Severe acute respiratory syndrome coronavirus 2 variants in patients with coronavirus disease 2019 and environmental sampling from the hospital and market during the coronavirus disease 2019 pandemic in Thailand

Abstract

Limited genomic surveillance data is available for SARS-CoV-2 in Thailand during the second and third wave outbreaks, including both patient and environmental samples. This study investigated the presence of SARS-CoV-2 RNA in patient samples, on frequently touched surfaces, and in environmental swab samples (EVSs) collected from urban markets in Bangkok between April 2021 and August 2022. A total of 78,159 nasopharyngeal swab samples from patients and 327 environmental swab samples from hospital and market settings were collected. SARS-CoV-2 RNA was detected in 3,706 of 78,159 patient samples and one of 327 environmental samples using real-time RT-PCR. In total, 54 patient samples and an environmental sample were subjected to whole-genome sequencing and mass array genotyping, respectively. Only 46 samples passed the quality assessment based on the analysis criteria. The lineages detected included B.1.1.529 (2 samples), B.1.1.7 (15 samples), B.1.351 (3 samples), B.1.36.16 (6 samples), B.1.617.2 (1 sample), AY.102 (1 sample), AY.4 (11 samples), AY.25 (1 sample), BA.1 (1 sample), BA.1.1 (3 samples), and BA.2 (2 samples). The phylogenetic analysis of the viral genome sequences revealed similar lineages during this study period.

Keywords: COVID-19; SARS-CoV-2 genome analysis; environmental contamination.