Tracing the new SARS-CoV-2 variant BA.2.86 in the community through wastewater surveillance in Bangkok, Thailand
2023; Elsevier BV; Volume: 23; Issue: 11 Linguagem: Inglês
10.1016/s1473-3099(23)00620-5
ISSN1474-4457
AutoresDhammika Leshan Wannigama, Mohan Amarasiri, Phatthranit Phattharapornjaroen, Cameron Hurst, Charin Modchang, Sudarat Chadsuthi, Suparinthon Anupong, Kazuhiko Miyanaga, Longzhu Cui, Stefan Fernandez, Angkana T. Huang, Puey Ounjai, Ratana Tacharoenmuang, Naveen Kumar Devanga Ragupathi, Daisuke Sano, Takashi Furukawa, Kazunari Sei, Asada Leelahavanichkul, Talerngsak Kanjanabuch, Paul G. Higgins, Asuka Nanbo, Anthony Kicic, Andrew C. Singer, Tanittha Chatsuwan, Sam Trowsdale, Aisha Khatib, Kenji Shibuya, Shuichi Abe, Hitoshi Ishikawa, Parichart Hongsing, Wanwara Thuptiang, Seyed Mohammad Ali Hosseini Rad, Porames Vatanaprasan, Dylan John Jay, Thammakorn Saethang, Sirirat Luk-in, Robin James Storer, Phitsanuruk Kanthawee,
Tópico(s)COVID-19 diagnosis using AI
ResumoAs SARS-CoV-2 evolves, emerging variants such as BA.2.86 raise public health concerns and challenge existing control measures due to the potential for increased transmissibility and immune escape.1Rasmussen M Møller FT Gunalan V et al.First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023.Euro Surveill. 2023; 282300460Crossref Scopus (9) Google Scholar By late July, 2023, a number of countries had detected BA.2.86. On Aug 17, 2023, it was classified as a variant under surveillance by WHO due to its significant number of mutations in the spike gene.1Rasmussen M Møller FT Gunalan V et al.First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023.Euro Surveill. 2023; 282300460Crossref Scopus (9) Google Scholar It is important to understand the prevalence and dynamics of BA.2.86. In the post-pandemic phase, clinical surveillance of SARS-CoV-2 variants has been affected due to a notable decrease in self-reports and clinical diagnoses. As of Aug 30, 2023, there have been no reported human cases of BA.2.86 in Asia, according to the Global Initiative on Sharing All Influenza Data. Hence, complementary surveillance methods such as wastewater-based epidemiological surveillance offer timely insights into virus circulation.2Wannigama DL Amarasiri M Hongsing P et al.COVID-19 monitoring with sparse sampling of sewered and non-sewered wastewater in urban and rural communities.iScience. 2023; 26107019Summary Full Text Full Text PDF Scopus (3) Google Scholar, 3Wannigama DL Amarasiri M Hurst C et al.Tracking COVID-19 with wastewater to understand asymptomatic transmission.Int J Infect Dis. 2021; 108: 296-299Summary Full Text Full Text PDF PubMed Scopus (23) Google Scholar, 4Wannigama DL Amarasiri M Hongsing P et al.Multiple traces of monkeypox detected in non-sewered wastewater with sparse sampling from a densely populated metropolitan area in Asia.Sci Total Environ. 2023; 858159816Crossref PubMed Scopus (13) Google Scholar, 5Wannigama DL Amarasiri M Phattharapornjaroen P et al.Tracing the transmission of mpox through wastewater surveillance in Southeast Asia.J Travel Med. 2023; 30taad096Crossref PubMed Scopus (1) Google Scholar To assess the emergence of BA.2.86 in the community, we analysed 432 wastewater samples collected in Bangkok, Thailand, between June and July, 2023, as part of our ongoing SARS-CoV-2 wastewater surveillance programme (appendix pp 6–7). Samples were collected twice a month (every 2 weeks) from 63 locations (shopping centres, condominium complexes, office complexes, food markets, wastewater treatment plants, and entertainment venues) in Bangkok province, covering 51 subdistricts. There was an increasing trend in viral RNA concentration from the second week of June (385·48 copies/mL) to the fourth week of July (533·14 copies/mL; figure A). On July 28, 2023 (the fourth week of July), there were five (1·15%) of 432 positive detections of the BA.2.86 variant (figure A). All the BA.2.86 positive locations were different commercial or public venues with closed, non-sewered sanitation systems (septic tanks; figure B). A phylogenetic analysis (figure C) shows that the five wastewater samples had co-occurrences of mutations in the exact genomic locations as those found in BA.2.86 genome sequences of human samples from South Africa, the USA, Denmark, and Israel (figure C). Four of the five sequences were identical (Wastewater|Thailand|wb-23-082|2023-07-28, Wastewater|Thailand|wb-23-074|2023-07-28, Wastewater|Thailand|wb-23-077|2023-07-28, and Wastewater|Thailand|wb-23-064|2023-07-28; figure B, C). Moreover, one sample (Wastewater|Thailand|wb-23-074|2023-07-28) had heterogeneity at position 23570 (appendix p 15).FigureOverview of SARS-CoV-2 BA.2.86 positive sites and RNA levels in wastewater, with Maximum-Likelihood PhylogenyShow full caption(A) SARS-CoV-2 RNA concentration in wastewater at each BA.2.86 positive locations from June to July 2023. (B) Wastewater sampling location in Bangkok, Thailand, with colours indicating at area where five positive samples were collected in Bangkok from June to July 2023. (C) Evolutionary history was inferred using the Maximum Likelihood method and Hasegawa-Kishino-Yano model. A discrete gamma distribution (+G) was used to model the evolutionary rate differences among sites (five categories; parameter=0·1000). Sequences obtained in this study are deposited with the Global Initiative on Sharing All Influenza Data. *Samples with identical sequences.View Large Image Figure ViewerDownload Hi-res image Download (PPT) (A) SARS-CoV-2 RNA concentration in wastewater at each BA.2.86 positive locations from June to July 2023. (B) Wastewater sampling location in Bangkok, Thailand, with colours indicating at area where five positive samples were collected in Bangkok from June to July 2023. (C) Evolutionary history was inferred using the Maximum Likelihood method and Hasegawa-Kishino-Yano model. A discrete gamma distribution (+G) was used to model the evolutionary rate differences among sites (five categories; parameter=0·1000). Sequences obtained in this study are deposited with the Global Initiative on Sharing All Influenza Data. *Samples with identical sequences. Our results show that the BA.2.86 variant is circulating in Thailand with numerous and noteworthy mutations, particularly substitutions and deletions within the spike protein gene of BA.2.86. Moreover, four identical sequences from different locations suggest parallel circulation across multiple areas. Furthermore, we identified two different sequences within the same short time frame and small geographical area. These sequences were found in different commercial or public venues, which poses a challenge in explaining their concurrent presence in the absence of epidemiological data. However, the proportion of BA.2.86 positive samples among the total samples has been small and cannot explain the increase in viral load by the fourth week of July. As regional tourism recovers from COVID-19 restrictions, the potential for new variants such as BA.2.86 to spread through international travel remains a concern, particularly in densely populated and popular tourist destinations in southeast Asia. Our continued research underscores the significance of wastewater-based epidemiological surveillance, even in regions with scarce resources and decentralised wastewater systems. We declare no competing interests. We confirm that the data supporting the findings of this study are available within this Correspondence and its additional information. All genome sequences and associated metadata in this study are published in GISAID's EpiCoV database under wastewater category under the accession identifiers EPI_ISL_18216960; Wastewater|Thailand|wb-23-082|2023-07-28, EPI_ISL_18216961; Wastewater|Thailand|wb-23-077|2023-07-28, EPI_ISL_18216959; Wastewater|Thailand|wb-23-064|2023-07-28, EPI_ISL_18216958; Wastewater|Thailand|wb-23-074|2023-07-28, and EPI_ISL_18217252; Wastewater|Thailand|wb-23-072|2023-07-28). We thank all the volunteers who kindly supported with sample collection. We also thank Ong-orn Prasarnphanich at the US Centers for Disease Control and Prevention (CDC) Thailand for technical support and the previous Chargé d'Affaires of the USA to Thailand (US Embassy and Consulate in Thailand), and Michael Heath for facilitating collaboration with the CDC and Armed Forces Research Institute of Medical Sciences. We also thank the LGBTQIA+ community in Thailand for generous support with the sample collection, the TEDxChiangMai team, and Martin Venzky-Stalling for facilitating a platform for collaboration, and marginalised, vulnerable indigenous communities in northern Thailand for support with the sample collection—special thanks to Nuttawut Kietchaiyakorn for helping with the illustrations. DLW was supported by Balvi Filantropic Fund and Chulalongkorn University (Second Century Fund–C2F Postdoctoral Fellowship), University of Western Australia (Overseas Research Experience Fellowship), and Yamagata Prefectural Central Hospital, Yamagata, Japan (Clinical Residency Fellowship). CM was supported by the Centre of Excellence in Mathematics, Ministry of Higher Education, Science, Research and Innovation, Thailand, Center of Excellence on Medical Biotechnology, and Thailand Center of Excellence in Physics. AK is a Rothwell Family Fellow. The funders had no role in study design, in the collection, analysis, and interpretation of data, in the writing of the report, or in the decision to submit the article for publication. We embrace inclusive, diverse, and equitable conduct of research. Our team comprises individuals who self-identify as under-represented ethnic minorities, gender minorities, members of the LGBTQIA+ community, and individuals living with disabilities. We actively promote gender balance in our reference list while maintaining scientific relevance. The Pathogen Hunters Research Team members are listed in the appendix (p 5). Download .pdf (2.61 MB) Help with pdf files Supplementary appendix
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