Omicron variant accounts for most of the sequences isolated in December, 2021 and locally circulating Omicron viruses most likely belong to BA.2 lineage.
Twenty-three (23) SARS-CoV-2 positive samples, from twenty-one (21) unique individuals residing at Laguna, Cavite, Batangas, Muntinlupa City, Quezon City, Las Piñas City, Makati City, and Pasig City, collected within December 16 – 28, 2021 were processed for whole genome sequencing (WGS) at the Research Institute for Tropical Medicine (RITM), under the GECO Philippines study.
Of these, 100% (23 of 23) were successfully assigned a SARS-CoV-2 lineage (refer to Appendix), and are included in this report. Three (3) of the samples processed for WGS came from one (1) patient, which have different sample collection dates, and identified as Delta variant. Furthermore, one (1) sample was identified as Alpha variant while the rest of the samples (19 of 23) were identified as Omicron variant sublineage BA.2. This report covers the analysis of these 23 whole genome sequences in the context of all Philippine SARS-CoV-2 whole genome sequences in GISAID as of time of writing.
The Omicron BA.2 detected in these recent set of sequences does not contain the HV 69/70 deletion that effects S gene target failure in some RT-PCR diagnostic kits (like TaqPath COVID-19 combo kit).
SARS-CoV-2 whole genome sequences were generated using Oxford Nanopore Mk1C sequencing machine and protocol analyzed using ncov-2019-artic-nf, a nextflow automation of the ARTIC network nCoV-2019 novel coronavirus bioinformatics protocol.