First sequences of Omicron variant were isolated from incoming travelers by Airport Diagnostic Laboratory and sequenced by the UP Philippine Genome Center. These samples were collected from on December 05 and 06, 2021 and submitted to GISAID on December 15, 2021.
Forty-six (46) SARS-CoV-2 positive samples from Batangas, Laguna, Marinduque, Parañaque, Quezon City, Batangas, Cavite and Southern Leyte, collected within September to October 2021 were processed for whole genome sequencing (WGS) at the Research Institute for Tropical Medicine (RITM), under the GECO Philippines study.
Of these, 84.7% (39 of 46) were successfully assigned a SARS-CoV-2 lineage (refer to Appendix), and are included in this report. All thirty-nine (39) samples successfully sequenced were identified as Delta variant.
SARS-CoV-2 whole genome sequences were generated using Oxford Nanopore Mk1C sequencing machine and analyzed using ncov2019-artic-nf, a nextflow automation of the ARTIC network nCoV-2019 novel coronavirus bioinformatics protocol.