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Munlela B, João ED, Strydom A, Bauhofer AFL, Chissaque A, Chilaúle JJ, Maurício IL, Donato CM, O’Neill HG, de Deus N. Whole-Genome Characterization of Rotavirus G9P[6] and G9P[4] Strains That Emerged after Rotavirus Vaccine Introduction in Mozambique. Viruses 2024; 16:1140. [PMID: 39066302 PMCID: PMC11281483 DOI: 10.3390/v16071140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Mozambique introduced the Rotarix® vaccine into the National Immunization Program in September 2015. Following vaccine introduction, rotavirus A (RVA) genotypes, G9P[4] and G9P[6], were detected for the first time since rotavirus surveillance programs were implemented in the country. To understand the emergence of these strains, the whole genomes of 47 ELISA RVA positive strains detected between 2015 and 2018 were characterized using an Illumina MiSeq-based sequencing pipeline. Of the 29 G9 strains characterized, 14 exhibited a typical Wa-like genome constellation and 15 a DS-1-like genome constellation. Mostly, the G9P[4] and G9P[6] strains clustered consistently for most of the genome segments, except the G- and P-genotypes. For the G9 genotype, the strains formed three different conserved clades, separated by the P type (P[4], P[6] and P[8]), suggesting different origins for this genotype. Analysis of the VP6-encoding gene revealed that seven G9P[6] strains clustered close to antelope and bovine strains. A rare E6 NSP4 genotype was detected for strain RVA/Human-wt/MOZ/HCN1595/2017/G9P[4] and a genetically distinct lineage IV or OP354-like P[8] was identified for RVA/Human-wt/MOZ/HGJM0644/2015/G9P[8] strain. These results highlight the need for genomic surveillance of RVA strains detected in Mozambique and the importance of following a One Health approach to identify and characterize potential zoonotic strains causing acute gastroenteritis in Mozambican children.
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Affiliation(s)
- Benilde Munlela
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Eva D. João
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
| | - Amy Strydom
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Avenue, Bloemfontein 9301, South Africa; (A.S.); (H.G.O.)
| | - Adilson Fernando Loforte Bauhofer
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Assucênio Chissaque
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Jorfélia J. Chilaúle
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
| | - Isabel L. Maurício
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal;
| | - Celeste M. Donato
- The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3000, Australia;
| | - Hester G. O’Neill
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Avenue, Bloemfontein 9301, South Africa; (A.S.); (H.G.O.)
| | - Nilsa de Deus
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
- Departamento de Ciências Biológicas, Universidade Eduardo Mondlane, Julius Nyerere Avenue, Maputo 3453, Mozambique
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Khakha SA, Varghese T, Giri S, Durbin A, Tan GS, Kalaivanan M, Prasad JH, Kang G. Whole-genome characterization of common rotavirus strains circulating in Vellore, India from 2002 to 2017: emergence of non-classical genomic constellations. Gut Pathog 2023; 15:44. [PMID: 37730725 PMCID: PMC10510252 DOI: 10.1186/s13099-023-00569-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/27/2023] [Indexed: 09/22/2023] Open
Abstract
Rotaviruses (RVs) are the most common etiological agent of acute gastroenteritis among young children, even after vaccine introduction in low-income countries. A whole-genome classification representing the 11 RV genes, was introduced for surveillance and characterization of RVs. This study characterized the common circulating strains in Vellore, India from 2002 to 2017 to understand rotavirus strain diversity and evolution using Whole genome sequencing (WGS) carried out on Illumina MiSeq. The 89% (92% of Wa-like, 86% of DS-1-like) of strains had classical constellations, while reassortant constellations were seen in 11% (8% of Wa-like, 14% of DS-1-like) of the strains. The rare E6-NSP4 in combination with DS-1 like G1P[8] and the emergence of the OP-354 subtype of P[8] were identified. Phylogenetics of RV strains revealed multiple subtypes circulating in the past 15 years, with strong evidence of animal to human gene transmission among several strains.
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Affiliation(s)
- Shainey Alokit Khakha
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Tintu Varghese
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Sidhartha Giri
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Alan Durbin
- J. Craig Venter Institute, La Jolla, San Diego, CA, 92037, USA
| | - Gene S Tan
- J. Craig Venter Institute, La Jolla, San Diego, CA, 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, San Diego, CA, 92037, USA
| | - Maheswari Kalaivanan
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | - Gagandeep Kang
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India.
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Kachooei A, Tava Koli A, Minaeian S, Hosseini M, Jalilvand S, Latifi T, Arashkia A, Ataei-Pirkooh A, Shoja Z. Molecular characterization of rotavirus infections in children less than 5 years of age with acute gastroenteritis in Tehran, Iran, 2021-2022: Emergence of uncommon G9P[4] and G9P[8] rotavirus strains. J Med Virol 2023; 95:e28529. [PMID: 36698258 DOI: 10.1002/jmv.28529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023]
Abstract
The present study was conducted to monitor the genotypes of circulating species A rotavirus (RVA) in Iran and investigate genetic linkages between specific RVA VP7, VP4, VP6, and NSP4 segments. For this purpose, 48 RVA strains were detected during the 2021-2022 seasons. The two combinations of G9P[4] and G9P[8] RVA strains were predominant. However, several other combinations of RVA also were detected. Based on the distribution of I and E genotypes (46 strains) with respect to G and P, the most common strains were G9P[4]-I2-E2 (19.5%), G9P[4]-I2-E1 (6.5%), G9P[4]-I1-E1 (4.3%), G9P[8]-I1-E1 (19.5%), and G9P[8]-I2-E2 (10.9%), which were followed by several other combinations of G and P RVA strains with different pattern of I-E genotypes and also emerging, rare and uncommon strains. The present study described the continued circulation of G9 strains with the emergence of uncommon G9P[4] and G9P[8] reassortants with three and two different I-E genotypes, respectively, which have not been reported previously in Iran. Our findings indicated that these uncommon strains exhibited a unique genotype pattern comprising a mixture of genogroup 1 and 2 genes and suggest the need for further analysis of rare, uncommon, and emerging strains of RVA at all 11 gene segments to determine intergenogroup and intragenotype reassortments.
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Affiliation(s)
- Atefeh Kachooei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Ahmad Tava Koli
- Rsearch Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Minaeian
- Antimicrobial Resistance Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Mahdieh Hosseini
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Tayebeh Latifi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Arashkia
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran.,Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Angila Ataei-Pirkooh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran.,Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
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Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016-2018. Virus Res 2022; 313:198715. [PMID: 35247484 DOI: 10.1016/j.virusres.2022.198715] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022]
Abstract
Species A Rotaviruses (RVA) still play a major role in causing acute diarrhea in children under five years old worldwide. Currently, an 11-gene classification system is used to designate the full genotypic constellations of circulating strains. Viral proteins and non-structural proteins in the order VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 are represented by the genotypes Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx, respectively. In Benin, ROTAVAC® vaccine was introduced into the Expanded Programme on Immunization in December 2019. To monitor circulating RVA strains for changes that may affect vaccine performance, in-depth analysis of strains prior to vaccine introduction are needed. Here we report, the whole-gene characterization (11 ORFs) for 72 randomly selected RVA strains of common and unusual genotypes collected in Benin from the 2016-2018 seasons. The sequenced strains were 15 G1P[8], 20 G2P[4], 5 G9P[8], 14 G12P[8], 9 G3P[6], 2 G1P[6], 3 G2P[6], 2 G9P[4], 1 G12P[6], and 1 G1G9P[8]/P[4]. The study strains exhibited two genetic constellations designed as Wa-like G1/G9/G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and DS-1-like G2/G3/G12-P[4]/P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Genotype G9P[4] strains possessed a DS-1-like genetic constellation with an E6 NSP4 gene, G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2. The mixed genotype showed both Wa-like and DS-1-like profiles with a T6 NSP3 gene G1/G9P[8]/[4]-I1/I2-R1/R2-C1/C2-M1/M2-A1/A2-N1/N2-T1/T6-E1/E6-H1/H2. At the allelic level, the analysis of the Benin strains, reference strains (with known alleles), vaccine strains (with known alleles) identified 2-13 and 1-17 alleles for DS-1-like and Wa-like strains, respectively. Most of the study strains clustered into previously defined alleles, but we defined 3 new alleles for the VP7 (G3=1 new allele and G12=2 new alleles) and VP4 (P[4]=1 new allele and P[6]=2 new alleles) genes which formed the basis of the VP7 and VP4 gene clusters, respectively. For the remaining 9 genes, 0-6 new alleles were identified for both Wa-like and DS-1-like strains. This analysis of whole genome sequences of RVA strains circulating in Benin described genetic point mutations and reassortment events as well as novel alleles. Further detailed studies on these new alleles are needed and these data can also provide a baseline for studies on RVA in the post-vaccination period.
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Rasebotsa S, Uwimana J, Mogotsi MT, Rakau K, Magagula NB, Seheri ML, Mwenda JM, Mphahlele MJ, Sabiu S, Mihigo R, Mutesa L, Nyaga MM. Whole-Genome Analyses Identifies Multiple Reassortant Rotavirus Strains in Rwanda Post-Vaccine Introduction. Viruses 2021; 13:v13010095. [PMID: 33445703 PMCID: PMC7828107 DOI: 10.3390/v13010095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 12/23/2022] Open
Abstract
Children in low-and middle-income countries, including Rwanda, experience a greater burden of rotavirus disease relative to developed countries. Evolutionary mechanisms leading to multiple reassortant rotavirus strains have been documented over time which influence the diversity and evolutionary dynamics of novel rotaviruses. Comprehensive rotavirus whole-genome analysis was conducted on 158 rotavirus group A (RVA) samples collected pre- and post-vaccine introduction in children less than five years in Rwanda. Of these RVA positive samples, five strains with the genotype constellations G4P[4]-I1-R2-C2-M2-A2-N2-T1-E1-H2 (n = 1), G9P[4]-I1-R2-C2-M2-A1-N1-T1-E1-H1 (n = 1), G12P[8]-I1-R2-C2-M1-A1-N2-T1-E2-H3 (n = 2) and G12P[8]-I1-R1-C1-M1-A2-N2-T2-E1-H1 (n = 1), with double and triple gene reassortant rotavirus strains were identified. Phylogenetic analysis revealed a close relationship between the Rwandan strains and cognate human RVA strains as well as the RotaTeq® vaccine strains in the VP1, VP2, NSP2, NSP4 and NSP5 gene segments. Pairwise analyses revealed multiple differences in amino acid residues of the VP7 and VP4 antigenic regions of the RotaTeq® vaccine strain and representative Rwandan study strains. Although the impact of such amino acid changes on the effectiveness of rotavirus vaccines has not been fully explored, this analysis underlines the potential of rotavirus whole-genome analysis by enhancing knowledge and understanding of intergenogroup reassortant strains circulating in Rwanda post vaccine introduction.
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Affiliation(s)
- Sebotsana Rasebotsa
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (S.R.); (M.T.M.); (S.S.)
| | - Jeannine Uwimana
- Department of Laboratory, Clinical Biology, Kigali University Teaching Hospital, P.O. Box 4285, Kigali, Rwanda;
| | - Milton T. Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (S.R.); (M.T.M.); (S.S.)
| | - Kebareng Rakau
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa; (K.R.); (N.B.M.); (M.L.S.); (M.J.M.)
| | - Nonkululeko B. Magagula
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa; (K.R.); (N.B.M.); (M.L.S.); (M.J.M.)
| | - Mapaseka L. Seheri
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa; (K.R.); (N.B.M.); (M.L.S.); (M.J.M.)
| | - Jason M. Mwenda
- World Health Organization, Regional Office for Africa, P.O. Box 06, Brazzaville, Congo; (J.M.M.); (R.M.)
| | - M. Jeffrey Mphahlele
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa; (K.R.); (N.B.M.); (M.L.S.); (M.J.M.)
- South African Medical Research Council, 1 Soutpansberg Road, Pretoria 0001, South Africa
| | - Saheed Sabiu
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (S.R.); (M.T.M.); (S.S.)
| | - Richard Mihigo
- World Health Organization, Regional Office for Africa, P.O. Box 06, Brazzaville, Congo; (J.M.M.); (R.M.)
| | - Leon Mutesa
- Centre for Human Genetics, University of Rwanda, College of Medicine and Health Sciences, P.O. Box 4285, Kigali, Rwanda;
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (S.R.); (M.T.M.); (S.S.)
- Correspondence: ; Tel.: +27-51-401-9158
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Tatte VS, Maran D, Walimbe AM, Gopalkrishna V. Rotavirus G9P[4], G9P[6] and G1P[6] strains isolated from children with acute gastroenteritis in Pune, western India, 2013-2015: evidence for recombination in genes encoding VP3, VP4 and NSP1. J Gen Virol 2019; 100:1605-1630. [PMID: 31553304 DOI: 10.1099/jgv.0.001323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species A rotaviruses (RVAs) are genetically diverse pathogens. These are the most evolutionarily adaptable organisms, with a multitude of mechanisms for evolutionary change. To date, full-genome classification has been proved to be an excellent tool for studying the evolution of unusual rotavirus strains. As limited data are available from Pune (Maharashtra), western India, the current study was undertaken with the aim of understanding the genetic diversity in three (G1P[6], G9P[4] and G9P[4]) unusual RVA strains circulating in Pune, India during 2013-2015. Full-genome analysis of these strains classified them as G1-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, G9-P[4]-I2-R2-C2-[M1-M2_R]-[A1-A2_R]-N2-T2-E6-H2 and G9-[P4-P6_R]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Sequencing and phylogenetic analysis of the structural and non-structural genes of these unusual RVA strains showed nucleotide/amino acid identities of 82.3-98.5 %/77.3-99.8 % and 86.6-97.6 %/89.6-97.8 % between the strains of the study. Evidence of recombination events was found within the genes encoding VP3, VP4 and NSP1, which showed a combination of genetic information for genogroup 1 [M1/P[6]/A1] and genogroup 2 [M2/P[4]/A2] strains. This study will facilitate future investigations into the molecular pathogenesis of such RVAs as the exchange of whole or partial genetic material between rotaviruses through recombination contributes directly to their diversification, adaptation and evolution.
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Affiliation(s)
- Vaishali S Tatte
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | - Deepthy Maran
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | - Atul M Walimbe
- Bioinformatics Group, National Institute of Virology, Pune, India
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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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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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Haque W, Haque J, Barai D, Rahman S, Moni S, Hossain ME, Faruque ASG, Ahmed S, Zaman K, Rahman M. Distribution of rotavirus genotypes in Dhaka, Bangladesh, 2012–2016: Re-emergence of G3P[8] after over a decade of interval. Vaccine 2018; 36:6393-6400. [DOI: 10.1016/j.vaccine.2018.08.081] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 01/11/2023]
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10
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Pradhan GN, Chitambar SD. Genetic analysis of rotavirus G2P[4] strains in Pune, Western India: circulation of a novel reassortant bearing E6 NSP4 genotype. Arch Virol 2018; 163:1391-1394. [PMID: 29411134 DOI: 10.1007/s00705-018-3710-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/01/2017] [Indexed: 11/29/2022]
Abstract
In India, G2P[4] strains are known to be the second most predominant group A rotaviruses causing acute gastroenteritis among children. This study was performed to determine the diversity within VP7(G), VP4(P), VP6(I) and NSP4(E) genes of 16 G2P[4] rotavirus strains detected in children hospitalized for acute gastroenteritis in Pune, Western India during 2009-2013. Fourteen strains showed G2-P[4]-I2-E2 and two strains showed G2-P[4]-I2-E6 genotype constellation. Phylogenetic analysis showed their clustering into G2-IV-a3, P[4]-5bi/ii, I2-3ii and E2-4i/ii or E6 genotypes/lineages. These data reveal inter- and/or intra-genotypic variations in a genogroup-2 constellation of G2P[4] rotavirus strains circulating in Pune, Western India, providing evidence of a novel G2P[4] reassortant bearing a rare NSP4 genotype, E6 during 2009-2013.
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Affiliation(s)
- Gauri N Pradhan
- National Institute of Virology, 20/A, Dr. Ambedkar Road. Post Box No. 11, Pune, 411001, India
| | - Shobha D Chitambar
- National Institute of Virology, 20/A, Dr. Ambedkar Road. Post Box No. 11, Pune, 411001, India.
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11
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Doan YH, Suzuki Y, Fujii Y, Haga K, Fujimoto A, Takai-Todaka R, Someya Y, Nayak MK, Mukherjee A, Imamura D, Shinoda S, Chawla-Sarkar M, Katayama K. Complex reassortment events of unusual G9P[4] rotavirus strains in India between 2011 and 2013. INFECTION GENETICS AND EVOLUTION 2017; 54:417-428. [PMID: 28750901 DOI: 10.1016/j.meegid.2017.07.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 11/16/2022]
Abstract
Rotavirus A (RVA) is the predominant etiological agent of acute gastroenteritis in young children worldwide. Recently, unusual G9P[4] rotavirus strains emerged with high prevalence in many countries. Such intergenogroup reassortant strains highlight the ongoing spread of unusual rotavirus strains throughout Asia. This study was undertaken to determine the whole genome of eleven unusual G9P[4] strains detected in India during 2011-2013, and to compare them with other human and animal global RVAs to understand the exact origin of unusual G9P[4] circulating in India and other countries worldwide. Of these 11 RVAs, four G9P[4] strains were double-reassortants with the G9-VP7 and E6-NSP4 genes on a DS-1-like genetic backbone (G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2). The other strains showed a complex genetic constellation, likely derived from triple reassortment event with the G9-VP7, N1-NSP2 and E6-NSP4 on a DS-1-like genetic backbone (G9-P[4]-I2-R2-C2-M2-A2-N1-T2-E6-H2). Presumably, these unusual G9P[4] strains were generated after several reassortment events between the contemporary co-circulating human rotavirus strains. Moreover, the point mutation S291L at the interaction site between inner and outer capsid proteins of VP6 gene may be important in the rapid spread of this unusual strain. The complex reassortment events within the G9[4] strains may be related to the high prevalence of mixed infections in India as reported in this study and other previous studies.
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Affiliation(s)
- Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Japan
| | - Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kei Haga
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Japan
| | - Akira Fujimoto
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Japan
| | - Reiko Takai-Todaka
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Japan
| | - Yuichi Someya
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mukti K Nayak
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Anupam Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Daisuke Imamura
- Collaborative Research Center of Okayama University for Infectious Diseases, India
| | - Sumio Shinoda
- Collaborative Research Center of Okayama University for Infectious Diseases, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Japan.
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