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The spread of the corona virus around the world has spurred travel restrictions and community lockdowns to manage the transmission of infection. In the Philippines, with a large population of overseas Filipino contract workers (OFWs), as well as foreign workers in the local online gaming industry and visitors from nearby countries, the first reported cases were from a Chinese couple visiting the country in mid-January 2020. Three months on, by mid-March, the COVID-19 cases in the Philippines had reached its first 100, before it exploded to the present 178,022 cases (as of August 20, 2020). Here, we report a genomic survey of six (6) whole genomes of the SARS-CoV-2 virus collected from COVID-19 patients seen at the Philippine General Hospital, the major referral hospital for COVID-19 cases in Metro Manila at about the time the Philippines had over a hundred cases. Analysis of commonly observed variants did not reveal a clear pattern of the virus evolving towards a more infectious and severe strain. When combined with other available viral sequences from the Philippines and from GISAID, phylogenomic analysis reveal that the sequenced Philippine isolates can be classified into three primary groups based on collection dates and possible infection sources: (1) January samples collected in the early phases of the pandemic that are closely associated with isolates from Wuhan, China; (2) March samples that are mainly linked to the M/V Diamond Princess Cruise Ship outbreak; and (3) June samples that clustered with European isolates, one of which already harbor the globally prevalent D614G mutation which initially circulated in Europe. The presence of community-acquired viral transmission amidst compulsory and strict quarantine protocols, particularly for repatriated Filipino workers, highlights the need for a refinement of the quarantine, testing, and tracing strategies currently being implemented to adapt to the current pandemic situation.

BackgroundThe Philippines has the fastest growing HIV epidemic in the Asia-Pacific. Concurrent with this is a subtype shift from B to CRF01_AE. We have previously documented transmitted drug resistance (TDR) locally. However, the lack of drug pressure and the insensitivity of Sanger-based sequencing (SBS) may leave archived drug-resistance mutations (DRMs) undetected. To better detect TDR, we performed next-generation sequencing (NGS) on treatment-naïve patients and compared this with SBS.MethodsFollowing ethics approval, newly-diagnosed adult Filipino HIV patients were recruited from the Philippine General Hospital HIV treatment hub. Demographic data were collected, and blood samples underwent SBS with a WHO-approved protocol. Whole-genome NGS was performed using Illumina HiSeq through a commercial provider (Macrogen, Korea). Genotype and DRMs were analyzed and scored using the Stanford HIV Drug Resistance Database.Results113 patients were analyzed. Median age was 29 years (range 19–68), mean CD4 count was 147 cells/µL (range 0–556) and median viral load was 2.8 × 106 copies/mL. Genotype distribution was: CRF01_AE (93), B (13), possible CRF01_AE/B recombinants (5), CRF02_AG (1), possible URF (1). TDR prevalence by SBS and NGS at different minority variant cutoffs are shown in Table 1. All DRMs on SBS were found on NGS. Some samples had multiple DRMs. No factors were significantly associated with TDR, genotype, viral load or baseline CD4 count.ConclusionNGS is a more sensitive tool for detecting TDR compared with SBS. Nearly double the DRMs were found at an NGS cutoff of ≥5%, including INSTI DRMs. With increasing HIV drug resistance worldwide, switching to NGS may help decrease rates of initial treatment failure, especially in settings with limited repertoires of ARVs.Table 1. TDR Prevalence by SBS and NGS (N = 113).MethodAll (%)NRTI (%)NNRTI (%)PI (%)INSTI (%)SBS11 (9.7)2 (1.8)7 (6.2)3 (2.7)0 (0)*NGS≥1%59 (52.2)15 (13.3)29 (25.7)19 (16.8)17 (15.0)≥2%39 (34.5)7 (6.2)19 (16.8)9 (8.0)10 (8.8)≥5%22 (19.5)3 (2.7)15 (13.3)5 (4.4)2 (1.8)≥10%19 (16.8)1 (0.9)14 (12.4)4 (3.5)2 (1.8)≥15%15 (13.3)1 (0.9)12 (10.6)3 (2.7)1 (0.9)≥20%13 (11.5)1 (0.9)10(8.8)2 (1.8)1 (0.9)*SBS for INSTI only done for those with INSTI DRM on NGS ≥ 1% minority variantDisclosures All authors: No reported disclosures.