Dataset Information

RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.

ABSTRACT: Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study utilized receptor-binding domain (RBD) amplicon sequencing of wastewater samples to monitor the SARS-CoV-2 community dynamics and evolution in El Paso, TX. Over 17 months, we identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Our findings demonstrated early detection of variants and identification of unreported outbreaks, while showing strong consistency with clinical genome sequencing data at the local, state, and national levels. Alpha diversity analyses revealed significant periodical variations, with the highest diversity observed in winter and the outbreak lag phases, likely due to lower competition among variants before the outbreak growth phase. The data underscores the importance of low transmission periods for rapid mutation and variant evolution. This study highlights the effectiveness of integrating RBD amplicon sequencing with wastewater surveillance in tracking viral evolution, understanding variant emergence, and enhancing public health preparedness.

SUBMITTER: Chen X

PROVIDER: S-EPMC11261926 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

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RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.

Chen Xingwen X Balliew John J Bauer Cici X CX Deegan Jennifer J Gitter Anna A Hanson Blake M BM Maresso Anthony W AW Tisza Michael J MJ Troisi Catherine L CL Rios Janelle J Mena Kristina D KD Boerwinkle Eric E Wu Fuqing F

medRxiv : the preprint server for health sciences 20240712

Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study utilized receptor-binding domain (RBD) amplicon sequencing of wastewater samples to monitor the SARS-CoV-2 community dynamics and evolution in El Paso, TX. Over 17 months, we identified 91 ...[more]

PMID: 39040200

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RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.

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RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.

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