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Sadiq A, Khan T, Bostan N, Yinda CK, Matthijnssens J. Antigenic epitope analysis of Pakistani G3 and G9 rotavirus strains compared to vaccine strains revealed multiple amino acid differences. Diagn Microbiol Infect Dis 2024; 109:116346. [PMID: 38759540 DOI: 10.1016/j.diagmicrobio.2024.116346] [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: 05/27/2022] [Revised: 08/13/2023] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Rotaviruses belong to genotype VP4-P[8] are a significant cause of severe loose diarrhea in infants and young children. In the present study, we characterised the complete genome of three of the Pakistani P[8]b RVA strains by Illumina HiSeq sequencing technology to determine the complete genotype constellation providing insight into the evolutionary dynamics of their genes using maximum likelihood analysis. The maximum genomic sequences of our study strains were similar to more recent human Wa-Like G1P[8]a, G3P[8]a, G4P[6], G4P[8], G9P[4], G9P[8]a, G11P[25],G12P[8]a and G12P[6] strains circulating around the world. Therefore, strains PAK274, PAK439 and PAK624 carry natively distinctive VP4 gene with universally common human Wa-Like genetic backbone. Comparing our study P[8]b strains with vaccines strains RotarixTM and RotaTeqTM, multiple amino acid differences were examined between vaccine virus antigenic epitopes and Pakistani isolates. Over time, these differences may result in the selection for strains that will escape the vaccine-induced RVA-neutralizing-antibody effect.
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Affiliation(s)
- Asma Sadiq
- Department of Microbiology, University of Jhang, Jhang, Pakistan
| | - Tariq Khan
- Department of Biosciences, COMSATS University (CUI), Park Road, Tarlai Kalan, Chak Shahzad, Islamabad,45550, Pakistan
| | - Nazish Bostan
- Department of Biosciences, COMSATS University (CUI), Park Road, Tarlai Kalan, Chak Shahzad, Islamabad,45550, Pakistan.
| | - Claude Kwe Yinda
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
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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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Thongprachum A, Khamrin P, Maneekarn N, Hayakawa S, Ushijima H. Epidemiology of gastroenteritis viruses in Japan: Prevalence, seasonality, and outbreak. J Med Virol 2015; 88:551-70. [PMID: 26387663 DOI: 10.1002/jmv.24387] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 12/11/2022]
Abstract
Acute gastroenteritis has been recognized as one of the most common diseases in humans and continues to be a major public health problem worldwide. Several groups of viruses have been reported as the causative agents of acute gastroenteritis, including rotavirus, norovirus, sapovirus, human astrovirus, adenovirus, and an increasing number of others which have been reported more recently. The epidemiology, prevalence, seasonality, and outbreaks of these viruses have been reviewed in a number of studies conducted in Japan over three decades. Rotavirus and norovirus were the two most common viruses detected almost equally in children under 5 years of age who were suffering from acute gastroenteritis. Like many other countries, the main rotavirus strains circulating in pediatric patients in Japan are G1P[8], G2P[4], G3P[8], and G9P[8]. Norovirus GII.4 was involved in most outbreaks in Japan and found to be associated with the emergence of new variants Sydney_2012. The classic human astrovirus, MLB, and VA clades astroviruses were also commonly found in pediatric patients with acute diarrhea. The sapovirus and adenovirus have been identified as the minor viral causative agents for acute gastroenteritis in Japan.
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Affiliation(s)
- Aksara Thongprachum
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Pattara Khamrin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Kulkarni R, Arora R, Arora R, Chitambar SD. Sequence analysis of VP7 and VP4 genes of G1P[8] rotaviruses circulating among diarrhoeic children in Pune, India: a comparison with Rotarix and RotaTeq vaccine strains. Vaccine 2015; 32 Suppl 1:A75-83. [PMID: 25091685 DOI: 10.1016/j.vaccine.2014.03.080] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND The G1P[8] rotaviruses are a common cause of rotavirus diarrhoea among children in India. Two rotavirus vaccines licensed in India, Rotarix and RotaTeq, contain strains with G1 and P[8] genotypes. A comparative analysis of these genotypes in the live rotavirus vaccines with circulating rotavirus strains is essential for assessment of rotavirus diversity. METHODS G1P[8] strains detected during rotavirus surveillance among diarrhoeic children hospitalized in Pune in 1992-1993 and 2006-2008, were included in the study. Amplification, sequencing and phylogenetic analysis of the VP7 and VP4 genes were carried out for identification of the G1 and P[8] lineages, respectively. Antigenic epitopes of VP7 and VP4 encoded proteins were compared to determine the differences between the G1P[8] strains from Pune and the vaccine strains. RESULTS G1-Lineage 1, P[8]-Lineage 3 strains were predominant in Pune during 1992-1993 and 2006-2008. Strains of G1-Lineage 2, P[8]-Lineage 3 and G1-Lineage 1, P[8]-Lineage 4 were detected at low levels during 2006-2008. The G1-Lineage 1, P[8]-Lineage 3 strains showed up to eight amino acid changes, each in the VP7 and VP4 epitopes, with respect to the Rotarix vaccine strain (G1-Lineage 2, P[8]-Lineage 1) and the G1 (Lineage-3) and P[8] (Lineage 2) components of the RotaTeq vaccine. The G1-Lineage 2 strains were closer to both vaccine strains with no or only two amino acid substitutions in the VP7 epitopes. The divergent P[8]-Lineage 4 (OP354-like) strains showed fourteen and fifteen amino acid differences, with Rotarix and RotaTeq vaccine strains, respectively, in the VP4 epitopes. CONCLUSION The differences between the G1P[8] strains in Pune and the G1 and P[8] components of the vaccine strains need to be described for appropriate evaluation of vaccine shedding. Continuous monitoring of the G1P[8] subgenotypic lineages would be necessary to study any long term impact of vaccine use on G1P[8] strain evolution.
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Affiliation(s)
- Ruta Kulkarni
- Enteric Viruses Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune-411001, India
| | - Ritu Arora
- Enteric Viruses Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune-411001, India
| | - Rashmi Arora
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, Ansari Nagar, New Delhi-110029, India
| | - Shobha D Chitambar
- Enteric Viruses Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune-411001, India.
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Kuzuya M, Fujii R, Hamano M, Kida K, Mizoguchi Y, Kanadani T, Nishimura K, Kishimoto T. Prevalence and molecular characterization of G1P[8] human rotaviruses possessing DS-1-like VP6, NSP4, and NSP5/6 in Japan. J Med Virol 2013; 86:1056-64. [DOI: 10.1002/jmv.23746] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2013] [Indexed: 01/17/2023]
Affiliation(s)
- Mitsutaka Kuzuya
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
| | - Ritsushi Fujii
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
| | - Masako Hamano
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
| | - Koji Kida
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
| | - Yoshinori Mizoguchi
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
| | - Tomohisa Kanadani
- Okayama Medical Center of National Hospital Organization; Okayama; Japan
| | - Keiko Nishimura
- Okayama Medical Center of National Hospital Organization; Okayama; Japan
| | - Toshio Kishimoto
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
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