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Fukuda Y, Kondo K, Nakata S, Morita Y, Adachi N, Kogawa K, Ukae S, Kudou Y, Adachi S, Yamamoto M, Fukumura S, Tsugawa T. Whole-genome analysis of human group A rotaviruses in 1980s Japan and evolutionary assessment of global Wa-like strains across half a century. J Gen Virol 2024; 105. [PMID: 38836747 DOI: 10.1099/jgv.0.001998] [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] [Indexed: 06/06/2024] Open
Abstract
Historically, the Wa-like strains of human group A rotavirus (RVA) have been major causes of gastroenteritis. However, since the 2010s, the circulation of non-Wa-like strains has been increasingly reported, indicating a shift in the molecular epidemiology of RVA. Although understanding RVA evolution requires the analysis of both current and historical strains, comprehensive pre-1980's sequencing data are scarce globally. We determined the whole-genome sequences of representative strains from six RVA gastroenteritis outbreaks observed at an infant home in Sapporo, Japan, between 1981 and 1989. These outbreaks were mainly caused by G1 or G3 Wa-like strains, resembling strains from the United States in the 1970s-1980s and from Malawi in the 1990s. Phylogenetic analysis of these infant home strains, together with Wa-like strains collected worldwide from the 1970s to 2020, revealed a notable trend: pre-2010 strains diverged into multiple lineages in many genomic segments, whereas post-2010 strains tended to converge into a single lineage. However, Bayesian skyline plot indicated near-constant effective population sizes from the 1970s to 2020, and selection pressure analysis identified positive selection only at amino acid 75 of NSP2. These results suggest that evidence supporting the influence of rotavirus vaccines, introduced globally since 2006, on Wa-like RVA molecular evolution is lacking at present, and phylogenetic analysis may simply reflect natural fluctuations in RVA molecular evolution. Evaluating the long-term impact of RV vaccines on the molecular evolution of RVA requires sustained surveillance.
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Affiliation(s)
- Yuya Fukuda
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shuji Nakata
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yasuyuki Morita
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriaki Adachi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Keiko Kogawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Susumu Ukae
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yoshimasa Kudou
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shuhei Adachi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masaki Yamamoto
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shinobu Fukumura
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
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Ushijima H, Pham NTK, Hoque SA, Nomura A, Kumthip K, Shimizu-Onda Y, Okitsu S, Kawata K, Hanaoka N, Müller WE, Maneekarn N, Hayakawa S, Khamrin P. Evaluation of a novel triplex immunochromatographic test for rapid simultaneous detection of norovirus, rotavirus, and adenovirus on a single strip test. J Infect Public Health 2024; 17:619-623. [PMID: 38417188 DOI: 10.1016/j.jiph.2024.02.010] [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: 09/15/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Acute gastroenteritis is one of the major causes of morbidity and mortality in young children worldwide. Among these, rotavirus, norovirus, and adenovirus have been reported as the primary viral pathogens associated with the disease. Rapid diagnosis of viral pathogens is crucial when diarrhea outbreaks occur to ensure the timely administration of appropriate treatment and control measures. METHODS We evaluated three immunochromatographic test kits designed for the detection of norovirus, rotavirus, and adenovirus in 71 stool specimens collected from children with diarrhea who visited clinics in Japan. The first kit is a triplex immunochromatographic test kit designed for simultaneous detections of norovirus, rotavirus, and adenovirus on a single strip (this kit was referred to as IC-A). The other two immunochromatographic test kits are a dual detection kit for rotavirus and adenovirus, and a single detection kit for norovirus (IC-B). The RT-PCR/PCR was used as the gold standard method. RESULTS The results revealed that both IC-A and IC-B kits exhibited the same level of sensitivity of detection for rotavirus (72.7%) and adenovirus (22.7%), although the detection rate was lower than that of the RT-PCR/PCR method. However, there was a slight difference in the sensitivity of detection for norovirus between IC-A and IC-B, at 86.7% and 93.3%, respectively. The sensitivity of detection for adenovirus of both kits was relatively lower than those of RT-PCR method. This could be due to low viral load of adenovirus in clinical specimens below the detection limit of IC-A and IC-B kits. However, both immunochromatographic test kits (IC-A and IC-B) exhibited 100% specificity for norovirus, rotavirus, and adenovirus. CONCLUSIONS The triplex immunochromatographic test kit (IC-A) designed for simultaneous detection of norovirus, rotavirus, and adenovirus has been proved to be more practical and convenient than the use of single or dual detection kits with more or less the same sensitivity and specificity of detections.
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Affiliation(s)
- Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.
| | - Ngan Thi Kim Pham
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; College of Industrial Technology, Nihon University, Chiba, Japan
| | - Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Bangladesh
| | - Akiko Nomura
- Immuno Probe Co. Ltd, Kamagata, Ranzanmachi,Saitama,Japan
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Yuko Shimizu-Onda
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Kimiko Kawata
- Midwifery and Maternal Health Nursing,School of Nursing, Graduate School of Medicine, Kagawa University,Kagawa,Japan
| | - Nozomu Hanaoka
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases,Tokyo,Japan
| | - Werner Eg Müller
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz,Germany
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand.
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Mansour Ghanaiee R, Fallah T, Karimi A, Sedighi I, Tariverdi M, Nazari T, Nahanmoghaddam N, Sedighi P, Nateghian A, Amirali A, Monavari SH, Fallahi M, Zahraei SM, Mahmoudi S, Elikaei A, Alebouyeh M. Multicenter Study of Rotavirus Infection, Diversity of Circulating Genotypes and Clinical Outcomes in Children ≤5 Years Old in Iran. Pediatr Infect Dis J 2024; 43:320-327. [PMID: 38190647 DOI: 10.1097/inf.0000000000004231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
BACKGROUND To determine the epidemiology of rotavirus group A (RVA) infection in symptomatic children, and analyze genotype diversity in association with clinical characteristics, geographical and seasonal changes. METHODS The stool samples of symptomatic children 5≥ years old were collected from 5 different hospitals during December 2020 and March 2022. Rotavirus stool antigen test was done and G and P genotypes of the positive samples were determined. Associations of the infection and genotype diversity with demographical and clinical data were assessed by statistical methods. RESULTS RVA infection was detected in 32.1% (300/934) of the patients (Ranges between 28.4% and 47.4%). An inverse association with age was detected, where the highest frequency was measured in children ≤12 months of age (175/482, 36.3%). The infection was more frequent during winter (124/284, 43.7%) and spring (64/187, 34.2%). Children who were exclusively fed with breast milk showed a lower rate of infection (72/251, 28.6%). Among the 46 characterized genotypes (17 single- and 29 mixed-genotype infections), G1P[8] and G9P[4] were more frequently detected in children <36 (67/234, 28.63%) and 36-60 (7/24, 29.16%) months of age children, respectively. A seasonal diversity in the circulating genotypes was detected in different cities. Children with G1P[8], G1P[6], and mixed-genotype infection experienced a shorter duration of hospitalization, and a higher frequency of nausea and severe diarrhea, respectively. CONCLUSIONS In this study high frequency of RVA infection was detected in symptomatic children in Iran. Moreover, genotype diversity according to geographic area, seasons, age groups, and clinical features of disease was detected.
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Affiliation(s)
- Roxana Mansour Ghanaiee
- From the Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tina Fallah
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Abdollah Karimi
- From the Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Iraj Sedighi
- Department of Pediatrics, Faculty of Medicine, Hamedan University of Medical Sciences, Hamedan, Iran
| | - Marjan Tariverdi
- Department of Pediatrics, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Tayebe Nazari
- From the Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Negin Nahanmoghaddam
- Department of Pediatrics, Bouali Hospital Children's Hospital, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Parinaz Sedighi
- Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran
- Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Alireza Nateghian
- Department of Pediatrics, Ali Asghar Children's hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Arezu Amirali
- From the Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Seyed Hamidreza Monavari
- Department of Medical Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahsa Fallahi
- Student Research Committee, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Seyed Mohsen Zahraei
- Center for Communicable Diseases Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Sussan Mahmoudi
- Center for Communicable Diseases Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Masoud Alebouyeh
- From the Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Zhong H, Jia R, Xu M, Liu P, Su L, Cao L, Zhu X, Lu L, Xu J. Emergence and high prevalence of unusual rotavirus G8P[8] strains in outpatients with acute gastroenteritis in Shanghai, China. J Med Virol 2024; 96:e29368. [PMID: 38180381 DOI: 10.1002/jmv.29368] [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: 07/04/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
Group A rotavirus (RVA) is considered an important cause of acute gastroenteritis (AGE) in all age groups, especially in children. We investigated the epidemiology of RVA in outpatients aged ≤ 16 years at the Children's Hospital of Fudan University, Shanghai, China. In this study, 16.6% (246/1482) were infected with RVA. The detection rate of RVA was significantly higher in the year of 2021 (20.3%, 147/725) compared to the year of 2020 (14.5%, 77/531) and 2022 (9.7%, 22/226) (p = 0.000). RVA infection was prevalent in all seasons from 2020 to 2022, with a different monthly distribution observed in different years. Among 246 RVA-positive samples, 14 different RVA genotypes were detected with different frequencies. Overall, G9P[8] (45.5%, 112/246) was the most common RVA genotype, followed by G8P[8] (37.4%, 92/246) and G3P[8] (4.1%, 10/246). The prevalence of G/P combinations varied from 2020 to 2022. G9P[8] was the most prevalent circulating genotype in 2020 (68.2%, 15/22) and 2021 (57.8%, 85/147). However, G8P[8] (68.8%, 53/77) suddenly became the most prevalent genotype in 2022 after being first identified in 2020 and prevalent in 2021. The G8 strains detected in the study were all clustered to DS-1-like G8 strains with the closest genetic distance to strains circulating in Southeast Asia. Our study demonstrated the diversity of circulating RVA genotypes in Shanghai. The sudden emergence and high prevalence of unusual G8P[8] strains deserve more concern and indicate the need for continuous surveillance of RVA in children with AGE in the future to refine future vaccine strategy.
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Affiliation(s)
- Huaqing Zhong
- Department of Pediatric Institute, Children's Hospital of Fudan University & National Children Medical Center, Shanghai, China
| | - Ran Jia
- Department of Clinical Laboratory, Children's Hospital of Fudan University & National Children Medical Center, Shanghai, China
| | - Menghua Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University & National Children Medical Center, Shanghai, China
| | - Pengcheng Liu
- Department of Clinical Laboratory, Children's Hospital of Fudan University & National Children Medical Center, Shanghai, China
| | - Liyun Su
- Department of Clinical Laboratory, Children's Hospital of Fudan University & National Children Medical Center, Shanghai, China
| | - Lingfeng Cao
- Department of Clinical Laboratory, Children's Hospital of Fudan University & National Children Medical Center, Shanghai, China
| | - Xunhua Zhu
- Department of Clinical Laboratory, Children's Hospital of Fudan University & National Children Medical Center, Shanghai, China
| | - Lijuan Lu
- Department of Clinical Laboratory, Children's Hospital of Fudan University & National Children Medical Center, Shanghai, China
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University & National Children Medical Center, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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Hoque SA, Saito H, Akino W, Kotaki T, Okitsu S, Onda Y, Kobayashi T, Hossian T, Khamrin P, Motomura K, Maneekarn N, Hayakawa S, Ushijima H. The Emergence and Widespread Circulation of Enteric Viruses Throughout the COVID-19 Pandemic: A Wastewater-Based Evidence. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:342-354. [PMID: 37898959 DOI: 10.1007/s12560-023-09566-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/30/2023] [Indexed: 10/31/2023]
Abstract
Growing evidence shed light on the importance of wastewater-based epidemiology (WBE) during the pandemic, when the patients rarely visited the clinics despite the fact that the infections were still prevalent in the community as before. The abundance of infections in the community poses a constant threat of the emergence of new epidemic strains. Herein, we investigated enteric viruses in raw sewage water (SW) from Japan's Tohoku region and compared them to those from the Kansai region to better understand the circulating strains and their distribution across communities during the COVID-19 pandemic. Raw SW was collected between 2019 and 2022, concentrated by polyethylene-glycol-precipitation method, and investigated for major AGE viruses by RT-PCR. Sequence-based analyses were used to assess genotypes and evolutionary relationships. The most commonly detected enteric virus was rotavirus A (RVA) at 63.8%, followed by astrovirus (AstV) at 61.1%, norovirus (NoV) GII and adenovirus (AdV) at 33.3%, sapovirus (SV) at 25.0%, enterovirus (EV) at 19.4%, and NoV GI at 13.9%. The highest prevalence (46.0%) was found in the spring. Importantly, enteric viruses did not decline during the pandemic. Rather, several strains like NoV GII.2, DS-1-like human G3 (equine) RVA, MLB1 AstV, and different F41 HAdV emerged throughout the pandemic and spread widely over the Tohoku and Kansai regions. Tohoku's detection rate remained lower than that of the Kansai area (36 vs 58%). This study provides evidence for the emergence and spread of enteric viruses during the pandemic.
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Affiliation(s)
- Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-ku, Tokyo, 173-8610, Japan
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Hiroyuki Saito
- Department of Microbiology, Akita Prefectual Research Center for Public Health and Environment, Akita, Japan
| | - Wakako Akino
- Department of Microbiology, Akita Prefectual Research Center for Public Health and Environment, Akita, Japan
| | - Tomohiro Kotaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Yuko Onda
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tania Hossian
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-ku, Tokyo, 173-8610, Japan.
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Morozova OV, Sashina TA, Epifanova NV, Velikzhanina EI, Novikova NA. Phylodynamic characteristics of reassortant DS-1-like G3P[8]-strains of rotavirus type A isolated in Nizhny Novgorod (Russia). Braz J Microbiol 2023; 54:2867-2877. [PMID: 37897627 PMCID: PMC10689624 DOI: 10.1007/s42770-023-01155-3] [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: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Since 2013, there has been an increase in reports of the spread of a double intergroup reassortant strain of rotavirus type A (RVA) with the genotype G3P[8] and other genes belonging to the second genogroup I2-R2-C2-M2-A2-N2-T2-E2-H2. In our study, we provide a molecular genetic characterization of rotaviruses with genotype G3P[8]-I2 isolated in Nizhny Novgorod. In our study, we used RT-PCR, Sanger sequencing, RNA-PAGE methods. Phylogenetic and phylodynamic analysis were performed using the Bayesian approach. According to our study, there was a significant increase in the proportion of G3P[8] from 15% during the period of 2020-2021 to 53% during the period of 2021-2022 in Nizhny Novgorod, Russia. Phylogenetic analysis based on the VP4 gene revealed that DS-1-like RVAs isolated in Nizhny Novgorod belong to different clusters of the P[8]-3.1 lineage, with a level of variation ranging from 1.1% to 1.3%. Based on the VP6 gene, the equine-like RVAs identified by us carry genetic variants belonging to three distinct clusters of the lineage I2-V, with a variation level ranging from 2.0% to 4.5%. These data indicate the genotypic diversity of circulating DS-1-like G3 RVAs. Phylogenetic analysis of the VP7 gene allowed us to assign the isolates identified in our study to the G3-1 lineage. We estimated that the circulation of the most recent common ancestor of the spreading strains dates back to 2002. Additionally, we determined the typical level of mutations in the VP7 gene, which amounted to 2.14*10-3 substitutions/per site/per year.
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Affiliation(s)
- Olga V Morozova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia.
| | - T A Sashina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N V Epifanova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - E I Velikzhanina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N A Novikova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
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Phan T, Hikita T, Okitsu S, Akari Y, Komoto S, Hayakawa S, Ushijima H. Whole genome sequencing and genomic characterization of a DS-1-like G2P[4] group A rotavirus in Japan. Virus Genes 2023; 59:688-692. [PMID: 37405556 DOI: 10.1007/s11262-023-02018-7] [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: 03/28/2023] [Accepted: 06/26/2023] [Indexed: 07/06/2023]
Abstract
After rotavirus was discovered in 1973, it became the leading pathogen in causing acute gastroenteritis in humans worldwide. In this study, we performed whole genome sequencing and genomic characterization of a DS-1-like G2P[4] group A rotavirus in feces of a Japanese child with acute gastroenteritis who was fully Rotarix® vaccinated. The genomic investigation determined a genomic constellation G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 of this rotavirus strain. Its antigenic epitopes of the VP7 and VP4 proteins had significant mismatches compared with the vaccine strains. Our study is the latest attempt to investigate the evolution of the VP7 and VP4 genes of emerging G2P[4] rotavirus in Japan.
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Affiliation(s)
- Tung Phan
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Shoko Okitsu
- Division of Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Yuki Akari
- 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
- Division of One Health, Research Center for Global and Local Infectious Diseases, Oita University, Yufu, Oita, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan.
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8
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Hoque SA, Pham NTK, Onda-Shimizu Y, Nishimura S, Sugita K, Kobayashi M, Islam MT, Okitsu S, Khamrin P, Maneekarn N, Hayakawa S, Ushijima H. Sapovirus infections in Japan before and after the emergence of the COVID-19 pandemic: An alarming update. J Med Virol 2023; 95:e29023. [PMID: 37543991 DOI: 10.1002/jmv.29023] [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: 01/17/2023] [Revised: 06/19/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
An increasing trend of sapovirus (SaV) infections in Japanese children during 2009-2019, particularly after the introduction of the voluntary rotavirus (RV)-vaccination program has been observed. Herein, we investigated the epidemiological situation of SaV infections from 2019 to 2022 when people adopted a precautionary lifestyle due to the emergence of the COVID-19 pandemic, and RV vaccines had been implemented as routine vaccines. Stool samples were collected from children who attended outpatient clinics with acute gastroenteritis and analyzed by reverse transcriptase-polymerase chain reaction to determine viral etiology. Among 961 stool samples, 80 (8.3%) were positive for SaV: 2019-2020 (6.5%), 2020-2021 (0%), and 2021-2022 (12.8%). The trend of SaV infection in Japanese children yet remained upward with statistical significance (p = 0.000). The major genotype was GI.1 (75%) which caused a large outbreak in Kyoto between December 2021 and February 2022. Phylogenetic, gene sequence and deduced amino acid sequence analyses suggested that these GI.1 strains detected in the outbreak and other places during 2021-2022 or 2019-2020 remained genetically identical and widely spread. This study reveals that SaV infection is increasing among Japanese children which is a grave concern and demands immediate attention to be paid before SaV attains a serious public health problem.
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Affiliation(s)
- Sheikh Ariful Hoque
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
- Cell and Tissue Culture Research, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Ngan Thi Kim Pham
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Yuko Onda-Shimizu
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shuichi Nishimura
- Cell and Tissue Culture Research, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Kumiko Sugita
- Division of Microbiology, Nihon University School of Medicine, Japanese Viral Gastritis Group, Tokyo, Japan
| | - Masaaki Kobayashi
- Division of Microbiology, Nihon University School of Medicine, Japanese Viral Gastritis Group, Tokyo, Japan
| | | | - Shoko Okitsu
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Thailand
| | - Satoshi Hayakawa
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
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9
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Hoque SA, Kotaki T, Pham NTK, Onda Y, Okitsu S, Sato S, Yuki Y, Kobayashi T, Maneekarn N, Kiyono H, Hayakawa S, Ushijima H. Genotype Diversity of Enteric Viruses in Wastewater Amid the COVID-19 Pandemic. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:176-191. [PMID: 37058225 PMCID: PMC10103036 DOI: 10.1007/s12560-023-09553-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/15/2023] [Indexed: 06/13/2023]
Abstract
Viruses remain the leading cause of acute gastroenteritis (AGE) worldwide. Recently, we reported the abundance of AGE viruses in raw sewage water (SW) during the COVID-19 pandemic, when viral AGE patients decreased dramatically in clinics. Since clinical samples were not reflecting the actual state, it remained important to determine the circulating strains in the SW for preparedness against impending outbreaks. Raw SW was collected from a sewage treatment plant in Japan from August 2018 to March 2022, concentrated by polyethylene-glycol-precipitation method, and investigated for major gastroenteritis viruses by RT-PCR. Genotypes and evolutionary relationships were evaluated through sequence-based analyses. Major AGE viruses like rotavirus A (RVA), norovirus (NoV) GI and GII, and astrovirus (AstV) increased sharply (10-20%) in SW during the COVID-19 pandemic, though some AGE viruses like sapovirus (SV), adenovirus (AdV), and enterovirus (EV) decreased slightly (3-10%). The prevalence remained top in the winter. Importantly, several strains, including G1 and G3 of RVA, GI.1 and GII.2 of NoV, GI.1 of SV, MLB1 of AstV, and F41 of AdV, either emerged or increased amid the pandemic, suggesting that the normal phenomenon of genotype changing remained active over this time. This study crucially presents the molecular characteristics of circulating AGE viruses, explaining the importance of SW investigation during the pandemic when a clinical investigation may not produce the complete scenario.
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Affiliation(s)
- Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, 1000, Bangladesh
| | - Tomohiro Kotaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Ngan Thi Kim Pham
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Yuko Onda
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Shintaro Sato
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
- Department of Microbiology and Immunology, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, 640-8156, Japan
| | - Yoshikazu Yuki
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba, Japan
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Kiyono
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba, Japan
- Research Institute of Disaster Medicine, Institute for Global Prominent Research, Institute for Advanced Academic Research, Chiba University, Chiba, Japan
- CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines (cMAV), Division of Gastroenterology, Department of Medicine, University of California, San Diego, USA
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 OyaguchiKamicho, Itabashi-Ku, Tokyo, 173-8610, Japan.
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10
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Abundance of viral gastroenteritis before and after the emergence of COVID-19: Molecular evidence on wastewater. J Infect 2022; 86:154-225. [PMID: 36402208 PMCID: PMC9671530 DOI: 10.1016/j.jinf.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022]
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11
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Lu L, Zhong H, Jia R, Su L, Xu M, Cao L, Liu P, Ao Y, Dong N, Xu J. Prevalence and genotypes distribution of group A rotavirus among outpatient children under 5 years with acute diarrhea in Shanghai, China, 2012-2018. BMC Gastroenterol 2022; 22:217. [PMID: 35505284 PMCID: PMC9066839 DOI: 10.1186/s12876-022-02288-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 04/20/2022] [Indexed: 11/10/2022] Open
Abstract
Background Group A rotavirus (RVA) remains the main causative agent of acute diarrhea among children under five years in countries that have not yet introduced the RVA vaccine worldwide. Long-term and continuous monitoring data on RVA infection in outpatient children were lacking in Shanghai. We investigated the prevalence and distribution of RVA genotypes in outpatient children with acute diarrhea in Shanghai from 2012 to 2018. Methods Stool specimens of outpatient children under five years were collected from the Children’s Hospital of Fudan University in Shanghai, China. All the samples enrolled in this study were detected and characterized for the P and G genotypes of RVA were determined using the semi-multiplex RT-PCR technique. Results Of 1814 children enrolled with acute diarrhea and having specimens collected, 246 (13.6%) were infected with RVA. The highest frequency of RVA was observed in children younger than two years old (87.0%, 214/246). Year-round RVA transmission was observed and the RVA detection rate peaked every winter and troughed in summer. In this study, 12 different RVA strains were identified in children. G9P[8] (49.2%, 121/246) was detected as the most prevalent genotype, followed by G–P[8] (22.8%, 56/246), G3P[8] (11.4%, 28/246), and G9P- (4.9%, 12/246). Although RVA strains detected in this study varied with the time, G9P[8] has been the most predominant circulating genotype since 2012. Furthermore, 12.2% (30/246) RVA positive samples were co-infected with other diarrhea viruses. Conclusion The present analysis showed that RVA was still a major cause of children with acute diarrhea in Shanghai from 2012 to 2018. A great diversity of RVA strains circulated in children with acute diarrhea with G9P[8] being the predominant genotype since 2012. Long-term and continuous monitoring of RVA genotypes is therefore indispensable to refine future vaccine strategy in Shanghai.
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Affiliation(s)
- Lijuan Lu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, People's Republic of China
| | - Huaqing Zhong
- Department of Pediatric Institute, Children's Hospital of Fudan University, Shanghai, 201102, People's Republic of China
| | - Ran Jia
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, People's Republic of China
| | - Liyun Su
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, People's Republic of China
| | - Menghua Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, People's Republic of China
| | - Lingfeng Cao
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, People's Republic of China
| | - Pengcheng Liu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, People's Republic of China
| | - Yuanyun Ao
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, People's Republic of China
| | - Niuniu Dong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, People's Republic of China
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, People's Republic of China.
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12
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Whole genome sequencing and evolutionary analysis of G8P [8] rotaviruses emerging in Japan. Virusdisease 2022; 33:215-218. [DOI: 10.1007/s13337-022-00765-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 04/03/2022] [Indexed: 10/18/2022] Open
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13
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Hoque SA, Wakana A, Shimizu H, Takanashi S, Okitsu S, Anwar KS, Hayakawa S, Maneekarn N, Okabe N, Ushijima H. Detection of Rotavirus Strains in Freshwater Clams in Japan. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:94-100. [PMID: 34981415 PMCID: PMC8722649 DOI: 10.1007/s12560-021-09505-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
Bivalve molluscan shellfish like clams and oysters, etc., are capable to bioaccumulate surrounding contaminants from waters into their digestive systems and posing serious threats of food poisoning. Detection of rotaviruses (RVs) in shellfish is of particular importance because RVs are prone to genome reassortment resulting in the emergence of new RV variants that may compromise vaccine safety. Herein, we have detected the wild-type RVs and Rotarix/RotaTeq vaccine strains in freshwater clams collected on the riverside, Kawasaki city, from July 2019 to January 2020 and correlated the detected genotypes with that of gastroenteritis cases of nearby clinics to understand the transmission of RVs in the environment. The wild-type RVs were detected in 62 (64.6%) out of 96 freshwater clams in every study month: July, September, November, and January that are considered as off-season for RV infections. The most frequent genotypes were G2 (42.9%), G8 (28.6%), G3 (14.3%), G1 (7.1%), and G10 (7.1%), which remained comparable with genotypic distribution found in the clinical samples over the last few years indicating that these RVs may accumulate in clams since a long time. However, G10 genotype was detected in clam but not in clinical samples suggesting the presence of asymptomatic infection or RVs could be carried out from a long distance. Importantly, vaccine strains, RotaTeq (1%) but not Rotarix (0%), were also detected in a clam. Attention must be paid to monitoring the potential transmission of wild-type and vaccine RV strains in the environment to prevent the emergence of new variants generated from genome reassortment with vaccine strains.
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Affiliation(s)
- Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Azumi Wakana
- Kawasaki City Institute for Public Health, Kawasaki City, Kanagawa, Japan
| | - Hideaki Shimizu
- Kawasaki City Institute for Public Health, Kawasaki City, Kanagawa, Japan
| | - Sayaka Takanashi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku-Ku, Tokyo, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Kazi Selim Anwar
- Ad-Din Women Medical College Hospital (AWMCH), Dhaka, Bangladesh
- Department of Public Health, Daffodil International University (DIU), Dhaka, Bangladesh
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nobuhiko Okabe
- Kawasaki City Institute for Public Health, Kawasaki City, Kanagawa, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan.
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14
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Hoque SA, Nishimura K, Thongprachum A, Khamrin P, Thi Kim Pham N, Islam MT, Khandoker N, Okitsu S, Onda-Shimizu Y, Dey SK, Maneekarn N, Kobayashi T, Hayakawa S, Ushijima H. An Increasing Trend of Human Sapovirus Infection in Japan, 2009 to 2019: An Emerging Public Health Concern. J Infect Public Health 2022; 15:315-320. [DOI: 10.1016/j.jiph.2022.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/21/2021] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
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15
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Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
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Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
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16
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Kawata K, Hoque SA, Nishimura S, Yagyu F, Islam MT, Sharmin LS, Pham NTK, Onda-Shimizu Y, Quang TD, Takanashi S, Okitsu S, Khamrin P, Maneekarn N, Hayakawa S, Ushijima H. Role of rotavirus vaccination on G9P[8] rotavirus strain during a seasonal outbreak in Japan. Hum Vaccin Immunother 2021; 17:3613-3618. [PMID: 34033735 DOI: 10.1080/21645515.2021.1925060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although two live oral rotavirus (RV) vaccines, Rotarix and RotaTeq, play a critical role toward reducing disease severity, hospitalization, and death rate in RV infections, regular monitoring of vaccine effectiveness (VE) is yet necessary because the segmented genome structure and reassortment capability of RVs pose considerable threats toward waning VE. In this study, we examined the VE by a test-negative study design against G9P[8]I2 strain during a seasonal outbreak in February-May, 2018, in an outpatient clinic in Kyoto Prefecture, Japan. It remains important because G9P[8]I2 strain remains partially heterotypic to these vaccines and predominating in post-vaccination era. During year-long surveillance, RV infections were detected only from February to May. During this outbreak, 33 (42.3%) children out of 78 with acute gastroenteritis (AGE) remained RV-positive, of which 29 (87.8%) children were infected with G9P[8]I2. Two immunochromatographic (IC) assay kits exhibited 100% sensitivity and specificity to detect G9P[8]I2 strain. Only 23.2% children were found to be vaccinated. Yet, significant VE 69.7% (95% CI: 2.5%-90.6%) was recognized against all RV strains that increased with disease severity. Similar significant VE 71.8% (95% CI: 1%-92%) was determined against G9P[8]I2 strain. The severity score remained substantially low in vaccinated children. Our data reveal that vaccine-preventable G9P[8]I2 strain yet may cause outbreak where vaccination coverage remains low. Thus, this study emphasizes the necessity of global introduction of RV-vaccines in national immunization programs of every country.
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Affiliation(s)
- Kimiko Kawata
- Division on Nursing Sciences, Midwifery, Department of Health Sciences, Faculty of Medical Sciences, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan
| | - Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Cell and Tissue Culture Research, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | | | - Fumihiro Yagyu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | | | | | - Ngan Thi Kim Pham
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Yuko Onda-Shimizu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Trinh Duy Quang
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine and Emerging and Re-emerging Diarrheal Viruses Research Center, Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine and Emerging and Re-emerging Diarrheal Viruses Research Center, 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
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17
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Jampanil N, Kumthip K, Yodmeeklin A, Kanai Y, Okitsu S, Kobayashi T, Ukarapol N, Ushijima H, Maneekarn N, Khamrin P. Epidemiology and genetic diversity of group A rotavirus in pediatric patients with acute gastroenteritis in Thailand, 2018-2019. INFECTION GENETICS AND EVOLUTION 2021; 95:104898. [PMID: 33971304 DOI: 10.1016/j.meegid.2021.104898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 12/12/2022]
Abstract
Group A rotaviruses (RVAs) are the major viruses that cause acute gastroenteritis in young children worldwide. The objective of this study was to investigate the prevalence and genotype diversity of RVAs circulating in children with acute gastroenteritis in Thailand in 2018-2019. A total of 1170 stool specimens were obtained from children admitted to hospitals with diarrhea and screened for RVAs by nested RT-PCR. The RVA genotypes were determined by multiplex-PCR or nucleotide sequencing and phylogenetic analysis. Out of 1170 stool specimens, 209 (17.9%) were positive for RVAs. The RVA G9P[8] genotype (24.4%) was the most dominant genotype, followed by G3P[8] (22.9%), G8P[8] (22.0%), G1P[8] (16.7%), G2P[4] (6.7%), G1P[6] (2.3%), G1P[4] (1.0%), G3P[4] (1.0%), G9P[4] (1.0%), mixed-infections of G1P[4] + G1P[8] (1.0%), and GXP[8] (0.5%). Moreover, an uncommon RVA G3P[10] genotype (0.5%), bearing bat-like VP7 and VP4 genes, was detected. This study reveals the prevalence and genetic diversity of RVA genotypes in children with acute gastroenteritis in Thailand. The knowledge obtained from this study is helpful for understanding the epidemiology of rotavirus in Thailand. The emergence of uncommon RVA strain G3P[10] provides an evidence for interspecies transmission of human and animal rotaviruses.
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Affiliation(s)
- Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Emerging and Re-emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Emerging and Re-emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai, Thailand
| | - Yuta Kanai
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shoko Okitsu
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Nuthapong Ukarapol
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; 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; Emerging and Re-emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Emerging and Re-emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai, Thailand; Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.
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18
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Cárcamo-Calvo R, Muñoz C, Buesa J, Rodríguez-Díaz J, Gozalbo-Rovira R. The Rotavirus Vaccine Landscape, an Update. Pathogens 2021; 10:520. [PMID: 33925924 PMCID: PMC8145439 DOI: 10.3390/pathogens10050520] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
Rotavirus is the leading cause of severe acute childhood gastroenteritis, responsible for more than 128,500 deaths per year, mainly in low-income countries. Although the mortality rate has dropped significantly since the introduction of the first vaccines around 2006, an estimated 83,158 deaths are still preventable. The two main vaccines currently deployed, Rotarix and RotaTeq, both live oral vaccines, have been shown to be less effective in developing countries. In addition, they have been associated with a slight risk of intussusception, and the need for cold chain maintenance limits the accessibility of these vaccines to certain areas, leaving 65% of children worldwide unvaccinated and therefore unprotected. Against this backdrop, here we review the main vaccines under development and the state of the art on potential alternatives.
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Affiliation(s)
- Roberto Cárcamo-Calvo
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
| | - Carlos Muñoz
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
| | - Javier Buesa
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
- Instituto de Investigación INCLIVA, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - Jesús Rodríguez-Díaz
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
- Instituto de Investigación INCLIVA, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - Roberto Gozalbo-Rovira
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
- Instituto de Investigación INCLIVA, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
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19
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Kim KG, Kee HY, Park HJ, Chung JK, Kim TS, Kim MJ. The Long-Term Impact of Rotavirus Vaccines in Korea, 2008-2020; Emergence of G8P[8] Strain. Vaccines (Basel) 2021; 9:406. [PMID: 33923945 PMCID: PMC8073504 DOI: 10.3390/vaccines9040406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/19/2022] Open
Abstract
This study evaluated the long-term impact of rotavirus vaccination on prevalence, seasonality, and genotype distribution in Gwangju, Korea for 13 seasons. Rotavirus was identified using ELISA and then sequenced for G and P genotypes by Reverse Transcription Polymerase Chain Reactions for diarrhoeagenic patient specimens from local hospitals between January 2008 and August2020. Of 26,902 fecal samples, 2919 samples (10.9%) were ELISA positive. The prevalence declined from 16.3% in pre-vaccine era to 5.4% in post-vaccine era. In the pre-vaccine period, G1P[8] was the most common genotype, followed by G2P[4], G3P[8], and G9P[8], etc. In the transitional period, the proportion of G2P[4] became the dominant genotype and G1P[8] was still commonly identified. In contrast, the novel genotype G8P[8] was predominant in the post-vaccine period. Meanwhile, G2P[4] and G8P[8] were major genotypes in both Rotarix and RotaTeq groups. The substantial decline of G1P[8] prevalence, reemergence of G1P[8], G3P[8], and G2P[4] rotavirus strains, and surge of the rare G8P[8] after vaccine introduction were interesting points to note. The continuous surveillance on the genotypes of RV will be needed to understand rotavirus epidemiology and their evolutionary patterns, as caution is required when interpreting temporal changes in RV genotype dynamic.
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Affiliation(s)
| | | | | | | | | | - Min Ji Kim
- Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (K.g.K.); (H.-y.K.); (H.j.P.); (J.K.C.); (T.s.K.)
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Cho SR, Chae SJ, Jung S, Choi W, Han MG, Yoo CK, Lee DY. Trends in acute viral gastroenteritis among children aged ≤5 years through the national surveillance system in South Korea, 2013-2019. J Med Virol 2021; 93:4875-4882. [PMID: 33219526 PMCID: PMC8360024 DOI: 10.1002/jmv.26685] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/04/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022]
Abstract
Acute gastroenteritis is a global public health concern. This study aimed to analyze the trend and characteristics of acute viral gastroenteritis through a national surveillance network. Enteric viruses were detected in 9510 of 31,750 (30.1%) cases assessed from 2013 to 2019 by EnterNet. The most prevalent pathogens were norovirus (15.2%) and group A rotavirus (9.7%); most infections were reported in 2017 (34.0%). Norovirus and rotavirus coinfections were the most common. Norovirus infections were prevalent among 1‐year‐old children (1835 out of 9510 cases) during winter, and group A rotavirus infections were common during spring. Seasonality was not observed among enteric adenovirus, astrovirus, and sapovirus. The prevalent viral genotypes detected included norovirus GII.4, enteric adenovirus F41, astrovirus genotype 1, and sapovirus GI.1. However, changes in enteric virus trends were noted during the study period. Norovirus prevalence extended into spring, and new genotypes of enteric adenovirus, astrovirus, and sapovirus were identified. These surveillance data elucidate enteric virus epidemiological characteristics.
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Affiliation(s)
- Seung-Rye Cho
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Su-Jin Chae
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Sunyoung Jung
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Wooyoung Choi
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Myung-Guk Han
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Cheon-Kwon Yoo
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Deog-Yong Lee
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, Chungcheongbuk-do, Republic of Korea
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Kyo K, Takano C, Kasuga Y, Ogawa E, Ishige M, Pham NTK, Okitsu S, Ushijima H, Urakami T, Fuchigami T, Hayakawa S, Morioka I. Severe rotavirus gastroenteritis in children older than 5 years after vaccine introduction. J Infect Chemother 2020; 27:598-603. [PMID: 33386258 DOI: 10.1016/j.jiac.2020.11.018] [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: 07/21/2020] [Revised: 10/29/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Rotavirus (RV) is the major pathogen responsible for acute gastroenteritis in infants. Since RV vaccines were introduced, a substantial decline in the incidence of severe RV infection has been reported. However, some burden still exists, even in developed countries, including Japan. METHODS We retrospectively surveyed 380 patients hospitalized for acute gastroenteritis from 2015 to 2019. In 2019, additional detailed clinical information of 21 patients with RV gastroenteritis was obtained to evaluate the efficacy of the RV vaccine. Nine fecal samples from those patients were collected to detect the RV genotypes. RESULTS Our data showed an increasing trend in hospitalizations for severe RV gastroenteritis in children older than 5 years. According to the Vesikari clinical severity scores in the older group (≥5 years), the gastrointestinal symptoms in vaccinated patients were less severe than those in unvaccinated patients (p = 0.014). The genotype analysis revealed that G9P[8]I1 was the major genotype in the recruited patients in 2019. CONCLUSIONS This report warns that children older than 5 years could be affected by severe RV infection and suggests prompt intervention for this age group, similar to that in infants. In the new period in which the RV vaccine is included in Japanese national immunization programs beginning October 2020, continuous monitoring of patient clinical characteristics and RV epidemiology is required to determine the role of vaccines.
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Affiliation(s)
- Kiyoshi Kyo
- Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Chika Takano
- Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan; Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan.
| | - Yuki Kasuga
- Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Erika Ogawa
- Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Mika Ishige
- Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Ngan Thi Kim Pham
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Tatsuhiko Urakami
- Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Tatsuo Fuchigami
- Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan; Department of Pediatrics, IMS Fujimi General Hospital, 1967-1, Tsuruma, Fujimi-shi, Saitama, 354-0021, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, 173-8610, Japan
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Reverse Genetics Approach for Developing Rotavirus Vaccine Candidates Carrying VP4 and VP7 Genes Cloned from Clinical Isolates of Human Rotavirus. J Virol 2020; 95:JVI.01374-20. [PMID: 33087468 DOI: 10.1128/jvi.01374-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
Species A rotaviruses (RVs) are a leading cause of severe acute gastroenteritis in infants and children younger than 5 years. Currently available RV vaccines were adapted from wild-type RV strains by serial passage of cultured cells or by reassortment between human and animal RV strains. These traditional methods require large-scale screening and genotyping to obtain vaccine candidates. Reverse genetics is a tractable, rapid, and reproducible approach to generating recombinant RV vaccine candidates carrying any VP4 and VP7 genes that provide selected antigenicity. Here, we developed a vaccine platform by generating recombinant RVs carrying VP4 (P[4] and P[8]), VP7 (G1, G2, G3, G8, and G9), and/or VP6 genes cloned from human RV clinical samples using the simian RV SA11 strain (G3P[2]) as a backbone. Neutralization assays using monoclonal antibodies and murine antisera revealed that recombinant VP4 and VP7 monoreassortant viruses exhibited altered antigenicity. However, replication of VP4 monoreassortant viruses was severely impaired. Generation of recombinant RVs harboring a chimeric VP4 protein for SA11 and human RV gene components revealed that the VP8* fragment was responsible for efficient infectivity of recombinant RVs. Although this system must be improved because the yield of vaccine viruses directly affects vaccine manufacturing costs, reverse genetics requires less time than traditional methods and enables rapid production of safe and effective vaccine candidates.IMPORTANCE Although vaccines have reduced global RV-associated hospitalization and mortality over the past decade, the multisegmented genome of RVs allows reassortment of VP4 and VP7 genes from different RV species and strains. The evolutionary dynamics of novel RV genotypes and their constellations have led to great genomic and antigenic diversity. The reverse genetics system is a powerful tool for manipulating RV genes, thereby controlling viral antigenicity, growth capacity, and pathogenicity. Here, we generated recombinant simian RVs (strain SA11) carrying heterologous VP4 and VP7 genes cloned from clinical isolates and showed that VP4- or VP7-substituted chimeric viruses can be used for antigenic characterization of RV outer capsid proteins and as improved seed viruses for vaccine production.
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Epidemiology of Acute Rotavirus Diarrhea Among Hospitalized Children Under Five Years of Age in Hefei, China, During 2015 - 2018. Jundishapur J Microbiol 2020. [DOI: 10.5812/jjm.105556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Rotavirus infection is still the leading cause of acute viral gastroenteritis in children under five years of age worldwide. It is also a serious public health concern in China. Objectives: This study aimed to obtain information about rotavirus diarrhea among hospitalized children in Hefei City, Anhui Province, China, in recent years. Methods: We conducted a retrospective study over four years (2015 - 2018) examining hospital admission records of rotavirus infections at the First Affiliated Hospital of Anhui Medical University in Hefei City of Anhui Province, China. Results: A total of 1,095 cases with acute viral gastroenteritis requiring hospital admission from January 2015 to December 2018 were analyzed. Among them, 276 cases were positive for rotavirus A infection, accounting for 25.21% of the total number of children suffering from acute diarrhea. The detection rate of rotavirus A was the highest in children aged 1 - 2 years. The peak month for rotavirus infection during 2015 - 2018 was December and January. The hospitalized children with rotavirus infection showed dehydration, electrolyte disorder, liver function abnormality, and myocardial enzyme abnormality. Conclusions: Rotavirus is still the first pathogen of acute viral diarrhea in children in Hefei, especially children < 2 years of age, which highlights the need for widespread rotavirus immunization in young children.
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Zhou N, Zhou L, Wang B. Genetic Characterizations and Molecular Evolution of VP7 Gene in Human Group A Rotavirus G1. Viruses 2020; 12:v12080831. [PMID: 32751603 PMCID: PMC7472278 DOI: 10.3390/v12080831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/20/2020] [Accepted: 07/29/2020] [Indexed: 01/01/2023] Open
Abstract
Rotavirus group A (RVA) G1 is one leading genotype circulating in humans worldwide, and related molecular information from a global perspective is still limited. Here, we present a comprehensive description of the genetic characterizations and molecular evolution of the RVA G1 VP7 gene. Our results show that RVA G1 can be divided into two lineages and multiple sub-lineages with a relatively high genetic diversity. Vaccine strains are phylogenetic, closer to lineage I. The evolutionary rate of the RVA G1 VP7 gene is 8.869 × 10-4 substitutions/site/year, and its most recent common ancestor was in 1933. The RVA G1 VP7 gene shows a linear evolution at the nucleotide level and a linear accumulation of difference at the amino acid level. Sub-lineage replacement of G1 VP7 gene is also observed and the effective population size of the G1 VP7 gene has had great change in the past decades and has remained stable in recent years. Altogether, the RVA G1 VP7 gene constantly evolves and there is no clear evidence that the evolution of the RVA G1 VP7 gene was influenced by vaccines. Continuous surveillance is still indispensable to evaluate the molecular epidemiology of RVA, especially in the post-vaccination era.
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Affiliation(s)
- Nan Zhou
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Statistics, School of Public Health, Southeast University, Nanjing 210009, China;
| | - Lu Zhou
- Department of Acute Infectious Diseases, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China;
| | - Bei Wang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Statistics, School of Public Health, Southeast University, Nanjing 210009, China;
- Correspondence: ; Tel.: +86-25-83272569
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