Genomic epidemiology and evolutionary analysis during XBB.1.16-predominant periods of SARS-CoV-2 omicron variant in Bangkok, Thailand: December 2022-August 2023

Abstract

The growing occurrence of novel recombinants, such as XBB.1.16, has emerged and become predominant, raising concerns about the impact of genomic recombination on the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study investigated the molecular epidemiological trends and evolution of the Omicron XBB.1.16 epidemic in Bangkok between December 2022 and August 2023. Partial spike and complete genome sequencing of SARS-CoV-2 samples collected from collaborating hospitals were performed. The analysis of 491 partial spike sequences identified 15 distinct lineages, with XBB.1.16 dominating the lineages beginning in March 2023. Phylogenetic analysis revealed at least four distinct XBB.1.16 lineages, suggesting multiple independent introductions into Bangkok. The estimated emergence of XBB.1.16 occurred approximately in January 2022, with an evolutionary rate of 0.79 × 10^-3 substitutions per site per year. Monitoring the genomic epidemiology and evolution of XBB.1.16 is vital for the early detection of new strains or emerging variants, which may guide vaccine design and the inclusion of new vaccine strains.

Figure 1

(a) Cases of confirmed SARS-CoV-2 infection reported in Thailand. (b) Timecourse of omicron variant distribution in Bangkok, Thailand, between December 2022 and August 2023.

Figure 2

Divergence times of phylogenetic trees of global XBB.1.5, XBB.1.16, and XBB viruses using molecular clock. A time-resolved maximum-likelihood phylogenetic tree of XBB.1.5, XBB.1.16, and XBB samples sequenced worldwide and sequences from this study is shown. The scale bar indicates nucleotide substitutions per site.

Figure 3

(a) Map of the regions in Thailand most affected by the SARS-CoV-2 outbreak from December 2022 to August 2023. Administrative divisions in the northern, central, northeastern, and southern areas are differentiated by blue, brown, red, and green color respectively. These colors represent the cumulative numbers of confirmed and suspected cases reported throughout the outbreak. (b) Root-to-tip regression of genetic distances against sampling time (month) for SARS-CoV-2 XBB.1.16 variant sequences based on a maximum likelihood tree. (c) Temporal phylogeny of all publicly accessible XBB.1.16 genomes in Thailand estimated using BEAST. Each tip is color-coded based on the probable region within the country where the patient was infected.