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Chen L, Chen A, Zhang XD, Saenz Robles MT, Han HS, Xiao Y, Xiao G, Pipas JM, Weitz DA. Targeted whole-genome recovery of single viral species in a complex environmental sample. Proc Natl Acad Sci U S A 2024; 121:e2404727121. [PMID: 39052829 PMCID: PMC11295033 DOI: 10.1073/pnas.2404727121] [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: 03/06/2024] [Accepted: 06/07/2024] [Indexed: 07/27/2024] Open
Abstract
Characterizing unknown viruses is essential for understanding viral ecology and preparing against viral outbreaks. Recovering complete genome sequences from environmental samples remains computationally challenging using metagenomics, especially for low-abundance species with uneven coverage. We present an experimental method for reliably recovering complete viral genomes from complex environmental samples. Individual genomes are encapsulated into droplets and amplified using multiple displacement amplification. A unique gene detection assay, which employs an RNA-based probe and an exonuclease, selectively identifies droplets containing the target viral genome. Labeled droplets are sorted using a microfluidic sorter, and genomes are extracted for sequencing. We demonstrate this method's efficacy by spiking two known viral genomes, Simian virus 40 (SV40, 5,243 bp) and Human Adenovirus 5 (HAd5, 35,938 bp), into a sewage sample with a final abundance in the droplets of around 0.1% and 0.015%, respectively. We achieve 100% recovery of the complete sequence of the spiked-in SV40 genome with uniform coverage distribution. For the larger HAd5 genome, we cover approximately 99.4% of its sequence. Notably, genome recovery is achieved with as few as one sorted droplet, which enables the recovery of any desired genomes in complex environmental samples, regardless of their abundance. This method enables single-genome whole-genome amplification and targeting characterizations of rare viral species and will facilitate our ability to access the mutational profile in single-virus genomes and contribute to an improved understanding of viral ecology.
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Affiliation(s)
- Liyin Chen
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Anqi Chen
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Xinge Diana Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | | | - Hee-Sun Han
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Yi Xiao
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Gao Xiao
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - James M. Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA15260
| | - David A. Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
- Department of Physics, Harvard University, Cambridge, MA02138
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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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Carmo dos Santos M, Cerqueira Silva AC, dos Reis Teixeira C, Pinheiro Macedo Prazeres F, Fernandes dos Santos R, de Araújo Rolo C, de Souza Santos E, Santos da Fonseca M, Oliveira Valente C, Saraiva Hodel KV, Moraes dos Santos Fonseca L, Sampaio Dotto Fiuza B, de Freitas Bueno R, Bittencourt de Andrade J, Aparecida Souza Machado B. Wastewater surveillance for viral pathogens: A tool for public health. Heliyon 2024; 10:e33873. [PMID: 39071684 PMCID: PMC11279281 DOI: 10.1016/j.heliyon.2024.e33873] [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: 01/03/2024] [Revised: 06/03/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
A focus on water quality has intensified globally, considering its critical role in sustaining life and ecosystems. Wastewater, reflecting societal development, profoundly impacts public health. Wastewater-based epidemiology (WBE) has emerged as a surveillance tool for detecting outbreaks early, monitoring infectious disease trends, and providing real-time insights, particularly in vulnerable communities. WBE aids in tracking pathogens, including viruses, in sewage, offering a comprehensive understanding of community health and lifestyle habits. With the rise in global COVID-19 cases, WBE has gained prominence, aiding in monitoring SARS-CoV-2 levels worldwide. Despite advancements in water treatment, poorly treated wastewater discharge remains a threat, amplifying the spread of water-, sanitation-, and hygiene (WaSH)-related diseases. WBE, serving as complementary surveillance, is pivotal for monitoring community-level viral infections. However, there is untapped potential for WBE to expand its role in public health surveillance. This review emphasizes the importance of WBE in understanding the link between viral surveillance in wastewater and public health, highlighting the need for its further integration into public health management.
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Affiliation(s)
- Matheus Carmo dos Santos
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Ana Clara Cerqueira Silva
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Carine dos Reis Teixeira
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Filipe Pinheiro Macedo Prazeres
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Rosângela Fernandes dos Santos
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Carolina de Araújo Rolo
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Emanuelle de Souza Santos
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Maísa Santos da Fonseca
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Camila Oliveira Valente
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Katharine Valéria Saraiva Hodel
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Larissa Moraes dos Santos Fonseca
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Bianca Sampaio Dotto Fiuza
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
| | - Rodrigo de Freitas Bueno
- Federal University of ABC. Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo, Brazil
| | - Jailson Bittencourt de Andrade
- University Center SENAI CIMATEC, SENAI CIMATEC, Salvador, 41650-010, Bahia, Brazil
- Centro Interdisciplinar de Energia e Ambiente – CIEnAm, Federal University of Bahia, Salvador, 40170-115, Brazil
| | - Bruna Aparecida Souza Machado
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CI-MATEC, Salvador, 41650-010, Bahia, Brazil
- University Center SENAI CIMATEC, SENAI CIMATEC, Salvador, 41650-010, Bahia, Brazil
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Wyler E, Lauber C, Manukyan A, Deter A, Quedenau C, Teixeira Alves LG, Wylezich C, Borodina T, Seitz S, Altmüller J, Landthaler M. Pathogen dynamics and discovery of novel viruses and enzymes by deep nucleic acid sequencing of wastewater. ENVIRONMENT INTERNATIONAL 2024; 190:108875. [PMID: 39002331 DOI: 10.1016/j.envint.2024.108875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024]
Abstract
Wastewater contains an extensive reservoir of genetic information, yet largely unexplored. Here, we analyzed by high-throughput sequencing total nucleic acids extracted from wastewater samples collected during a 17 month-period in Berlin, Germany. By integrating global wastewater datasets and applying a novel computational approach to accurately identify viral strains within sewage RNA-sequencing data, we demonstrated the emergence and global dissemination of a specific astrovirus strain. Astrovirus abundance and sequence variation mirrored temporal and spatial patterns of infection, potentially serving as footprints of specific timeframes and geographical locations. Additionally, we revealed more than 100,000 sequence contigs likely originating from novel viral species, exhibiting distinct profiles in total RNA and DNA datasets and including undescribed bunyaviruses and parvoviruses. Finally, we identified thousands of new CRISPR-associated protein sequences, including Transposase B (TnpB), a class of compact, RNA-guided DNA editing enzymes. Collectively, our findings underscore the potential of high-throughput sequencing of total nucleic acids derived from wastewater for a broad range of applications.
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Affiliation(s)
- Emanuel Wyler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Chris Lauber
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, A Joint Venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Artür Manukyan
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Aylina Deter
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Claudia Quedenau
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Luiz Gustavo Teixeira Alves
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Tatiana Borodina
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Janine Altmüller
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany; Berlin Institute of Health at Charité, Berlin, Germany
| | - Markus Landthaler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany.
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5
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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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