novel G2P[8] reassortant possessing 7 EQL-G3-associated genes and 3 genes from a locally-circulating G2P[4] strain. Phylogenetic/genetic analyses of VP7 gene sequences revealed nine G3 lineages (I-IX) with newly-assigned lineage IX encompassing all reported human EQL-G3 strains along with the ancestral equine strain. VP1 and NSP2 gene phylogenies suggest that EQL-G3P[8] strains were introduced into the Dominican Republic from Thailand. The emergence of EQL-G3P[8] strains in the Dominican Republic and their reassortment with locally-circulating RVA could have implications for current vaccination strategies.
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Affiliation(s)
- Eric M Katz
- Cherokee Nation Assurance, Contracting Agency to the Division of Viral Diseases, Centers for Disease Control and Prevention, Arlington, VA, USA; Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mathew D Esona
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Naga S Betrapally
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Yenny R Neira
- Pan American Health Organization/World Health Organization, Santo Domingo, Dominican Republic
| | - Gloria J Rey
- Pan American Health Organization, Washington, D.C, USA
| | - Michael D Bowen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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50
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Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains. PLoS One 2019; 14:e0217422. [PMID: 31150425 PMCID: PMC6544246 DOI: 10.1371/journal.pone.0217422] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022] Open
Abstract
Recent increase in the detection of unusual G1P[8], G3P[8], G8P[8], and G9P[4] Rotavirus A (RVA) strains bearing the DS-1-like constellation of the non-G, non-P genes (hereafter referred to as the genotype 2 backbone) requires better understanding of their evolutionary relationship. However, within a genotype, there is lack of a consensus lineage designation framework and a set of common sequences that can serve as references. Phylogenetic analyses were carried out on over 8,500 RVA genotype 2 genes systematically retrieved from the rotavirus database within the NCBI Virus Variation Resource. In line with previous designations, using pairwise comparison of cogent nucleotide sequences and stringent bootstrap support, reference lineages were defined. This study proposes a lineage framework and provides a dataset ranging from 34 to 145 sequences for each genotype 2 gene for orderly lineage designation of global genotype 2 genes of RVAs detected in human and animals. The framework identified five to 31 lineages depending on the gene. The least number of lineages (five to seven) were observed in genotypes A2 (NSP1), T2 (NSP3) and H2 (NSP5) which are limited to human RVA whereas the most number of lineages (31) was observed in genotype E2 (NSP4). Sharing of the same lineage constellations of the genotype 2 backbone genes between recently-emerging, unusual G1P[8], G3P[8], G8P[8] and G9P[4] reassortants and many contemporary G2P[4] strains provided strong support to the hypothesis that unusual genotype 2 strains originated primarily from reassortment events in the recent past involving contemporary G2P[4] strains as one parent and ordinary genotype 1 strains or animal RVA strains as the other. The lineage framework with selected reference sequences will help researchers to identify the lineage to which a given genotype 2 strain belongs, and trace the evolutionary history of common and unusual genotype 2 strains in circulation.
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