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Zhang Z, He F, Yi L, Deng Z, Wang R, Shen L, Fu S. Wastewater surveillance together with metaviromic data revealed the unusual resurgence of infectious diseases after the first wave of the COVID-19 outbreak. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134635. [PMID: 38772110 DOI: 10.1016/j.jhazmat.2024.134635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/01/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
How to address public health priorities after COVID-19 is becoming a critical task. To this end, we conducted wastewater surveillance for six leading pathogens, namely, SARS-CoV-2, norovirus, rotavirus, influenza A virus (IAV), enteroviruses and respiratory syncytial virus (RSV), in Nanchang city from January to April 2023. Metaviromic sequencing was conducted at the 1st, 4th, 7th, 9th, 12th and 14th weeks to reveal the dynamics of viral pathogens that were not covered by qPCR. Amplicon sequencing of the conserved region of norovirus GI and GII and the rotavirus and region encoding nonstructural protein of RSV was also conducted weekly. The results showed that after a rapid decrease in SARS-CoV-2 sewage concentrations occurred in January 2023, surges of norovirus, rotavirus, IAV and RSV started at the 6th, 7th, 8th and 11th weeks, respectively. The dynamics of the sewage concentrations of norovirus, rotavirus, IAV and RSV were consistent with the off-season resurgence of the above infectious diseases. Notably, peak sewage concentrations of norovirus GI, GII, rotavirus, IAV and RSV were found at the 6th, 3rd, 7th, 7th and 8th weeks, respectively. Astroviruses also resurge after the 7th week, as revealed by metaviromic data, suggesting that wastewater surveillance together with metaviromic data provides an essential early warning tool for revealing patterns of infectious disease resurgence.
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Affiliation(s)
- Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China
| | - Fenglan He
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, Jiangxi, China
| | - Liu Yi
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, Jiangxi, China
| | - Zhiqiang Deng
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, Jiangxi, China
| | - Rui Wang
- Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, Dalian Ocean University, Dalian 116023, China
| | - Lixin Shen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China.
| | - Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China.
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Peng L, Yang F, Shi J, Pan L, Liu Y, Mao D, Luo Y. Molecular characterization of human bocavirus in municipal wastewaters using amplicon target sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170674. [PMID: 38316309 DOI: 10.1016/j.scitotenv.2024.170674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/22/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Human bocavirus (HBoV) is an emerging health concern worldwide, associated with range of clinical manifestations, including gastroenteritis and respiratory infections. Therefore, it is crucial to comprehend and minimize their prevalence in different systems. In this study, we conducted regular sampling throughout the year in two different sizes and work processes of wastewater treatment plants (WWTPs) in Tianjin, China. Our objective was to investigate the occurrence, prevalence, and endurance of HBoV in wastewater, while also evaluating the efficacy of amplicon target sequencing in directly detecting HBoV in wastewater. At two WWTPs, HBoV2 (45.51 %-45.67 %) and HBoV3 (38.30 %-40.25 %) were the most common genotypes identified, and the mean concentration range of HBoV was 2.54-7.40 log10 equivalent copies/l as determined by multiplex real-time quantitative PCR assay. A positive rate of HBoV was found in 96.6 % (29/30) samples of A-WWTP, and 96.6 % (26/27) samples of B-WWTP. The phylogenetic analysis indicated that the nucleotide similarity between the HBoV DNA sequences to the reference HBoV sequences published globally ranged from 90.14 %-100 %. A significant variation in the read abundance of HBoV2 and HBoV3 in two wastewater treatment plants (p < 0.05) was detected, specifically in the Winter and Summer seasons. The findings revealed a strong correlation between the genotypes detected in wastewater and the clinical data across various regions in China. In addition, it is worth mentioning that HBoV4 was exclusively detected in wastewater and not found in the clinical samples from patients. This study highlights the high prevalence of human bocavirus in municipal wastewater. This finding illustrates that amplicon target sequencing can amplify a wide variety of viruses, enabling the identification of newly discovered viruses.
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Affiliation(s)
- Liang Peng
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Jingliang Shi
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Liuzhu Pan
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yixin Liu
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; State Key Laboratory of Pollution Control and Resource reuse, School of the Environment, Nanjing university, Nanjing 210093, China.
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Tang J, Zhang X, Zhang J, Zhao Z, Ding Z. Environmental surveillance reveals co-circulation of distinctive lineages of enteroviruses in southwest China's border cities, 2020-2022. J Appl Microbiol 2024; 135:lxae060. [PMID: 38471668 DOI: 10.1093/jambio/lxae060] [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: 09/28/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
AIMS Enteroviruses are significant human pathogens associated with a range of mild to severe diseases. This study aims to understand the diversity and genetic characterization of enteroviruses circulated in southwest China's border cities by using environmental surveillance. METHODS AND RESULTS A total of 96 sewage samples were collected in three border cities and a port located in Yunnan Province, China from July 2020 to June 2022. After cell culture and VP1 sequencing, a total of 590 enterovirus isolates were identified, belonging to 21 types. All PV strains were Sabin-like with ≤6 nucleotide mutations in the VP1 coding region. Echovirus 6, echovirus 21 (a rare serotype in previous studies), and coxsackievirus B5 were the predominant serotypes, which accounted for 21.19%, 18.31%, and 13.39% of the total isolates, respectively. The prevalence of the common serotypes varied across different border cities and periods. Phylogenetic analysis revealed the presence of multiple evolutionary lineages for E21, E6, and E30, some of which formed distinct branches. CONCLUSIONS High diversity of enteroviruses and distinct lineages of predominant serotypes circulated in southwest China's border cities.
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Affiliation(s)
- Jingjing Tang
- Yunnan Center for Disease Control and Prevention, No. 158 Dongsi Road, Kunming 650022, People's Republic of China
| | - Xiaodie Zhang
- Kunming Center for Disease Control and Prevention, No. 4 Ziyun Road, Kunming 650228, People's Republic of China
| | - Jie Zhang
- Yunnan Center for Disease Control and Prevention, No. 158 Dongsi Road, Kunming 650022, People's Republic of China
| | - Zhixian Zhao
- Yunnan Center for Disease Control and Prevention, No. 158 Dongsi Road, Kunming 650022, People's Republic of China
| | - Zhengrong Ding
- Yunnan Center for Disease Control and Prevention, No. 158 Dongsi Road, Kunming 650022, People's Republic of China
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Lin X, Xu M, Zhao Y, Ji F, Liu Y, Wang S, Chen M, Zhang W, Tao Z, Xu A. Environmental Surveillance of Human Astroviruses in Jinan City of China, 2020-2021. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:50-57. [PMID: 38212480 DOI: 10.1007/s12560-023-09576-x] [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: 06/05/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Human astroviruses (HAstVs) are a significant etiological agent of acute gastroenteritis in children. In order to investigate the circulation of HAstVs during the COVID-19 pandemic, a 2-year environmental surveillance was conducted in Jinan between 2020 and 2021. A total of 24 sewage samples were collected and concentrated. Real-time PCR indicated a positive rate of 83.3%, 79.2% (19/24), and 62.5% for classic, MLB, and VA types of HAstV in sewage samples, respectively, with genomic copies ranging from 6.4 × 103 to 3.7 × 107, 3.2 × 104 to 2.2 × 106, and 1.2 × 104 to 1.6 × 107 l-1. Next-generation sequencing (NGS) analysis on complete ORF2 amplicons from each sewage concentrate revealed the presence of 11 HAstV types, including HAstV-1, -2, -4, -5, MLB1, and VA1 to VA6, as well as non-human animal astroviruses. The most abundant HAstV types were HAstV-1, -4, and -5, which accounted for 70.3%, 12.6%, and 9.1% of total HAstV reads, respectively. Phylogenetic analysis revealed that the sequences obtained in this study were segregated into multiple transmission lineages, yet exhibited less genetic divergence among themselves than with foreign strains. These findings provide insight into the genotype diversity and genetic characterization of HAstVs during the COVID-19 pandemic, and highlight the effectiveness of utilizing NGS approaches to investigate sewage HAstVs.
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Affiliation(s)
- Xiaojuan Lin
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Mingyi Xu
- Shandong Academy of Occupational Health and Occupational Medicine, Jinan, 250062, China
| | - Yun Zhao
- School of Public Health, Shandong University Cheeloo College of Medicine, Jinan, China
| | - Feng Ji
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Yao Liu
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Suting Wang
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Meng Chen
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Wenqiang Zhang
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Zexin Tao
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China.
| | - Aiqiang Xu
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China.
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Kumthip K, Khamrin P, Ushijima H, Maneekarn N. Detection of Six Different Human Enteric Viruses Contaminating Environmental Water in Chiang Mai, Thailand. Microbiol Spectr 2023; 11:e0351222. [PMID: 36533933 PMCID: PMC9927274 DOI: 10.1128/spectrum.03512-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
A 2-year surveillance study into enteric viruses contaminating environmental water samples was conducted in the city of Chang Mai, Thailand. The aim of the study was to investigate the prevalence of six different human enteric viruses, specifically, adenovirus (AdV), astrovirus (AstV), enteroviruses (EVs), human parechovirus (HPeV), rotavirus (RV), and saffold virus (SAFV), contaminating several types of environmental water using PCR and reverse transcription-PCR (RT-PCR) methods. All targeted viruses were detected with different levels of prevalence. The levels ranged from 0.8 to 4.8% (AdV, 0.8%; AstV, 4.8%; EV, 0.8%; HPeV, 3.2%; RV, 0.8%; SAFV, 3.2%). A wide variety of human enteric virus genotypes, including AdV-41, AstV-MLB1, coxsackievirus A, HPeV1, 5, and 6, RV G4[P8], and SAFV-2 and 3 were detected. The overall picture of the 13 human enteric viruses that were detected in environmental water in Chiang Mai, Thailand, is also summarized in this study. The data and the findings of this study will provide a better understanding of the viral dynamics in environmental water. The detection of these viruses in environmental water indicates there is the potential for human infection from this source. IMPORTANCE Human enteric viruses are a major cause of gastrointestinal illness, and these viruses can be introduced into environmental water through various routes. Viral contamination in water could play a significant role in human health. This study demonstrated the prevalence of six different enteric viruses, adenovirus, astrovirus, enteroviruses, human parechovirus, rotavirus, and saffold virus, contaminating environmental water. We also analyzed the overall prevalence of other enteric viruses that were in this area, and the findings revealed a wide diversity of the enteric viruses contaminating environmental water. The data provide a better understanding of the epidemiologic importance of viral contamination of the water and highlight the need for better management of wastewater disposal and effective environmental water treatment to prevent the human population from infection.
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Affiliation(s)
- Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, The University of Tokyo, School of International Health, Graduate School of Medicine, Tokyo, Japan
- 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
- Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
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