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Usman M, Rana MS, Salman M, Alam MM, Khurshid A, Umair M, Ullah N, Anas M, Ahmed M, Ayub A, Habib S, Zohaib A, Javed A. Molecular characterization of rotavirus indicates predominance of G9P[4] genotype among children with acute gastroenteritis: First report after vaccine introduction in Pakistan. J Med Virol 2024; 96:e29761. [PMID: 38924137 DOI: 10.1002/jmv.29761] [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: 03/08/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Globally, Group A rotavirus (RVA) is the leading cause of acute gastroenteritis in children under 5 years old, with Pakistan having the highest rates of RVA-related morbidity and mortality. The current study aims to determine the genetic diversity of rotavirus and evaluate the impact of Rotarix-vaccine introduction on disease epidemiology in Pakistan. A total of 4749 children, hospitalized with acute gastroenteritis between 2018 and 2020, were tested at four hospitals in Lahore and Karachi. Of the total, 19.3% (918/4749) cases were tested positive for RVA antigen, with the positivity rate varying annually (2018 = 22.7%, 2019 = 14.4%, 2020 = 20.9%). Among RVA-positive children, 66.3% were under 1 year of age. Genotyping of 662 enzyme-linked immuno sorbent assay-positive samples revealed the predominant genotype as G9P[4] (21.4%), followed by G1P[8] (18.9%), G3P[8] (11.4%), G12P[6] (8.7%), G2P[4] (5.7%), G2P[6] (4.8%), and 10.8% had mixed genotypes. Among vaccinated children, genotypes G9P[4] and G12P[6] were more frequently detected, whereas a decline in G2P[4] was observed. Phylogenetic analysis confirmed the continued circulation of indigenous genotypes detected earlier in the country except G9 and P[6] strains. Our findings highlight the predominance of G9P[4] genotype after the vaccine introduction thus emphasizing continual surveillance to monitor the disease burden, viral diversity, and their impact on control of rotavirus gastroenteritis in children.
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Affiliation(s)
- Muhammad Usman
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | | | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | | | - Adnan Khurshid
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Nadeem Ullah
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Anas
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muzzamil Ahmed
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Aaima Ayub
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Sabahat Habib
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Ali Zohaib
- Department of Microbiology, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus, Bahawalpur, Pakistan
| | - Aneela Javed
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Gutierrez MB, de Assis RMS, Arantes I, Fumian TM. Full genotype constellations analysis of unusual DS-1-like G12P[6] and G6P[8] rotavirus strains detected in Brazil, 2019. Virology 2022; 577:74-83. [PMID: 36323046 DOI: 10.1016/j.virol.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022]
Abstract
Rotavirus A (RVA) is a major cause of acute gastroenteritis (AGE) in children worldwide. We report unusual RVA G12P[6] and G6P[8] strains isolated from fecal samples from Brazilian children hospitalized for AGE. The characterized RVA have genome segments backbone: G12-P[6]/ G6-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 of DS-1-like genogroup. Our study describes the first identification of G6P[8], a DS-1-like genogroup strain. Nucleotide analysis of VP7 and VP4 genes revealed that all G12 Brazilian strains clustered into the sub-lineages IIIB, mostly associated with P[6] lineage I. Additionally, our G6 lineage I strains were closely related to German G6 genotypes, bound with P[8] lineage III, differing from both vaccine strains. The comparative sequence analysis of our strains with vaccine strains revealed amino acid substitutions located in immunodominant regions of VP7 and VP4 proteins. Continuous monitoring of RVA genotypes is essential to evaluate the impact of vaccination on the dynamic nature of RVA evolution.
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Affiliation(s)
- Meylin Bautista Gutierrez
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Av. Brasil, 4365, Rio de Janeiro, RJ 21040-360, Brazil
| | - Rosane Maria Santos de Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Av. Brasil, 4365, Rio de Janeiro, RJ 21040-360, Brazil
| | - Ighor Arantes
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Av. Brasil, 4365, Rio de Janeiro, RJ 21040-360, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Av. Brasil, 4365, Rio de Janeiro, RJ 21040-360, Brazil.
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Varghese T, Alokit Khakha S, Giri S, Nair NP, Badur M, Gathwala G, Chaudhury S, Kaushik S, Dash M, Mohakud NK, Ray RK, Mohanty P, Kumar CPG, Venkatasubramanian S, Arora R, Raghava Mohan V, E. Tate J, D. Parashar U, Kang G. Rotavirus Strain Distribution before and after Introducing Rotavirus Vaccine in India. Pathogens 2021; 10:pathogens10040416. [PMID: 33915946 PMCID: PMC8066972 DOI: 10.3390/pathogens10040416] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 12/13/2022] Open
Abstract
In April 2016, an indigenous monovalent rotavirus vaccine (Rotavac) was introduced to the National Immunization Program in India. Hospital-based surveillance for acute gastroenteritis was conducted in five sentinel sites from 2012 to 2020 to monitor the vaccine impact on various genotypes and the reduction in rotavirus positivity at each site. Stool samples collected from children under 5 years of age hospitalized with diarrhea were tested for group A rotavirus using a commercial enzyme immunoassay, and rotavirus strains were characterized by RT-PCR. The proportion of diarrhea hospitalizations attributable to rotavirus at the five sites declined from a range of 56–29.4% in pre-vaccine years to 34–12% in post-vaccine years. G1P[8] was the predominant strain in the pre-vaccination period, and G3P[8] was the most common in the post-vaccination period. Circulating patterns varied throughout the study period, and increased proportions of mixed genotypes were detected in the post-vaccination phase. Continuous long-term surveillance is essential to understand the diversity and immuno-epidemiological effects of rotavirus vaccination.
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Affiliation(s)
- Tintu Varghese
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore 632004, India; (T.V.); (S.A.K.); (S.G.); (N.P.N.)
| | - Shainey Alokit Khakha
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore 632004, India; (T.V.); (S.A.K.); (S.G.); (N.P.N.)
| | - Sidhartha Giri
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore 632004, India; (T.V.); (S.A.K.); (S.G.); (N.P.N.)
| | - Nayana P. Nair
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore 632004, India; (T.V.); (S.A.K.); (S.G.); (N.P.N.)
| | - Manohar Badur
- Department of Pediatrics, Sri Venkateshwara Medical College, Tirupati 517507, India;
| | - Geeta Gathwala
- Department of Pediatrics, Post Graduate Institute of Medical Sciences, Medical Road, Rohtak, Haryana 124001, India;
| | - Sanjeev Chaudhury
- Department of Pediatrics, Dr Rajendra Prasad Government Medical College, Tanda, Himachal Pradesh 176001, India;
| | - Shayam Kaushik
- Department of Pediatrics, Indira Gandhi Medical College, Shimla, Himachal Pradesh 171001, India;
| | - Mrutunjay Dash
- Department of Pediatrics, Institute of Medical Sciences and SUM Hospital, Bhubaneswar, Odisha 751003, India;
| | - Nirmal K. Mohakud
- Department of Pediatrics, Kalinga Institute of Medical Sciences, 5 KIIT Road, Bhubaneswar, Odisha 751024, India;
| | - Rajib K. Ray
- Department of Pediatrics, Hi-Tech Hospital, Bhubaneswar, Odisha 751025, India; (R.K.R.); (P.M.)
| | - Prasantajyoti Mohanty
- Department of Pediatrics, Hi-Tech Hospital, Bhubaneswar, Odisha 751025, India; (R.K.R.); (P.M.)
| | | | | | - Rashmi Arora
- Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India;
| | | | - Jacqueline E. Tate
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Umesh D. Parashar
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Gagandeep Kang
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore 632004, India; (T.V.); (S.A.K.); (S.G.); (N.P.N.)
- Correspondence:
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Reslan L, Mishra N, Finianos M, Zakka K, Azakir A, Guo C, Thakka R, Dbaibo G, Lipkin WI, Zaraket H. The origins of G12P[6] rotavirus strains detected in Lebanon. J Gen Virol 2020; 102. [PMID: 33331815 DOI: 10.1099/jgv.0.001535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The G12 rotaviruses are an increasingly important cause of severe diarrhoea in infants and young children worldwide. Seven human G12P[6] rotavirus strains were detected in stool samples from children hospitalized with gastroenteritis in Lebanon during a 2011-2013 surveillance study. Complete genomes of these strains were sequenced using VirCapSeq-VERT, a capture-based high-throughput viral-sequencing method, and further characterized based on phylogenetic analyses with global RVA and vaccine strains. Based on the complete genomic analysis, all Lebanese G12 strains were found to have Wa-like genetic backbone G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Phylogenetically, these strains fell into two clusters where one of them might have emerged from Southeast Asian strains and the second one seems to have a mixed backbone between North American and Southeast Asian strains. Further analysis of these strains revealed high antigenic variability compared to available vaccine strains. To our knowledge, this is the first report on the complete genome-based characterization of G12P[6] emerging in Lebanon. Additional studies will provide important insights into the evolutionary dynamics of G12 rotaviruses spreading in Asia.
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Affiliation(s)
- Lina Reslan
- Center for Infectious Diseases Research, American University of Beirut, Faculty of Medicine, Beirut, Lebanon.,Department of Pediatrics and Adolescent Medicine, American University of Beirut, Faculty of Medicine, Beirut, Lebanon
| | - Nischay Mishra
- Center for Infection and the Immunity, Mailman School of Public Health, Columbia University, NY 10032, New York
| | - Marc Finianos
- Center for Infectious Diseases Research, American University of Beirut, Faculty of Medicine, Beirut, Lebanon
| | - Kimberley Zakka
- Center for Infectious Diseases Research, American University of Beirut, Faculty of Medicine, Beirut, Lebanon
| | - Amanda Azakir
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut, Faculty of Medicine, Beirut, Lebanon
| | - Cheng Guo
- Center for Infection and the Immunity, Mailman School of Public Health, Columbia University, NY 10032, New York
| | - Riddhi Thakka
- Center for Infection and the Immunity, Mailman School of Public Health, Columbia University, NY 10032, New York
| | - Ghassan Dbaibo
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Faculty of Medicine, Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut, Faculty of Medicine, Beirut, Lebanon
| | - W Ian Lipkin
- Center for Infection and the Immunity, Mailman School of Public Health, Columbia University, NY 10032, New York
| | - Hassan Zaraket
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut, Faculty of Medicine, Beirut, Lebanon
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Satayarak J, Strauss ST, Duangdee C, Charunwatthana P, Jiamsomboon K, Kosoltanapiwat N, Srinukham S, Boonnak K. Prevalence and diversity of human rotavirus among Thai adults. J Med Virol 2020; 92:2582-2592. [PMID: 32470142 DOI: 10.1002/jmv.26076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/17/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
Abstract
Rotavirus infections have become one of the most common causes of infectious gastroenteritis in children. Although rotavirus infections have been intensively studied in infants and young children, the study in adults has been limited. As such, this study assessed the prevalence of rotaviruses and performed the molecular characterization of rotaviruses circulating in Thai adults experiencing acute gastroenteritis between January 2018 and December 2018. Group A human rotaviruses were detected in 100 feces samples by rapid immunochromatography. The peak incidence of infection occurred in February and began to decline in the summer months. From January 2018 to December 2018, there were 1344 acute gastroenteritis adult cases in the Hospital for Tropical Diseases, Bangkok, Thailand. Among these, 310 cases were rotavirus-suspected cases. Only 100 samples tested positive for rotavirus via an immunochromatography test. Twentynine out of the 100 rotavirus-positive samples were further characterized by real-time polymerase chain reaction. The G3[P8] strain was identified as the most prevalent (31.0%) followed by G1P[8], G8P[8] and G9P[8], and G2P[8], which accounted for 20.8%, 17.2%, and 13.8%, respectively. Because of the detection of rare rotavirus genotypes, such as G8, the surveillance of rotavirus epidemiology is crucial in monitoring new emergences of rotavirus strains, leading to a better understanding of the effects of strain variation for further vaccine development.
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Affiliation(s)
- Jantawan Satayarak
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Stefan Thomas Strauss
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chatnapa Duangdee
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Prakaykaew Charunwatthana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Nakhon Pathom, Thailand
| | - Kultida Jiamsomboon
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sompan Srinukham
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kobporn Boonnak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Motamedi-Rad M, Farahmand M, Arashkia A, Jalilvand S, Shoja Z. VP7 and VP4 genotypes of rotaviruses cocirculating in Iran, 2015 to 2017: Comparison with cogent sequences of Rotarix and RotaTeq vaccine strains before their use for universal mass vaccination. J Med Virol 2019; 92:1110-1123. [PMID: 31774174 DOI: 10.1002/jmv.25642] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 11/23/2019] [Indexed: 12/17/2022]
Abstract
The present study was conducted to analyze the genotypic diversity of circulating species A rotavirus (RVA) strains in Iran and also to investigate comparative analysis between the genotypes of VP4 and VP7 of cocirculating RVA and vaccine strains before the vaccine is introduced in the national immunization program. The G3-lineage I was found in this study as the most common G genotype which was followed by G9-lineage III, G1-lineages I, II, G12-lineage III, G2-lineage IV, and G4-lineage I. Also, P[8]-lineages III, IV was found as the predominant P genotype which was followed by P[4]-lineage V, and P[6]-lineage I. Overally, G3P[8] was determined as the most common combination. Moreover, the analysis of the VP7 antigenic epitopes showed that several amino acid differences existed between circulating Iranian and the vaccine strains. The comparison of genotype G1 of Iranian and vaccine strains (RotaTeq and Rotarix), and genotypes G2, G3, and G4 of Iranian and RotaTeq vaccine strains revealed three to five amino acids differences on the VP7 antigenic epitopes. Furthermore, analyzing of the VP8* epitopes of Iranian P[8] strains indicated that they contained up to 11 and 14 amino acid differences with Rotarix and RotaTeq, respectively. Based on different patterns of amino acid substitutions in circulating and vaccine strains, the emergence of antibody escaping mutants and potentially the decrease of immune protection might ensue in vaccinated children. However, considering the broad cross-protective activity of RVA vaccines, their efficacy should be monitored after the introduction in Iran.
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Affiliation(s)
| | - Mohammad Farahmand
- 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
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
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Satter SM, Aliabadi N, Gastañaduy PA, Haque W, Mamun A, Flora MS, Zaman K, Rahman M, Heffelfinger JD, Luby SP, Gurley ES, Parashar UD. An update from hospital-based surveillance for rotavirus gastroenteritis among young children in Bangladesh, July 2012 to June 2017. Vaccine 2018; 36:7811-7815. [PMID: 29793894 PMCID: PMC9169511 DOI: 10.1016/j.vaccine.2018.05.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/08/2018] [Accepted: 05/04/2018] [Indexed: 11/29/2022]
Abstract
INTRODUCTION In preparation for the introduction of a rotavirus vaccine into the routine immunization program of Bangladesh in 2018, we report data and highlight evolving genotypes from five years of active hospital-based rotavirus surveillance which began in July 2012. METHODS We enrolled and collected fresh stool from every fourth child < 5 years admitted with acute gastroenteritis (AGE) at 8 participating surveillance hospitals. Rotavirus infections were detected by enzyme immune assay. Twenty-five percent of rotavirus isolates were genotyped using reverse transcription polymerase chain reaction. RESULTS We found that 64% (4832/7562) of children < 5 years of age admitted with AGE had evidence of rotavirus infection. The majority (57%) of patients with rotavirus infection were <12 months of age. The most common strains were G1P[8] (43%), G12P[8] (15%) and G9P[8] (9%); 11% of children had mixed infection.G3P[8], which has not been reported in Bangladesh since 2001, was documented for the first time in our surveillance system. CONCLUSIONS The high burden of rotavirus-associated hospitalizations highlights the potential value of rotavirus vaccination in Bangladesh. Continued surveillance is important for monitoring the impact of vaccination as well as monitoring evolving genotypes.
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Affiliation(s)
| | - Negar Aliabadi
- Centers for Disease Control and Prevention(CDC), Atlanta, USA
| | | | | | | | - Meerjady S Flora
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | | | | | | | - Stephen P Luby
- Center for Innovation in Global Health, Stanford University, USA
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