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Kachooei A, Mirhoseinian M, Jalilvand S, Latifi T, Feizi M, Shahosseini Z, Arashkia A, Marashi SM, Shoja Z. Molecular characterization of human astrovirus infection in children under 5 years of age with acute gastroenteritis in Tehran, Iran, 2021-2022: co-infection with rotavirus. Virus Genes 2024; 60:357-369. [PMID: 38744749 DOI: 10.1007/s11262-024-02075-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024]
Abstract
Human astroviruses (HAstVs) are considered important causative pathogens of acute gastroenteritis (AGE) in children under 5 years of age worldwide, along with group A rotavirus (RVA), norovirus (NoV), and enteric adenovirus (EAdV). The present study was aimed to both detect HAstV and its co-infections and investigate genetic analysis of circulating HAstV and co-infected virus in hospitalized children under 5 years of age with AGE in Iran. Accordingly, a sum of 200 stool specimens were screened by PCR for HAstV during 2021-2022. The HAstV was found in 0.5% of 200 specimens (n = 1) while was co-infected with RVA. The genetic and phylogenetic analysis indicated HAstV1 genotype, which clustered with viruses from lineage 1b, which has not been previously reported in Iran. The detected RVA strain belonged to G1 lineage II/P[8]-lineage III, which has been reported previously in Iran as the most common strain. The further genetic analysis of RVA VP6 and NSP4 demonstrated an atypical genotype pattern G1P[8]-I1-E2, as a mono-reassortant of a Wa-like genogroup, which appeared to be reassorted with the NSP4 gene of E2 genotype of the G2P[4] DS-1 genogroup. Although the clinical outcomes of the AGE-causing viruses co-infection is not yet entirely clear, it seems that future studies will be helpful to merge clinical and epidemiological data of co-infecting viruses for a more accurate medical and clinical relevance in symptomatic children.
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Affiliation(s)
- Atefeh Kachooei
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahtab Mirhoseinian
- Department of Virology, School of Public Health, Tehran 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 Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Mahsa Feizi
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Arash Arashkia
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Sayed Mahdi Marashi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of 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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Dellis C, Tatsi EB, Koukou DM, Filippatos F, Vetouli EE, Zoumakis E, Michos A, Syriopoulou V. Genotyping and Molecular Characterization of VP6 and NSP4 Genes of Unusual Rotavirus Group A Isolated from Children with Acute Gastroenteritis. Adv Virol 2024; 2024:3263228. [PMID: 38993264 PMCID: PMC11239230 DOI: 10.1155/2024/3263228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/29/2024] [Accepted: 05/27/2024] [Indexed: 07/13/2024] Open
Abstract
Group A rotavirus (RVA), which causes acute gastroenteritis (AGE) in children worldwide, is categorized mainly based on VP7 (genotype G) and VP4 (genotype P) genes. Genotypes that circulate at <1% are considered unusual. Important genes also include VP6 (genotype I) and NSP4 (genotype E). VP6 establishes the group and affects immunogenicity, while NSP4, as an enterotoxin, is responsible for the clinical symptoms. The aim of this study was to genotype the VP6 and NSP4 genes and molecularly characterize the NSP4 and VP6 genes of unusual RVA. Unusual RVA strains extracted from fecal samples of children ≤16 years with AGE were genotyped in VP6 and NSP4 genes with Sanger sequencing. In a 15-year period (2007-2021), 54.8% (34/62) of unusual RVA were successfully I and E genotyped. Three different I and E genotypes were identified; I2 (73.5%, 25/34) and E2 (35.3%, 12/34) were the most common. E3 genotype was detected from 2017 onwards. The uncommon combination of I2-E3 was found in 26.5% (9/34) of the strains and G3-P[9]-I2-E3 remained the most frequent G-P-I-E combination (20.6%, 7/34). Children infected with RVA E2 strains had a statistically higher frequency of dehydration (50%) than those infected with RVA E3 strains (p = 0.019). Multiple substitutions were detected in NSP4, but their functional effect remains unknown. The result indicates the genetic diversity of RVA strains. Continuous surveillance of the RVA based on the whole genome will provide better knowledge of its evolution.
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Affiliation(s)
- Charilaos Dellis
- First Department of Pediatrics Infectious Diseases and Chemotherapy Research Laboratory Medical School National and Kapodistrian University of Athens "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Elizabeth-Barbara Tatsi
- First Department of Pediatrics Infectious Diseases and Chemotherapy Research Laboratory Medical School National and Kapodistrian University of Athens "Aghia Sophia" Children's Hospital, Athens, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, Athens, Greece
| | - Dimitra-Maria Koukou
- First Department of Pediatrics Infectious Diseases and Chemotherapy Research Laboratory Medical School National and Kapodistrian University of Athens "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Filippos Filippatos
- First Department of Pediatrics Infectious Diseases and Chemotherapy Research Laboratory Medical School National and Kapodistrian University of Athens "Aghia Sophia" Children's Hospital, Athens, Greece
| | | | - Emmanouil Zoumakis
- First Department of Pediatrics Infectious Diseases and Chemotherapy Research Laboratory Medical School National and Kapodistrian University of Athens "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Athanasios Michos
- First Department of Pediatrics Infectious Diseases and Chemotherapy Research Laboratory Medical School National and Kapodistrian University of Athens "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Vasiliki Syriopoulou
- First Department of Pediatrics Infectious Diseases and Chemotherapy Research Laboratory Medical School National and Kapodistrian University of Athens "Aghia Sophia" Children's Hospital, Athens, Greece
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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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Almeida TNV, Fiaccadori FS, Souza M, Borges AMT, Cardoso DDDDP. Molecular characterization of group A rotavirus before and after the introduction of vaccines in Brazil. Rev Soc Bras Med Trop 2015; 48:599-602. [PMID: 26516971 DOI: 10.1590/0037-8682-0023-2015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/14/2015] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION In this study, the molecular characteristics of group A rotavirus (RVA) were compared in samples obtained before and after RVA vaccine-introduction in Brazil. METHODS Eighty samples were screened for the presence of RVA. Positive samples were molecularly analyzed. RESULTS RVA positivity was 16.9%, with a predominance of G2P[4]. Periods: pre-vaccination: predominance of IId (G1), IId (G2) lineages, and I1 and E1 genotypes; post-vaccination: predominance of Ib (G1), IIa, and IIc (G2) lineages and I2 and E2 genotypes. CONCLUSIONS Although changes in RVA-circulation pattern were observed in the post-vaccination period, it could not be attributed to vaccination process.
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Affiliation(s)
- Tâmera Nunes Vieira Almeida
- Departamento de Microbiologia, Imunologia, Parasitologia e Patologia Geral, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Fabíola Souza Fiaccadori
- Departamento de Microbiologia, Imunologia, Parasitologia e Patologia Geral, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Menira Souza
- Departamento de Microbiologia, Imunologia, Parasitologia e Patologia Geral, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Ana Maria Tavares Borges
- Departamento de Microbiologia, Imunologia, Parasitologia e Patologia Geral, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Divina das Dôres de Paula Cardoso
- Departamento de Microbiologia, Imunologia, Parasitologia e Patologia Geral, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
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Bertol JW, Fregolente MCD, Caruzo TAR, Silva MJD, Munford V, Sáfadi MAP, Rácz ML, Gatti MSV. Molecular characterisation of the NSP4 gene of group A human rotavirus G2P[4] strains circulating in São Paulo, Brazil, from 1994 and 2006 to 2010. Mem Inst Oswaldo Cruz 2015; 110:786-92. [PMID: 26517658 PMCID: PMC4667582 DOI: 10.1590/0074-02760150199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/20/2015] [Indexed: 11/22/2022] Open
Abstract
Group A human rotaviruses (HuRVA) are causative agents of acute gastroenteritis. Six viral structural proteins (VPs) and six nonstructural proteins (NSPs) are produced in RV-infected cells. NSP4 is a diarrhoea-inducing viral enterotoxin and NSP4 gene analysis revealed at least 15 (E1-E15) genotypes. This study analysed the NSP4 genetic diversity of HuRVA G2P[4] strains collected in the state of São Paulo (SP) from 1994 and 2006-2010 using reverse transcription-polymerase chain reaction, sequencing and phylogenetic analysis. Forty (97.6%) G2P[4] strains displayed genotype E2; one strain (2.4%) displayed genotype E1. These results are consistent with the proposed linkage between VP4/VP7 (G2P[4]) and the NSP4 (E2) genotype of HuRVA. NSP4 phylogenetic analysis showed distinct clusters, with grouping of most strains by their genotype and collection year, and most strains from SP were clustered together with strains from other Brazilian states. A deduced amino acid sequence alignment for E2 showed many variations in the C-terminal region, including the VP4-binding domain. Considering the ability of NSP4 to generate host immunity, monitoring NSP4 variations, along with those in the VP4 or VP7 protein, is important for evaluating the circulation and pathogenesis of RV. Finally, the presence of one G2P[4]E1 strain reinforces the idea that new genotype combinations emerge through reassortment and independent segregation.
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Affiliation(s)
- Jéssica Wildgrube Bertol
- Departamento de Genética, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | | | | | - Márcio José da Silva
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Veridiana Munford
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
| | | | - Maria Lucia Rácz
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Maria Silvia Viccari Gatti
- Departamento de Genética, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
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Theamboonlers A, Maiklang O, Thongmee T, Chieochansin T, Vuthitanachot V, Poovorawan Y. Complete genotype constellation of human rotavirus group A circulating in Thailand, 2008–2011. INFECTION GENETICS AND EVOLUTION 2014; 21:295-302. [DOI: 10.1016/j.meegid.2013.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 01/26/2023]
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Chaimongkol N, Khamrin P, Malasao R, Thongprachum A, Ushijima H, Maneekarn N. Genotypic linkages of gene segments of rotaviruses circulating in pediatric patients with acute gastroenteritis in Thailand. INFECTION GENETICS AND EVOLUTION 2012; 12:1381-91. [PMID: 22564696 DOI: 10.1016/j.meegid.2012.04.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/11/2012] [Accepted: 04/14/2012] [Indexed: 12/11/2022]
Abstract
Rotavirus is a major cause of morbidity and mortality of infants and young children with diarrhea throughout the world. In Thailand, extensive studies of rotavirus infections have been reported continually and rotavirus diarrhea remains a common illness. To monitor the epidemiological situation of rotavirus in Chiang Mai, Thailand, surveillance of rotavirus circulating in pediatric patients was conducted. A total of 160 fecal specimens collected from children hospitalized with diarrhea were tested for rotaviruses groups A, B, and C by RT-PCR and their genotypes were identified by multiplex PCR and nucleotide sequencing. Group A rotavirus was detected at 29.4% but none of group B and C was found in this study. Molecular characterizations of G- and P-genotypes revealed three different G-P combinations, G1P[8] was the most predominant genotype with the prevalence of 72.3% followed by G2P[4] at 19.2%, and G3P[8] at 8.5%. Phylogenetic analyses of VP7 and VP4 genes of the representative strains detected in the present study, G1, G2, G3, and P[4] and P[8], respectively, revealed that G1 belonged to G1-Ic and G1-II, G2 belonged to G2-II, and G3 belonged to G3-III-S4 lineages while P[4] and P[8] were identified as P[4]-V and P[8]-III lineages. Analyses of VP6, NSP4, and NSP5 genes demonstrated that these representative strains belonged to genotypes I1 and I2, E1 and E2, and H1 and H2, respectively. Analyzing the association of G- and P-genotypes with I, E, H genotypes revealed unique patterns of genotypic linkage. The G1P[8] and G3P[8] were intimately linked with I1, E1, H1 genotypes and displayed the genetic features of G1-P[8]-I1-E1-H1 and G3-P[8]-I1-E1-H1, respectively, while G2P[4] was closely linked to I2, E2, H2 genotypes and showed the genetic pattern of G2-P[4]-I2-E2-H2. This study provides epidemiological information and insight into the genetic background of rotaviruses circulating in pediatric patients in Chiang Mai, Thailand.
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Affiliation(s)
- Natthawan Chaimongkol
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
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