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França Y, Medeiros RS, Viana E, de Azevedo LS, Guiducci R, da Costa AC, Luchs A. Genetic diversity and evolution of G12P[6] DS-1-like and G12P[9] AU-1-like Rotavirus strains in Brazil. Funct Integr Genomics 2024; 24:92. [PMID: 38733534 DOI: 10.1007/s10142-024-01360-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/31/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
In the early 2000s, the global emergence of rotavirus (RVA) G12P[8] genotype was noted, while G12P[6] and G12P[9] combinations remained rare in humans. This study aimed to characterize and phylogenetically analyze three Brazilian G12P[9] and four G12P[6] RVA strains from 2011 to 2020, through RT-PCR and sequencing, in order to enhance our understanding of the genetic relationship between human and animal-origin RVA strains. G12P[6] strains displayed a DS-1-like backbone, showing a distinct genetic clustering. G12P[6] IAL-R52/2020, IAL-R95/2020 and IAL-R465/2019 strains clustered with 2019 Northeastern G12P[6] Brazilian strains and a 2018 Benin strain, whereas IAL-R86/2011 strain grouped with 2010 Northern G12P[6] Brazilian strains and G2P[4] strains from the United States and Belgium. These findings suggest an African genetic ancestry and reassortments with co-circulating American strains sharing the same DS-1-like constellation. No recent zoonotic reassortment was observed, and the DS-1-like constellation detected in Brazilian G12P[6] strains does not seem to be genetically linked to globally reported intergenogroup G1/G3/G9/G8P[8] DS-1-like human strains. G12P[9] strains exhibited an AU-1-like backbone with two different genotype-lineage constellations: IAL-R566/2011 and IAL-R1151/2012 belonged to a VP3/M3.V Lineage, and IAL-R870/2013 to a VP3/M3.II Lineage, suggesting two co-circulating strains in Brazil. This genetic diversity is not observed elsewhere, and the VP3/M3.II Lineage in G12P[9] strains seems to be exclusive to Brazil, indicating its evolution within the country. All three G12P[9] AU-1-like strains were closely relate to G12P[9] strains from Paraguay (2006-2007) and Brazil (2010). Phylogenetic analysis also highlighted that all South American G12P[9] AU-1-like strains had a common origin and supports the hypothesis of their importation from Asia, with no recent introduction from globally circulating G12P[9] strains or reassortments with local G12 strains P[8] or P[6]. Notably, certain genes in the Brazilian G12P[9] AU-1-like strains share ancestry with feline/canine RVAs (VP3/M3.II, NSP4/E3.IV and NSP2/N3.II), whereas NSP1/A3.VI likely originated from artiodactyls, suggesting a history of zoonotic transmission with human strains. This genomic data adds understanding to the molecular epidemiology of G12P[6] and G12P[9] RVA strains in Brazil, offering insights into their genetic diversity and evolution.
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Affiliation(s)
- Yasmin França
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Ellen Viana
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Raquel Guiducci
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Antonio Charlys da Costa
- Medical Parasitology Laboratory (LIM/46), São Paulo Tropical Medicine Institute, University of Sao Paulo, Sao Paulo, Brazil
| | - Adriana Luchs
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil.
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Cao M, Yuan F, Zhang W, Wang X, Ma J, Ma X, Kuai W, Ma X. Genomic analysis of two rare human G3P[9] rotavirus strains in Ningxia, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105518. [PMID: 37890809 DOI: 10.1016/j.meegid.2023.105518] [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: 09/22/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
G3P (Matthijnssens et al., 2008b [9]) is a rare combination of human rotavirus VP7/VP4 genotypes with a complex evolutionary pattern but limited related studies. Detailed genomic characterisation and genetic evolutionary analyses of G3P (Matthijnssens et al., 2008b [9]) rotaviruses have helped to enhance our understanding of rotavirus diversity. For the first time, we detected two human G3P (Matthijnssens et al., 2008b [9]) Rotavirus A (RVA) strains, RVA/Human-tc/CHN/2020999/2020/G3P (Matthijnssens et al., 2008b [9]) and RVA/Human-wt/CHN/23582009/2023/G3P (Matthijnssens et al., 2008b [9]), in diarrhoea patients from the Ningxia region of China, and carried out a whole-genome analysis of these strains. 2,020,999 and 23,582,009 have identical gene constellations: G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3, and this genotypic constellation was reported first time in China. They are closely related in 11 genome segments. The genotypes of these two strains are different from the human RVA strains L621 and E2451, which are only G3P (Matthijnssens et al., 2008b [9]) strains reported so far in China, but are identical to those of the Thai feline strain Meesuk and the Korean human strain CAU12-2-51.Phylogenetic analysis showed that the VP6, VP1-VP3, and NSP2 genes of the two strains in this study clustered with human/bovine and feline/bovine rotavirus strains to form a sublineage distinct from the common DS-1-like G2 human rotavirus. In contrast, the VP7, VP4, NSP1, and NSP3-NSP5 gene segments were closely associated with human/feline rotavirus and feline rotavirus strains. These findings suggest that the evolutionary origin of the G3P (Matthijnssens et al., 2008b [9]) human rotavirus found in Ningxia, China, is consistent with the Meesuk and CAU12-2-51 strains, may have arisen through reassortment between uncommon human/bovine, feline/bovine rotavirus strains and human/feline, feline rotaviruses. However, VP1-VP2 gene segments did not have the same lineage as strains Meesuk and CAU12-2-51, suggesting that these genes might be derived from additional reassortment event.
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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
| | - Wei Zhang
- Ningxia center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Xiuqin Wang
- 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
| | - Wenhe Kuai
- 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.
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Azevedo LS, Costa FF, Ghani MBA, Viana E, França Y, Medeiros RS, Guiducci R, Morillo SG, Primo D, Lopes RD, Gomes-Gouvêa MS, da Costa AC, Luchs A. Full genotype characterization of Brazilian canine G3P[3] strains during a 10-year survey (2012-2021) of rotavirus infection in domestic dogs and cats. Arch Virol 2023; 168:176. [PMID: 37306860 DOI: 10.1007/s00705-023-05807-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/25/2023] [Indexed: 06/13/2023]
Abstract
There is a dearth of information on the molecular epidemiology of rotaviruses in pets in Brazil. The aim of this study was to monitor rotavirus infections in household dogs and cats, determine full-genotype constellations, and obtain data on evolutionary relationships. Between 2012 and 2021, 600 fecal samples from dogs and cats (516 and 84, respectively) were collected at small animal clinics in São Paulo state, Brazil. Rotavirus screening was conducted using ELISA, PAGE, RT-PCR, sequencing, and phylogenetic analysis. Rotavirus type A (RVA) was detected in 0.5% (3/600) of the animals. No non-RVA types were detected. The three canine RVA strains were found to have a novel genetic constellation, G3-P[3] -I2-R3-C2-M3-A9-N2-T3-E3-H6, which has never been reported in dogs. As expected, all of the viral genes, except those encoding NSP2 and VP7, were closely related to the corresponding genes from canine, feline, and canine-like-human RVA strains. A novel N2 (NSP2) lineage was identified, grouping together Brazilian canine, human, rat and bovine strains, suggesting that genetic reassortment had occurred. Uruguayan G3 strains obtained from sewage contained VP7 genes that were phylogenetically close to those of the Brazilian canine strains, which suggests that these strains are widely distributed in pet populations in South American countries. For the NSP2 (I2), NSP3 (T3), NSP4 (E3), NSP5 (H6), VP1 (R3), VP3 (M3), and VP6 (I2) segments, phylogenetic analysis revealed possibly new lineages. The epidemiological and genetic data presented here point out the necessity for collaborative efforts to implement the One Health strategy in the field of RVA research and to provide an updated understanding of RVA strains circulating canines in Brazil.
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Affiliation(s)
- Lais Sampaio Azevedo
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | - Ellen Viana
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | - Yasmin França
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Raquel Guiducci
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Dieli Primo
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Michele Soares Gomes-Gouvêa
- Laboratorio de Gastroenterologia e Hepatologia Tropical-LIM07, Departamento de Gastroenterologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Laboratorio de Parasitologia Médica-LIM46, Departamento de Doenças Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Luchs
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil.
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil.
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Albuquerque MA, Deus DRD, Lobo PS, Teixeira DM, Maués MAC, Cardoso JF, Silva LDD, Gabbay YB, Resque HR, Silva Soares LD, Siqueira JAM, Guerra SFS. Detection of G3 human-like rotavirus in institutionalized dogs from Brazil. Braz J Microbiol 2023; 54:1295-1301. [PMID: 37076753 PMCID: PMC10234945 DOI: 10.1007/s42770-023-00972-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/07/2023] [Indexed: 04/21/2023] Open
Abstract
Viral gastroenteritis is a common clinical problem in dogs and group A rotavirus (RVA) is one of the agents involved in this etiology. It mainly affects dogs in the first 6 months of life, and these animals are considered an important reservoir and potential transmitters of the virus to other susceptible hosts, such as humans. Among the different types of RVA, G3 is the most detected in dogs, and this genotype is also involved in infections in other animals, including humans. Thus, the present study aims to investigate the presence of RVA in samples of dogs from a public kennel. A total of 64 fecal samples from dogs with diarrhea were analyzed, collected from April 2019 to March 2020, from the kennel of the Zoonosis Control Center, located in Belém, a city in the North of Brazil. The extracted genetic material was subjected to reverse transcription followed by real-time PCR (RT-qPCR); the positives were tested by RT-PCR with a specific primer for the RVA VP7 gene, after nucleotide sequencing and phylogenetic analysis. One sample was subjected to high-performance sequencing. A positivity of 7.8% (5/64) was observed for RVA, all characterized as G3, grouping in the G3-III lineage, with greater similarity to human samples. Different regions of the RVA genome fragments were found. These results emphasize the need for animal health surveillance to better understand the global strain dispersion of RVA and elucidate possible interspecies transmission events, monitoring the genetic diversity of this pathogen.
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Affiliation(s)
| | | | - Patrícia Santos Lobo
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | - Dielle Monteiro Teixeira
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | | | - Jedson Ferreira Cardoso
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | - Luciana Damascena da Silva
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | - Yvone Benchimol Gabbay
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | - Hugo Reis Resque
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | - Luana da Silva Soares
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil
| | | | - Sylvia Fátima Santos Guerra
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Pará, Ananindeua, Brazil.
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A G3P[9] rotavirus strain with an unusual genome constellation in a diarrheic cat in Thailand. Arch Virol 2023; 168:24. [PMID: 36593426 PMCID: PMC9807420 DOI: 10.1007/s00705-022-05641-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/28/2022] [Indexed: 01/04/2023]
Abstract
Rotavirus infection can cause diarrhea in many animal species. A 2-year-old indoor female Siamese cat with bloody mucoid diarrhea tested positive for rotavirus (RV) group A by real-time reverse transcription polymerase chain reaction (RT-PCR). Subsequent conventional RT-PCR amplification of the 11 RV segments and sequencing revealed a G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3 genome constellation. Phylogenetic analysis showed that the VP4, VP7, NSP1, NSP3, NSP4, and NSP5 genes were closely related to those of human feline-like rotaviruses, while the VP1, VP2, VP3, VP6, and NSP2 genes were genetically closest to those of human bovine-like rotaviruses, suggesting that genetic reassortment had occurred. The uniqueness of this G3P[9] feline rotavirus strain expands our knowledge about feline rotaviruses.
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Miao Q, Pan Y, Gong L, Guo L, Wu L, Jing Z, Zhang G, Tian J, Feng L. Full genome characterization of a human-porcine reassortment G12P[7] rotavirus and its pathogenicity in piglets. Transbound Emerg Dis 2022; 69:3506-3517. [PMID: 36150417 DOI: 10.1111/tbed.14712] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/13/2022] [Accepted: 09/17/2022] [Indexed: 02/04/2023]
Abstract
In recent years, increasing numbers of cases of acute gastroenteritis caused by Group A rotavirus (RVA) G12 strains have been reported in humans from many countries around the world, but G12 RVA detection in animals is currently less reported. Pigs are an important animal reservoir of zoonotic RVs and a mixing vessel for RVs. In 2020, RVA infection cases in piglets increased in China, which attracted more attention. During an epidemiological survey, a new type of porcine G12P[7] strain (CN127) was detected in pig farms across several provinces. Complete genome analyses revealed that strain CN127 possessed a Wa-like backbone with a genotype constellation of G12-P[7]-I1-C1-M1-R1-A8-N1-T1-E1-H1. The A8 genotype is indicative of its porcine rotavirus origin. Sequence identities and phylogenetic analyses showed that the VP2, VP4, NSP1, NSP4 and NSP5 genes were most closely related to those of porcine rotaviruses, but the VP1, VP6, VP7 and NSP2-3 genes were most closely related to those of human rotaviruses. CN127 likely emerged due to genetic reassortment between porcine and human rotavirus. In vivo experiments showed that CN127 infection caused gastrointestinal tract lesions in piglets and histopathological changes in the lung, liver and mesenteric lymph nodes (MLNs). In the small intestine, RVA antigen was detected in the duodenum and jejunum but not in the ileum. In the extra-intestinal tissues, RVA antigen was detected in the lung but not in the MLNs. Viral RNA was detected in the intestinal and extra-intestinal tissues as well as blood. This study reveals that RVA G12P[7] may become an epidemic strain in China and also provides further evidence that cocirculating human and porcine strains could produce new genotype rotaviruses with high virulence in piglets.
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Affiliation(s)
- Qian Miao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Yudi Pan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Lang Gong
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, People's Republic of China
| | - Longjun Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Ling Wu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Zhaoyang Jing
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Guihong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, People's Republic of China
| | - Jin Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
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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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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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9
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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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10
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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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11
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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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12
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Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events. Sci Rep 2018; 8:6011. [PMID: 29662148 PMCID: PMC5902508 DOI: 10.1038/s41598-018-24511-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/05/2018] [Indexed: 01/02/2023] Open
Abstract
After the introduction of two global rotavirus vaccines, RotaTeq in 2007 and Rotarix in 2008 in South Korea, G1[P8] rotavirus was the major rotavirus genotype in the country until 2012. However, in this study, an emergence of G2P[4] as the dominant genotype during the 2013 to 2015 season has been reported. Genetic analysis revealed that these viruses had typical DS-1-like genotype constellation and showed evidence of re-assortment in one or more genome segments, including the incorporation of NSP4 genes from strains B-47/2008 from a cow and R4/Haryana/2007 from a buffalo in India, and the VP1 and VP3 genes from strain GO34/1999 from a goat in Bangladesh. Compared to the G2 RotaTeq vaccine strain, 17–24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.
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13
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Dian Z, Wang B, Fan M, Dong S, Feng Y, Zhang AM, Liu L, Niu H, Li Y, Xia X. Completely genomic and evolutionary characteristics of human-dominant G9P[8] group A rotavirus strains in Yunnan, China. J Gen Virol 2017; 98:1163-1168. [PMID: 28613141 DOI: 10.1099/jgv.0.000807] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
G9P[8] rotavirus A (RVA) has been identified as the predominant genotype circulating in Yunnan, China. To elucidate the molecular characteristics of its genetic composition at the whole-genome level, the genomes of 12 strains isolated from paediatric patients with diarrhoea were fully sequenced and characterized. Eleven of the 12 strains were genotyped as G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, which is closely related to the Wa-like genotype 1 constellation. In contrast, one strain was genotyped as G9-P[8]-I1-R1-C1-M1-A1-N2-T1-E1-H1, with the NSP2 gene characterized as a DS-1 like genotype. Bayesian phylogenetic analysis indicated that G9 strains had emerged in 1932 with an estimated average evolutionary rate of 1.63×10-3 substitutions/site/year. Considering the high prevalence and fast evolutionary rate of G9P[8] rotaviruses, our results suggest that G9P[8] RVA should be strictly monitored in China.
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Affiliation(s)
- Ziqin Dian
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan 650500, PR China
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Yunnan 650032, PR China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan 650500, PR China
| | - Mao Fan
- Department of Clinical Laboratory, Kunming Children's Hospital, Yunnan 650034, PR China
| | - Shuwei Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan 650500, PR China
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan 650500, PR China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan 650500, PR China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan 650500, PR China
| | - Hua Niu
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Yunnan 650032, PR China
| | - Yuanyue Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan 650500, PR China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan 650500, PR China
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14
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Saikruang W, Khamrin P, Malasao R, Kumthip K, Ushijima H, Maneekarn N. Complete genome analysis of a rare G12P[6] rotavirus isolated in Thailand in 2012 reveals a prototype strain of DS-1-like constellation. Virus Res 2016; 224:38-45. [PMID: 27565028 DOI: 10.1016/j.virusres.2016.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/29/2016] [Accepted: 08/02/2016] [Indexed: 12/22/2022]
Abstract
Species A rotaviruses (RVAs) are a major cause of severe diarrhea in children worldwide. G12 RVA detection is currently increasing and has been reported from many countries around the world. However, few studies have reported whole genome sequences of G12 RVAs. In the present study, the complete genome sequence of a G12P[6] RVA strain (RVA/Human-wt/THA/CMHN49-12/2012/G12P[6]) detected in a stool sample from a child with acute gastroenteritis in 2012 in Thailand was analyzed. In the CMHN49-12 strain, all genome segments had a DS-1-like backbone: G12-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2 indicates that it is most likely the prototype strain of G12P[6] with a DS-1-like genotype constellation. Based on a Bayesian evolutionary analysis of VP7 nucleotide sequence, G12 RVA strains reported previously from Thailand during the period of 2007-2012 could be divided into 3 clusters, indicating that they originated from at least 3 different ancestral G12 strains. The evolutionary rate of G12 calculated by Bayesian Markov Chain Monte Carlo analysis indicated that the nucleotide substitution rate of G12 was 1.11×10(-3) mutations/site/year. The finding of a G12P[6] RVA possessing a DS-1-like backbone provides insights into the evolution of global G12 RVAs.
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Affiliation(s)
- Wilaiporn Saikruang
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Rungnapa Malasao
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
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15
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Evidence of multiple reassortment events of feline-to-human rotaviruses based on a rare human G3P[9] rotavirus isolated from a patient with acute gastroenteritis. Comp Immunol Microbiol Infect Dis 2016; 46:53-9. [DOI: 10.1016/j.cimid.2016.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 12/11/2022]
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16
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Silva FDF, Gregori F, McDonald SM. Distinguishing the genotype 1 genes and proteins of human Wa-like rotaviruses vs. porcine rotaviruses. INFECTION GENETICS AND EVOLUTION 2016; 43:6-14. [PMID: 27180895 DOI: 10.1016/j.meegid.2016.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 11/16/2022]
Abstract
Group A rotaviruses (RVAs) are 11-segmented, double-stranded RNA viruses and important causes of gastroenteritis in the young of many animal species. Previous studies have suggested that human Wa-like RVAs share a close evolutionary relationship with porcine RVAs. Specifically, the VP1-VP3 and NSP2-5/6 genes of these viruses are usually classified as genotype 1 with >81% nucleotide sequence identity. Yet, it remains unknown whether the genotype 1 genes and proteins of human Wa-like strains are distinguishable from those of porcine strains. To investigate this, we performed comprehensive bioinformatic analyses using all known genotype 1 gene sequences. The RVAs analyzed represent wildtype strains isolated from humans or pigs at various geographical locations during the years of 2004-2013, including 11 newly-sequenced porcine RVAs from Brazil. We also analyzed archival strains that were isolated during the years of 1977-1992 as well as atypical strains involved in inter-species transmission between humans and pigs. We found that, in general, the genotype 1 genes of typical modern human Wa-like RVAs clustered together in phylogenetic trees and were separate from those of typical modern porcine RVAs. The only exception was for the NSP5/6 gene, which showed no host-specific phylogenetic clustering. Using amino acid sequence alignments, we identified 34 positions that differentiated the VP1-VP3, NSP2, and NSP3 genotype 1 proteins of typical modern human Wa-like RVAs versus typical modern porcine RVAs and documented how these positions vary in the archival/unusual isolates. No host-specific amino acid positions were identified for NSP4, NSP5, or NSP6. Altogether, the results of this study support the notion that human Wa-like RVAs and porcine RVAs are evolutionarily related, but indicate that some of their genotype 1 genes and proteins have diverged over time possibly as a reflection of sequestered replication and protein co-adaptation in their respective hosts.
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Affiliation(s)
- Fernanda D F Silva
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Brazil
| | - F Gregori
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Brazil
| | - Sarah M McDonald
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA; Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA.
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17
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The prevalence and genotype diversity of Human Rotavirus A circulating in Thailand, 2011-2014. INFECTION GENETICS AND EVOLUTION 2015; 37:129-36. [PMID: 26593177 DOI: 10.1016/j.meegid.2015.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 11/06/2015] [Accepted: 11/14/2015] [Indexed: 01/11/2023]
Abstract
Human rotavirus A (RVA) is the major infectious virus causing acute watery diarrhea in children, especially those younger than 5 years of age, and is a major public health problem in Thailand. Outbreaks of this virus have been reported worldwide. Besides the common genotypes, unusual genotypes providing evidence of inter-species transmission have also been described. Therefore, the aim of this study was to investigate the prevalence and genotypes of RVA in Thailand. A total of 688 samples were collected from children who were hospitalized with acute diarrhea in Chumphae Hospital in Khon Kaen and Chulalongkorn Hospital in Bangkok. RVA was detected using one-step RT-PCR and the genotypes were evaluated by sequencing. Overall, 204 of the 688 samples (30%) were positive for RVA. Nine genotypes were identified: three common in humans (G1P[8] [53%], G2P[4] [18%], G3P[8] [12%]), one feline-like (G3P[9] [1%]), four porcine-like (G4P[6] [0.5%], G5P[6] [0.5%], G9P[8] [0.5%], G12P[6] [1.5%]), and one bovine-like (G8P[8] [13%]). The variation in virus genotypes and the animal-like genotypes detected in this study suggested that a high diversity of RVA types is circulating in the Thai population. Therefore, continuous molecular epidemiological monitoring of RVA is essential and has implications for the national vaccination program.
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18
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Komoto S, Tacharoenmuang R, Guntapong R, Ide T, Haga K, Katayama K, Kato T, Ouchi Y, Kurahashi H, Tsuji T, Sangkitporn S, Taniguchi K. Emergence and Characterization of Unusual DS-1-Like G1P[8] Rotavirus Strains in Children with Diarrhea in Thailand. PLoS One 2015; 10:e0141739. [PMID: 26540260 PMCID: PMC4634990 DOI: 10.1371/journal.pone.0141739] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/12/2015] [Indexed: 12/11/2022] Open
Abstract
The emergence and rapid spread of unusual DS-1-like G1P[8] rotaviruses in Japan have been recently reported. During rotavirus surveillance in Thailand, three DS-1-like G1P[8] strains (RVA/Human-wt/THA/PCB-180/2013/G1P[8], RVA/Human-wt/THA/SKT-109/2013/G1P[8], and RVA/Human-wt/THA/SSKT-41/2013/G1P[8]) were identified in stool specimens from hospitalized children with severe diarrhea. In this study, we sequenced and characterized the complete genomes of strains PCB-180, SKT-109, and SSKT-41. On whole genomic analysis, all three strains exhibited a unique genotype constellation including both genogroup 1 and 2 genes: G1-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. This novel genotype constellation is shared with Japanese DS-1-like G1P[8] strains. Phylogenetic analysis revealed that the G/P genes of strains PCB-180, SKT-109, and SSKT-41 appeared to have originated from human Wa-like G1P[8] strains. On the other hand, the non-G/P genes of the three strains were assumed to have originated from human DS-1-like strains. Thus, strains PCB-180, SKT-109, and SSKT-41 appeared to be derived through reassortment event(s) between Wa-like G1P[8] and DS-1-like human rotaviruses. Furthermore, strains PCB-180, SKT-109, and SSKT-41 were found to have the 11-segment genome almost indistinguishable from one another in their nucleotide sequences and phylogenetic lineages, indicating the derivation of the three strains from a common origin. Moreover, all the 11 genes of the three strains were closely related to those of Japanese DS-1-like G1P[8] strains. Therefore, DS-1-like G1P[8] strains that have emerged in Thailand and Japan were assumed to have originated from a recent common ancestor. To our knowledge, this is the first report on whole genome-based characterization of DS-1-like G1P[8] strains that have emerged in an area other than Japan. Our observations will provide important insights into the evolutionary dynamics of emerging DS-1-like G1P[8] rotaviruses.
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Affiliation(s)
- Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- * E-mail:
| | | | - Ratigorn Guntapong
- Department of Medical Sciences, National Institute of Health, Nonthaburi, Thailand
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Yuya Ouchi
- Genome and Transcriptome Analysis Center, Fujita Health University, Toyoake, Aichi, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
- Genome and Transcriptome Analysis Center, Fujita Health University, Toyoake, Aichi, Japan
| | - Takao Tsuji
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Somchai Sangkitporn
- Department of Medical Sciences, National Institute of Health, Nonthaburi, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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19
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Otto PH, Rosenhain S, Elschner MC, Hotzel H, Machnowska P, Trojnar E, Hoffmann K, Johne R. Detection of rotavirus species A, B and C in domestic mammalian animals with diarrhoea and genotyping of bovine species A rotavirus strains. Vet Microbiol 2015. [DOI: 10.1016/j.vetmic.2015.07.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Doan YH, Nakagomi T, Agbemabiese CA, Nakagomi O. Changes in the distribution of lineage constellations of G2P[4] Rotavirus A strains detected in Japan over 32years (1980–2011). INFECTION GENETICS AND EVOLUTION 2015; 34:423-33. [DOI: 10.1016/j.meegid.2015.05.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 05/19/2015] [Accepted: 05/27/2015] [Indexed: 01/27/2023]
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21
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Ide T, Komoto S, Higo-Moriguchi K, Htun KW, Myint YY, Myat TW, Thant KZ, Thu HM, Win MM, Oo HN, Htut T, Wakuda M, Dennis FE, Haga K, Fujii Y, Katayama K, Rahman S, Nguyen SV, Umeda K, Oguma K, Tsuji T, Taniguchi K. Whole Genomic Analysis of Human G12P[6] and G12P[8] Rotavirus Strains that Have Emerged in Myanmar. PLoS One 2015; 10:e0124965. [PMID: 25938434 PMCID: PMC4418666 DOI: 10.1371/journal.pone.0124965] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/20/2015] [Indexed: 11/18/2022] Open
Abstract
G12 rotaviruses are emerging rotavirus strains causing severe diarrhea in infants and young children worldwide. However, the whole genomes of only a few G12 strains have been fully sequenced and analyzed. In this study, we sequenced and characterized the complete genomes of six G12 strains (RVA/Human-tc/MMR/A14/2011/G12P[8], RVA/Human-tc/MMR/A23/2011/G12P[6], RVA/Human-tc/MMR/A25/2011/G12P[8], RVA/Human-tc/MMR/P02/2011/G12P[8], RVA/Human-tc/MMR/P39/2011/G12P[8], and RVA/Human-tc/MMR/P43/2011/G12P[8]) detected in six stool samples from children with acute gastroenteritis in Myanmar. On whole genomic analysis, all six Myanmarese G12 strains were found to have a Wa-like genetic backbone: G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 for strains A14, A25, P02, P39, and P43, and G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 for strain A23. Phylogenetic analysis showed that most genes of the six strains examined in this study were genetically related to globally circulating human G1, G3, G9, and G12 strains. Of note is that the NSP4 gene of strain A23 exhibited the closest relationship with the cognate genes of human-like bovine strains as well as human strains, suggesting the occurrence of reassortment between human and bovine strains. Furthermore, strains A14, A25, P02, P39, and P43 were very closely related to one another in all the 11 gene segments, indicating derivation of the five strains from a common origin. On the other hand, strain A23 consistently formed distinct clusters as to all the 11 gene segments, indicating a distinct origin of strain A23 from that of strains A14, A25, P02, P39, and P43. To our knowledge, this is the first report on whole genome-based characterization of G12 strains that have emerged in Myanmar. Our observations will provide important insights into the evolutionary dynamics of spreading G12 rotaviruses in Asia.
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Affiliation(s)
- Tomihiko Ide
- 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:
| | - Kyoko Higo-Moriguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Khaing Win Htun
- Nay Pyi Taw General Hospital (Central Myanmar), Nay Pyi Taw, Myanmar
| | - Yi Yi Myint
- Department of Medical Research (Upper Myanmar), Pyin Oo Lwin, Myanmar
| | | | - Kyaw Zin Thant
- Department of Medical Research (Lower Myanmar), Yangon, Myanmar
| | - Hlaing Myat Thu
- Department of Medical Research (Lower Myanmar), Yangon, Myanmar
| | - Mo Mo Win
- Department of Medical Research (Lower Myanmar), Yangon, Myanmar
| | - Htun Naing Oo
- Department of Traditional Medicine (Central Myanmar), Nay Pyi Taw, Myanmar
| | - Than Htut
- Ministry of Health (Central Myanmar), Nay Pyi Taw, Myanmar
| | - Mitsutaka Wakuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Francis Ekow Dennis
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Shofiqur Rahman
- Immunology Research Institute in Gifu, EW Nutrition Japan, Gifu, Japan
| | - Sa Van Nguyen
- Immunology Research Institute in Gifu, EW Nutrition Japan, Gifu, Japan
| | - Kouji Umeda
- Immunology Research Institute in Gifu, EW Nutrition Japan, Gifu, Japan
| | - Keiji Oguma
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Takao Tsuji
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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22
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Tsugawa T, Rainwater-Lovett K, Tsutsumi H. Human G3P[9] rotavirus strains possessing an identical genotype constellation to AU-1 isolated at high prevalence in Brazil, 1997-1999. J Gen Virol 2014; 96:590-600. [PMID: 25467218 DOI: 10.1099/vir.0.071373-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rotavirus (RV) A is a very common cause of acute diarrhoea in infants and young children worldwide. Most human strains are classified into two major Wa-like and DS-1-like genotype constellations, whilst a minor third strain, AU-1, was described in 1989 among human RV isolates from Japan. AU-1 demonstrates a high degree of homology to a feline RV, FRV-1, which suggests interspecies transmission of feline RV. However, there has been no subsequent report of RVs possessing the AU-1 genotype throughout all 11 genes of the genome. Between March 1997 and December 1999, 157 RV-positive stool samples were collected from Brazilian children, and 16 of the RVs (10.2 %) were P[9] genotype. We analysed eight strains by almost full-genome sequencing. These eight strains were divided into two groups: five AU-1-like and three Wa-like strains. Four of the five AU-1-like strains had the AU-1-like genotype constellation throughout the 11 genes. The remaining AU-1-like strain was considered to be a reassortant strain comprosed of nine, two and one genes from the AU-1-like, Wa-like and G9 strains, respectively. The three Wa-like strains were considered to be reassortants comprising seven to eight genes and three to four genes from Wa-like and non-Wa-like strains, respectively. This report of human G3P[9] RV strains possessing the AU-1 genotype constellation throughout all genes demonstrates the stability and infectivity of the AU-1-like strain with its original genotype over distance and time.
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Affiliation(s)
- Takeshi Tsugawa
- Rotavirus Vaccine Development Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
| | - Kaitlin Rainwater-Lovett
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.,Rotavirus Vaccine Development Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hiroyuki Tsutsumi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
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23
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Ndze VN, Esona MD, Achidi EA, Gonsu KH, Dóró R, Marton S, Farkas S, Ngeng MB, Ngu AF, Obama-Abena MT, Bányai K. Full genome characterization of human Rotavirus A strains isolated in Cameroon, 2010–2011: Diverse combinations of the G and P genes and lack of reassortment of the backbone genes. INFECTION GENETICS AND EVOLUTION 2014; 28:537-60. [DOI: 10.1016/j.meegid.2014.10.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/09/2014] [Accepted: 10/11/2014] [Indexed: 12/17/2022]
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24
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Mullick S, Mukherjee A, Ghosh S, Pazhani GP, Sur D, Manna B, Nataro JP, Levine MM, Ramamurthy T, Chawla-Sarkar M. Community based case-control study of rotavirus gastroenteritis among young children during 2008-2010 reveals vast genetic diversity and increased prevalence of G9 strains in Kolkata. PLoS One 2014; 9:e112970. [PMID: 25401757 PMCID: PMC4234499 DOI: 10.1371/journal.pone.0112970] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 10/17/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Group A Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children (<5 years) worldwide. Although rotavirus vaccines have been successfully administered in many countries, in India the introduction of rotavirus vaccine in national immunization program was approved in 2014. Since high disease burden and large number of genetic variants have been reported from low income countries including India, monitoring of rotavirus was initiated prior to implementation of the vaccine in the region. METHODS A total number of 3,582 stool samples were collected from an urban slum community in Kolkata, among which 1,568 samples were obtained from children of ≤ 5 years of age, with moderate to severe diarrhoea and 2,014 samples were collected from age-sex matched healthy neighbourhood controls. Rotavirus positive samples were typed by multiplex semi-nested PCR and nucleotide sequencing. Circulating strains were phylogenetically analyzed. RESULTS Among 1,568 children with diarrhoea, 395 (25.2%), and among 2,014 asymptomatic children, 42 (2%) were rotavirus positive. G1P[8] was identified as the most common strain (32%) followed by G9P[8] (16.9%), G2P[4] (13.5%) and G9P[4] (10.75%). G12 strains with combinations of P[4], P[6] and P[8] comprised 11.9% of total positive strains. The rest (<10%) were rare and uncommon strains like G1P[4], G1P[6], G2P[8] and animal-like strains G4P[6], G6P[14] and G11P[25]. The 42 rotavirus positive samples from asymptomatic children revealed common genotypes like G1, G2 and G9. CONCLUSION This community based case-control study showed increased predominance of genotype G9 in Kolkata. It also confirmed co-circulation of a large number of genetic variants in the community. Asymptomatic rotavirus positive children though low in number can also be a source of dispersal of infection in the community. This study provides background information to the policy makers for implementation of rotavirus vaccines in this region.
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Affiliation(s)
- Satarupa Mullick
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Anupam Mukherjee
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Santanu Ghosh
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Dipika Sur
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Byomkesh Manna
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - James P. Nataro
- Department of Paediatrics, University of Virginia, School of Medicine, Charlottesville, Virginia, United States of America
| | - Myron M. Levine
- Center for Vaccine Development, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
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25
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Papp H, Marton S, Farkas SL, Jakab F, Martella V, Malik YS, Palya V, Bányai K. Classification and characterization of a laboratory chicken rotavirus strain carrying G7P[35] neutralization antigens on the genotype 4 backbone gene configuration. Biologicals 2014; 42:299-304. [PMID: 25284347 DOI: 10.1016/j.biologicals.2014.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/30/2014] [Accepted: 08/18/2014] [Indexed: 12/23/2022] Open
Abstract
The laboratory rotavirus strain, BRS/115, has been used for more than two decades to monitor rotaviruses in specific pathogen free flocks of laying hens. However, the virus strain has not been characterized in detail. Therefore we aimed at the description of molecular features of BRS115 by using random primed reverse transcription-PCR of the genomic RNA followed by massive parallel sequencing using the semiconductor sequencing technology. Over 64,000 trimmed reads mapped to reference sequences obtained from GenBank. The strain classified into the species Rotavirus A and genotyped G7-P[35]-I4-R4-C4-M4-A16-N4-T4-E11-H4 according to guidelines of the Rotavirus Classification Working Group. Phylogenetic analysis identified shared features with chicken, turkey and pigeon origin rotaviruses. This study demonstrates the robustness of next generation sequencing in the characterization of reference virus materials used in specialized laboratories.
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Affiliation(s)
- Hajnalka Papp
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
| | - Szilvia L Farkas
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
| | - Ferenc Jakab
- Institute of Biology, Faculty of Sciences, University of Pécs, Ifjúság útja 6., H-7624 Pécs, Hungary; János Szentágothai Research Center, University of Pécs, Ifjúság útja 20., H-7624 Pécs, Hungary
| | - Vito Martella
- Department of Veterinary Public Health, University of Bari, S.p. per Casamassima km 3, 70010 Valenzano, Bari, Italy
| | - Yashpal S Malik
- Division of Biological Standardisation, Indian Veterinary Research Institute (IVRI), Izatnagar, 243 122 Bareilly, Uttar Pradesh, India
| | - Vilmos Palya
- Ceva-Phylaxia Veterinary Biologicals Co. Ltd., Szállás u. 5., H-1107 Budapest, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary.
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26
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Analysis of human rotaviruses from a single location over an 18-year time span suggests that protein coadaption influences gene constellations. J Virol 2014; 88:9842-63. [PMID: 24942570 DOI: 10.1128/jvi.01562-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
UNLABELLED Rotaviruses (RVs) are 11-segmented, double-stranded RNA viruses that cause severe gastroenteritis in children. In addition to an error-prone genome replication mechanism, RVs can increase their genetic diversity by reassorting genes during host coinfection. Such exchanges allow RVs to acquire advantageous genes and adapt in the face of selective pressures. However, reassortment may also impose fitness costs if it unlinks genes/proteins that have accumulated compensatory, coadaptive mutations and that operate best when kept together. To better understand human RV evolutionary dynamics, we analyzed the genome sequences of 135 strains (genotype G1/G3/G4-P[8]-I1-C1-R1-A1-N1-T1-E1-H1) that were collected at a single location in Washington, DC, during the years 1974 to 1991. Intragenotypic phylogenetic trees were constructed for each viral gene using the nucleotide sequences, thereby defining novel allele level gene constellations (GCs) and illuminating putative reassortment events. The results showed that RVs with distinct GCs cocirculated during the vast majority of the collection years and that some of these GCs persisted in the community unchanged by reassortment. To investigate the influence of protein coadaptation on GC maintenance, we performed a mutual information-based analysis of the concatenated amino acid sequences and identified an extensive covariance network. Unexpectedly, amino acid covariation was highest between VP4 and VP2, which are structural components of the RV virion that are not thought to directly interact. These results suggest that GCs may be influenced by the selective constraints placed on functionally coadapted, albeit noninteracting, viral proteins. This work raises important questions about mutation-reassortment interplay and its impact on human RV evolution. IMPORTANCE Rotaviruses are devastating human pathogens that cause severe diarrhea and kill >450,000 children each year. The virus can evolve by accumulating mutations and by acquiring new genes from other strains via a process called reassortment. However, little is known about the relationship between mutation accumulation and gene reassortment for rotaviruses and how it impacts viral evolution. In this study, we analyzed the genome sequences of human strains found in clinical fecal specimens that were collected at a single hospital over an 18-year time span. We found that many rotaviruses did not reassort their genes but instead maintained them as specific sets (i.e., constellations). By analyzing the encoded proteins, we discovered concurrent amino acid changes among them, which suggests that they are functionally coadapted to operate best when kept together. This study increases our understanding of how rotaviruses evolve over time in the human population.
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