Early SARS-CoV-2 variant detection relies on testing and genomic
surveillance. The Omicron variant (B.1.1.529) has quickly become the
dominant type among the previous circulating variants worldwide. Several
subvariants have emerged exhibiting greater infectivity and immune
evasion. In this study we aimed at studying the prevalence of the
Omicron subvariants during the flu season and beyond in Lebanon through
genomic screening and at determining the overall standing and trajectory
of the pandemic in the country. A total of 155 RNA samples were
sequenced and 39 Omicron variants were detected. XBB.1.5 (23.29%) was
the most common, followed by XBB.1.9.1 (10.96%) and XBB.1.42 (7.5%).
The first batch collected between September and November 2022, included
the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages.
Between December 2022 and January 2023, those lineages were replaced by
BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK.
Starting February 2023, we observed a gradual emergence and dominance of
the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2,
XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and
XBB.1.42). The timely detection and characterization of SARS-CoV-2
variants is important to reduce transmission through established disease
control measures and to avoid introductions into animal populations that
could lead to serious public health implications.