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2. Genotype Diversity of Enteric Viruses in Wastewater Amid the COVID-19 Pandemic.

Author

Hoque, Sheikh, Kotaki, Tomohiro, Pham, Ngan, Onda, Yuko, Okitsu, Shoko, Sato, Shintaro, Yuki, Yoshikazu, Kobayashi, Takeshi, Maneekarn, Niwat, Kiyono, Hiroshi, Hayakawa, Satoshi, and Ushijima, Hiroshi

Subjects
COVID-19 pandemic, Enteric viruses, Genotypes, Raw sewage, Humans, Wastewater, Pandemics, Sewage, COVID-19, Gastroenteritis, Viruses, Rotavirus, Enterovirus, Norovirus, Sapovirus, RNA Viruses, Enterovirus Infections, Adenoviridae, Genotype, Phylogeny, Feces
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.

Published
2023

19. Epidemiology of Enterovirus Genotypes in Association with Human Diseases.

Author

Xie, Zhenfeng, Khamrin, Pattara, Maneekarn, Niwat, and Kumthip, Kattareeya

Subjects
INFANT diseases, COMMUNICABLE diseases, GENOTYPES, SEROPREVALENCE, ENTEROVIRUSES
Abstract

Enteroviruses (EVs) are well-known causes of a wide range of infectious diseases in infants and young children, ranging from mild illnesses to severe conditions, depending on the virus genotypes and the host's immunity. Recent advances in molecular surveillance and genotyping tools have identified over 116 different human EV genotypes from various types of clinical samples. However, the current knowledge about most of these genotypes, except for those of well-known genotypes like EV-A71 and EV-D68, is still limited due to a lack of comprehensive EV surveillance systems. This limited information makes it difficult to understand the true burden of EV-related diseases globally. Furthermore, the specific EV genotype associated with diseases varies according to country, population group, and study period. The same genotype can exhibit different epidemiological features in different areas. By integrating the data from established EV surveillance systems in the USA, Europe, Japan, and China, in combination with other EV infection studies, we can elaborate a better understanding of the distribution of prevalent EV genotypes and the diseases associated with EV. This review analyzed the data from various EV surveillance databases and explored the EV seroprevalence and the association of specific EV genotypes with human diseases. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Molecular Evolution of GII.P31/GII.4_Sydney_2012 Norovirus over a Decade in a Clinic in Japan

Author

Ushijima, Hiroshi, primary, Hoque, Sheikh Ariful, additional, Akari, Yuki, additional, Pham, Ngan Thi Kim, additional, Phan, Tung, additional, Nishimura, Shuichi, additional, Kobayashi, Masaaki, additional, Sugita, Kumiko, additional, Okitsu, Shoko, additional, Komoto, Satoshi, additional, Thongprachum, Aksara, additional, Khamrin, Pattara, additional, Maneekarn, Niwat, additional, and Hayakawa, Satoshi, additional

Published
2024
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23. Enterovirus genotype diversity with emergence of coxsackievirus A2 circulating in pediatric patients with acute gastroenteritis in Thailand, 2019-2022.

Author

Zhenfeng Xie, Khamrin, Pattara, Jampanil, Nutthawadee, Yodmeeklin, Arpaporn, Ukarapol, Nuthapong, Maneekarn, Niwat, and Kumthip, Kattareeya

Subjects
CHILD patients, GASTROENTERITIS, COVID-19 pandemic, ELECTRIC vehicle industry, GENOTYPES, COVID-19, COXSACKIEVIRUS diseases
Abstract

Introduction: Enteroviruses (EVs) are recognized as potential causative agents of acute gastroenteritis (AGE) in children worldwide. This study aimed to investigate the epidemiology and molecular characteristics of EV infection in children admitted to hospitals with AGE in Chiang Mai, Thailand from 2019 to 2022. Methods: A total of 1,148 fecal samples collected from patients with AGE were screened for the presence of EV using RT-PCR. The prevalence, co-infection with common diarrheal viruses, and seasonal pattern of EV were examined. The genotypes of EV were identified based on the VP1 sequence and phylogenetic analysis. Results: The overall prevalence of EV in AGE patients was 8.8% (101/1,148). After the COVID-19 outbreak in 2019, a significant decrease in the EV infection rate and genotype diversity was observed (p < 0.05). EV infection alone was observed in 68.3% (69/101) of cases while co-infection with other enteric viruses was 31.7% (32/101). The seasonal pattern of EV infection showed a peak prevalence during the rainy season. EV species A was the most prevalent (37.5%), followed by species B (32.3%), species C (29.2%), and species D (1.0%). Twenty-five genotypes of EV were identified with the most predominant of the coxsackievirus A2 (CVA2) (13.5%), CV-B2 (7.3%) and CV-A24 (5.2%). Conclusion: Our data demonstrate a significant decrease in the prevalence and diversity of EV circulating in AGE patients during the COVID-19 pandemic and highlight the emergence of CV-A2 during this study period. These findings contribute to a better understanding of the molecular epidemiology and diversity of EV in patients with AGE and provide useful information for further investigation into the potential association between specific EV genotypes and AGE in future studies. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Sapovirus infections in Japan before and after the emergence of the COVID‐19 pandemic: An alarming update

Author

Hoque, Sheikh Ariful, primary, Pham, Ngan Thi Kim, additional, Onda‐Shimizu, Yuko, additional, Nishimura, Shuichi, additional, Sugita, Kumiko, additional, Kobayashi, Masaaki, additional, Islam, Mohammad Tajul, additional, Okitsu, Shoko, additional, Khamrin, Pattara, additional, Maneekarn, Niwat, additional, Hayakawa, Satoshi, additional, and Ushijima, Hiroshi, additional

Published
2023
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35. Triple Intergenotype Recombination of Human Astrovirus 5, Human Astrovirus 8, and Human Astrovirus 1 in the Open Reading Frame 1a, Open Reading Frame 1b, and Open Reading Frame 2 Regions of the Human Astrovirus Genome

Author

Wei, Hongyu, primary, Kumthip, Kattareeya, additional, Khamrin, Pattara, additional, Yodmeeklin, Arpaporn, additional, Jampanil, Nutthawadee, additional, Phengma, Phitchakorn, additional, Xie, Zhenfeng, additional, Ukarapol, Nuthapong, additional, Ushijima, Hiroshi, additional, and Maneekarn, Niwat, additional

Published
2023
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36. Kobuviruses

Author

Kumthip, Kattareeya, primary, Khamrin, Pattara, additional, and Maneekarn, Niwat, additional

Published
2018
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37. Sapovirus

Author

Okitsu, Shoko, primary, Khamrin, Pattara, additional, Maneekarn, Niwat, additional, and Ushijima, Hiroshi, additional

Published
2018
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41. Abundance of viral gastroenteritis before and after the emergence of COVID-19: Molecular evidence on wastewater

Author

Hoque, Sheikh Ariful, primary, Kotaki, Tomohiro, additional, Pham, Ngan Thi Kim, additional, Onda, Yuko, additional, Okitsu, Shoko, additional, Sato, Shintaro, additional, Yuki, Yoshikazu, additional, Kobayashi, Takeshi, additional, Maneekarn, Niwat, additional, Kiyono, Hiroshi, additional, Hayakawa, Satoshi, additional, and Ushijima, Hiroshi, additional

Published
2023
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42. Evaluation of an Immunochromatographic Test for Rapid Detection of Astrovirus in Acute Gastroenteritis Pediatric Patients

Author

Khamrin, Pattara, primary, Pham, Ngan, additional, Shimizu-Onda, Yuko, additional, Trinh, Quang, additional, Hoque, Sheikh, additional, Kumthip, Kattareeya, additional, Nomura, Akiko, additional, Okitsu, Shoko, additional, Maneekarn, Niwat, additional, Müller, Werner, additional, Hayakawa, Satoshi, additional, and Ushijima, Hiroshi, additional

Published
2023
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50. Emerging norovirus GII.4 Sydney[P31] causing acute gastroenteritis outbreak in children in Japan, during COVID-19, 2021

Author

Pham, Ngan Thi Kim, primary, Nishimura, Shuichi, additional, Shimizu-Onda, Yuko, additional, Trinh, Quang Duy, additional, Komine-Aizawa, Shihoko, additional, Khamrin, Pattara, additional, Okitsu, Shoko, additional, Sato, Shintaro, additional, Kobayashi, Takeshi, additional, Maneekarn, Niwat, additional, Hayakawa, Satoshi, additional, and Ushijima, Hiroshi, additional

Published
2022
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