1902. Whole Genome Sequence analysis of early community transmission SARS-CoV-2 samples in the Philippines

Abstract

Abstract Background The Philippines has recorded nearly 3.7 million COVID-19 cases and more than 60,000 deaths. The first three cases of COVID-19 in the country were reported in January 2020 (1 lineage A, 2 lineage B, all Chinese tourists), with the first death outside China occurring among these cases. No cases were reported in February 2020. The first Filipino cases were reported March 2020. With over one million overseas Filipinos repatriated, tracking the introduction of waves of variants and subsequent community spread is important in order to improve future control efforts. Methods We analyzed 35 archived samples collected from March to September 2020 at the Philippines National Institutes of Health. SARS-CoV2 RT-PCR positive samples with Ct values from 15 to 25 were sequenced using Illumina HiSeq and analyzed using an in-house bioinformatics pipeline. Lineages were assigned using PANGOLIN. 14 whole genome sequences were generated with sufficient coverage. These were analyzed with 439 whole genome sequences from February to September 2020 that were publicly available on ViruSurf and GISAID to generate transmission maps. Results Transmission maps are shown in Figure 1. The earliest community transmission of COVID-19 in the Philippines was from lineage B.6 in March 2020 most closely related to B.6 from India. There is no evidence of onward transmission from the initial reported cases in January 2020 (lineage A and B). In June 2020, the predominant lineage switched to B.1 and its sublineages from Europe, coincident with a surge in cases. Figure 1.Alignment of the whole genome sequences from early Philippine samples and related SARS-COV2 sequences from ViruSurf and GISAID. Conclusion Transmission maps are shown in Figure 1. The earliest community transmission of COVID-19 in the Philippines was from lineage B.6 in March 2020 most closely related to B.6 from India. There is no evidence of onward transmission from the initial reported cases in January 2020 (lineage A and B). In June 2020, the predominant lineage switched to B.1 and its sublineages from Europe, coincident with a surge in cases. Disclosures Edsel Maurice Salvana, MD, MSD: Advisor/Consultant|MSD: Honoraria|Pfizer: Advisor/Consultant|Pfizer: Honoraria.