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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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Ushijima H, Hoque SA, Akari Y, Pham NTK, Phan T, Nishimura S, Kobayashi M, Sugita K, Okitsu S, Komoto S, Thongprachum A, Khamrin P, Maneekarn N, Hayakawa S. Molecular Evolution of GII.P31/GII.4_Sydney_2012 Norovirus over a Decade in a Clinic in Japan. Int J Mol Sci 2024; 25:3619. [PMID: 38612429 PMCID: PMC11011564 DOI: 10.3390/ijms25073619] [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: 01/31/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Norovirus (NoV) genogroup II, polymerase type P31, capsid genotype 4, Sydney_2012 variant (GII.P31/GII.4_Sydney_2012) has been circulating at high levels for over a decade, raising the question of whether this strain is undergoing molecular alterations without demonstrating a substantial phylogenetic difference. Here, we applied next-generation sequencing to learn more about the genetic diversity of 14 GII.P31/GII.4_Sydney_2012 strains that caused epidemics in a specific region of Japan, with 12 from Kyoto and 2 from Shizuoka, between 2012 and 2022, with an emphasis on amino acid (aa) differences in all three ORFs. We found numerous notable aa alterations in antigenic locations in the capsid region (ORF2) as well as in other ORFs. In all three ORFs, earlier strains (2013-2016) remained phylogenetically distinct from later strains (2019-2022). This research is expected to shed light on the evolutionary properties of dominating GII.P31/GII.4_Sydney_2012 strains, which could provide useful information for viral diarrhea prevention and treatment.
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Affiliation(s)
- Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
| | - Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka 1000, Bangladesh
| | - Yuki Akari
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Ngan Thi Kim Pham
- College of Industrial Technology, Nihon University, Narashino, Chiba 275-8575, Japan;
| | - Tung Phan
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | | | | | - Kumiko Sugita
- Sugita Children Clinic, Ibaraki, Osaka 567-0035, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
- Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan
- Division of One Health, Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University, Yufu, Oita 879-5593, Japan
| | | | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine and Emerging and Re-Emerging Diarrheal Viruses Research Center, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine and Emerging and Re-Emerging Diarrheal Viruses Research Center, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
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Hazan G, Goldstein Y, Greenberg D, Khalde F, Mahajna R, Keren-Naos A, Hershkovitz E, Faingelernt Y, Givon-Lavi N, Danino D. Comparing single versus multiple virus detection in pediatric acute gastroenteritis postimplementation of routine multiplex RT-PCR diagnostic testing. J Med Virol 2024; 96:e29344. [PMID: 38149453 DOI: 10.1002/jmv.29344] [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: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Utilizing multiplex real time polymerase chain reaction (RT-PCR) for rapid diagnosis of gastroenteritis, enables simultaneous detection of multiple pathogens. A comparative analysis of disease characteristics was conducted between cases with single and multiple viruses. Rotavirus vaccine was introduced in 2010, reaching a 70% coverage in 2 years. All rectal swabs collected from diarrheic children (<5 years) between December 2017 and March 2022 were included. Detection of the same viruses within 2 months was considered a single episode. Episodes with positive stool bacterial PCR were excluded. A total of 5879 samples were collected, revealing 86.9% (1509) with single virus detection and 13.1% (227) with multiple viruses. The most frequent combination was rotavirus and norovirus (27.8%), these infections followed a winter-spring seasonality akin to rotavirus. Children with multivirus infections exhibited higher immunodeficiency (OR 2.06) rates, but lower food allergy (OR 0.45) and prematurity rates (OR 0.55) compared to single infections. Greater disease severity, evaluated by the Vesikari score, was observed in multivirus episodes (p < 0.001, OR 1.12). Multivirus infections accounted for 13.1% of symptomatic cases in hospitalized young children. Despite vaccination efforts, rotavirus remained prominent, frequently in co-infections with norovirus. Overall, multivirus infections were linked to more severe diseases than single virus cases.
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Affiliation(s)
- Guy Hazan
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Pulmonary Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Yoav Goldstein
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - David Greenberg
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Firas Khalde
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Rofaida Mahajna
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Ayelet Keren-Naos
- Clinical Virology Laboratory, Soroka University Medical Center, Beer Sheva, Israel
| | - Eli Hershkovitz
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Yaniv Faingelernt
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Gastroenterology Hepatology and Nutrition Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Noga Givon-Lavi
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Dana Danino
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
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Michael F, Mirambo MM, Lyimo D, Salehe A, Kyesi F, Msanga DR, Mahamba D, Nyawale H, Kwiyolecha E, Okamo B, Mwanyika PJ, Maghina V, Bendera E, Salehe M, Hokororo A, Mwipopo E, Khamis AC, Nyaki H, Magodi R, Mujuni D, Konje ET, Katembo B, Wilillo R, Mshana SE. Rotavirus genotype diversity in Tanzania during Rotavirus vaccine implementation between 2013 and 2018. Sci Rep 2023; 13:21795. [PMID: 38066194 PMCID: PMC10709589 DOI: 10.1038/s41598-023-49350-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
The study aims to determine Rotavirus genotypes between 2013 and 2018 during implementation of ROTARIX vaccine in Tanzania. The analysis of surveillance data obtained between 2013 and 2018 was done to determine circulating genotypes after introduction of Rotarix vaccine. From 2013 to 2018, a total of 10,557 samples were collected and screened for Rotavirus using an enzyme immunoassay. A significant decrease in Rotavirus positivity (29.3% to 17.8%) from 2013 to 2018 (OR 0.830, 95% CI 0.803-0.857, P < 0.001) was observed. A total of 766 randomly selected Rotavirus positive samples were genotyped. Between 2013 and 2018, a total of 18 Rotavirus genotypes were detected with G1P [8] being the most prevalent. The G1P [8] strain was found to decrease from 72.3% in 2015 to 13.5% in 2018 while the G9P [4] strain increased from 1 to 67.7% in the same years. G2P [4] was found to decrease from 59.7% in 2013 to 6.8% in 2018 while G3P [6] decreased from 11.2% in 2014 to 4.1% in 2018. The data has clearly demonstrated that ROTARIX vaccine has provided protection to varieties of the wild-type Rotavirus strains. Continuous surveillance is needed to monitor the circulation of Rotavirus strains during this era of vaccine implementation.
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Affiliation(s)
- Fausta Michael
- Ministry of Health, Immunization and Vaccine Development Program, Dodoma, Tanzania
| | - Mariam M Mirambo
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania.
| | - Dafrossa Lyimo
- Ministry of Health, Immunization and Vaccine Development Program, Dodoma, Tanzania
| | - Abdul Salehe
- Ministry of Health, Immunization and Vaccine Development Program, Zanzibar, Tanzania
| | - Furaha Kyesi
- Ministry of Health, Immunization and Vaccine Development Program, Dodoma, Tanzania
| | - Delfina R Msanga
- Department of Paediatrics and Child Health, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Dina Mahamba
- Department of Pediatrics and Child Health, College of Health Sciences, University of Dodoma, P.O. Box 395, Dodoma, Tanzania
| | - Helmut Nyawale
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Elizabeth Kwiyolecha
- Department of Paediatrics and Child Health, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Bernard Okamo
- Department of Biochemistry and Molecular Biology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Paul J Mwanyika
- Department of Pediatrics and Child Health, Mbeya Zonal Referral Hospital, P.O. Box 419, Mbeya, Tanzania
| | - Victoria Maghina
- Department of Pediatrics and Child Health, Mbeya Zonal Referral Hospital, P.O. Box 419, Mbeya, Tanzania
| | - Elice Bendera
- Department of Pediatrics and Child Health, Muheza Designated District Hospital, Tanga, Tanzania
| | - Mohammed Salehe
- Department of Pediatrics and Child Health, Bombo Regional Referral Hospital, Tanga, Tanzania
| | - Adolfine Hokororo
- Department of Paediatrics and Child Health, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Ernestina Mwipopo
- Department of Pediatrics and Child Health, Mwananyamala Regional Referral Hospital, Dar es Salaam, Tanzania
| | - Asha C Khamis
- Department of Pediatrics and Child Health, Temeke Regional Referral Hospital, Dar es Salaam, Tanzania
| | - Honest Nyaki
- Ministry of Health, Immunization and Vaccine Development Program, Dodoma, Tanzania
| | - Richard Magodi
- Ministry of Health, Immunization and Vaccine Development Program, Dodoma, Tanzania
| | - Delphius Mujuni
- Ministry of Health, Immunization and Vaccine Development Program, Dodoma, Tanzania
| | - Eveline T Konje
- Department of Epidemiology and Biostatistics, School of Public Health, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Betina Katembo
- National Public Health Laboratory, Dar es Salaam, Tanzania
| | - Ritha Wilillo
- World Health Organization, Country Office, Dar es Salaam, Tanzania
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
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5
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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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6
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Danino D, Hazan G, Mahajna R, Khalde F, Farraj L, Avni YS, Greenberg D, Hershkovitz E, Faingelernt Y, Givon-Lavi N. Implementing a multiplex-PCR test for the diagnosis of acute gastroenteritis in hospitalized children: Are all enteric viruses the same? J Clin Virol 2023; 167:105577. [PMID: 37651826 DOI: 10.1016/j.jcv.2023.105577] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Multiplex-PCR is a valuable tool for diagnosing viral acute gastroenteritis (AGE), enabling the detection of multiple pathogens. However, distinguishing between active disease and shedding poses challenges. This study aimed to evaluate viral AGE epidemiology and compare clinical characteristics among the five most common viruses. METHODS Rotavirus vaccine was introduced in 2010, with 70% coverage achieved in southern Israel in two years. All rectal swabs for multiplex-PCR targeting rotavirus, norovirus, adenovirus, astrovirus and sapovirus from hospitalized diarrheic children <5 years were included, from December 2017 through March 2022. Detection of the same virus within two months was considered a single episode. Clinical analysis included episodes with single-virus detection and negative bacterial PCR. RESULTS Among 5,879 rectal swabs, 2,662 (45.3%) tested positive for at least one virus, with 245 (9.2%) showing multiple virus detection. Rotavirus was the most prevalent. While rotavirus exhibited typical winter-spring seasonality in 2018-19, an unusual off-season surge was observed during the second year of the COVID-19 pandemic. Among negative bacterial PCR episodes, 34.6% had mucus stool, 5.9% had bloody stool, and 29.3% received antibiotics. Astrovirus or sapovirus infections were associated with higher rates of hospital-acquired AGE and immunodeficiency (P<0.05), whereas rotavirus infections had higher rates of dehydration severity and acute kidney injury (P<0.05). DISCUSSION Enteric viruses were detected in 45.3% of rectal swabs from hospitalized children with diarrhea. Despite vaccination efforts, rotavirus remained prevalent and caused more severe disease. Continuous surveillance using multiplex-PCR is crucial for accurate management and future prevention strategies for viral AGE.
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Affiliation(s)
- Dana Danino
- Ben Gurion University, Faculty of Health Sciences, Beer Sheva, Israel; Soroka University Medical Center, Pediatric Infectious Diseases Unit, Beer Sheva, Israel.
| | - Guy Hazan
- Ben Gurion University, Faculty of Health Sciences, Beer Sheva, Israel; Soroka University Medical Center, Pediatric Department D, Beer Sheva, Israel
| | - Rofaida Mahajna
- Soroka University Medical Center, Pediatric Department D, Beer Sheva, Israel
| | - Firas Khalde
- Soroka University Medical Center, Pediatric Department D, Beer Sheva, Israel
| | - Lama Farraj
- Ben Gurion University, Faculty of Health Sciences, Beer Sheva, Israel
| | - Yonat Shemer Avni
- Soroka University Medical Center, Clinical Virology Laboratory, Beer-Sheva, Israel
| | - David Greenberg
- Ben Gurion University, Faculty of Health Sciences, Beer Sheva, Israel; Soroka University Medical Center, Pediatric Infectious Diseases Unit, Beer Sheva, Israel
| | - Eli Hershkovitz
- Ben Gurion University, Faculty of Health Sciences, Beer Sheva, Israel; Soroka University Medical Center, Clinical Virology Laboratory, Beer-Sheva, Israel
| | - Yaniv Faingelernt
- Ben Gurion University, Faculty of Health Sciences, Beer Sheva, Israel; Soroka University Medical Center, Pediatric Gastroenterology Hepatology and Nutrition Unit, Beer Sheva, Israel
| | - Noga Givon-Lavi
- Ben Gurion University, Faculty of Health Sciences, Beer Sheva, Israel
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7
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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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8
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Differentiation between Wild-Type Group A Rotaviruses and Vaccine Strains in Cases of Suspected Horizontal Transmission and Adverse Events Following Vaccination. Viruses 2022; 14:v14081670. [PMID: 36016292 PMCID: PMC9416126 DOI: 10.3390/v14081670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/18/2022] Open
Abstract
Human group A rotaviruses (RVA) are important enteric pathogens, as they are a leading cause of acute gastroenteritis (AGE) in children worldwide. Since 2013, the German Standing Committee on vaccination recommended the routine rotavirus vaccination for infants in Germany. While vaccination has significantly decreased RVA cases and worldwide mortality, in some cases, infants can develop acute gastroenteritis as an adverse reaction after immunization with an attenuated live vaccine. Pediatricians, as well as clinicians and diagnostic laboratories, contacted the Consultant Laboratory for Rotaviruses and inquired whether cases of RVA-positive AGE after vaccination were associated with vaccine or with wild-type RVA strains. A testing algorithm based on distinguishing PCRs and confirmative sequencing was designed, tested, and applied. Diagnostic samples from 68 vaccinated children and six cases where horizontal transmission was suspected were investigated in this study. Using a combination of real-time PCR, fragment-length analysis of amplicons from multiplex PCRs and confirmative sequencing, vaccine-like virus was detected in 46 samples and wild-type RVA was detected in 6 samples. Three mixed infections of vaccine and wild-type RVA were detectable, no RVA genome was found in 19 samples. High viral loads (>1.0 × 107 copies/g stool) were measured in most RVA-positive samples. Furthermore, information on co-infections with other AGE pathogens in the vaccinated study population was of interest. A commercial multiplex PCR and in-house PCRs revealed three co-infections of vaccinated infants with bacteria (two samples with Clostridioides difficile and one sample with enteropathogenic E. coli) and six co-infections with norovirus in a subset of the samples. Human astrovirus was detected in one sample, with suspected horizontal transmission. The cases of suspected horizontal transmission of vaccine RVA strains could not be confirmed, as they either involved wild-type RVA or were RVA negative. This study shows that RVA-positive AGE after vaccination is not necessarily associated with the vaccine strain and provides a reliable workflow to distinguish RVA vaccine strains from wild-type strains.
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9
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Mitra S, Lo M, Saha R, Deb AK, Debnath F, Miyoshi S, Dutta S, Chawla‐Sarkar M. Epidemiology of major entero‐pathogenic viruses and genetic characterization of Group A rotaviruses among children (≤5 years) with acute gastroenteritis in eastern India, 2018‐2020. J Appl Microbiol 2022; 133:758-783. [DOI: 10.1111/jam.15594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Suvrotoa Mitra
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
| | - Mahadeb Lo
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
| | - Ritubrita Saha
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
| | - Alok K. Deb
- Division of Epidemiology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Falguni Debnath
- Division of Epidemiology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Shin‐Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences Okayama University Okayama Japan
- Collaborative Research Centre of Okayama University for Infectious Disease ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Shanta Dutta
- Regional Virus Research and Diagnostic Laboratory, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Mamta Chawla‐Sarkar
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
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