key: cord-0868212-lezayth4 authors: Velasco, John Mark; Chinnawirotpisan, Piyawan; Joonlasak, Khajohn; Manasatienkij, Wudtichai; Huang, Angkana; Valderama, Maria Theresa; Diones, Paula Corazon; Leonardia, Susie; Timbol, Maria Leanor; Navarro, Fatima Claire; Villa, Vicente; Tabinas, Henry; Chua, Domingo; Fernandez, Stefan; Jones, Anthony; Klungthong, Chonticha title: Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines date: 2020-10-22 journal: Microbiol Resour Announc DOI: 10.1128/mra.01031-20 sha: 0dcef4c6aa2161b0ec7e602accd8a94352b3f5ab doc_id: 868212 cord_uid: lezayth4 Here, we report the coding-complete genome sequences of 23 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples from the Philippines. Sequences were obtained from nasopharyngeal and oropharyngeal swabs from coronavirus disease 2019 (COVID-19)-positive patients. Mutation analysis showed the presence of the D614G mutation in the spike protein in 22 of 23 genomes. None of the Philippine SARS-CoV-2 sequences in GISAID (accessed 22 August 2020) with a collection date before 25 June 2020 (15, 16) contained the D614G mutation. From the same set of data, lineage B.1.1 containing D614G was found in a sample collected on 25 June 2020. This observation coincides with our findings that the D614G mutation was observed in samples collected in June 2020 (16) . Our findings show the presence of lineages B.6, B.1.1, and B1.1.28, with the latter being first reported in the Philippines in this study. The D614G mutation is currently the most prevalent variant worldwide and is associated with higher viral RNA levels and titers of pseudoviruses (17) . In this study, all patients had no history of travel outside the country and acquired the disease in the National Capital Region, Region 3, or Region 4A (Table 1) , providing evidence of local transmission. Multiple lineages and strains could have been introduced by travelers and Filipino repatriates (18) . The D614G mutation is replacing and rapidly surpassing in prevalence the original strain circulating prior to June 2020 and may partially explain the rapid rise of cases in the Philippines. Data availability. The SARS-CoV-2 genomes from the Philippines were deposited in the GenBank database (accession no. MT919768 to MT919790). The raw reads have been deposited in the NCBI Sequence Read Archive (SRA accession no. SRS7273360 to SRS7273382). The BioProject accession no. is PRJNA659293. The BioSample accession no. are SAMN15903138 to SAMN15903160. China Novel Coronavirus Investigating and Research Team. 2020. A novel coronavirus from patients with pneumonia in China COVID-19) situation reports: weekly epidemiological update and weekly operational update COVID-19 ARTIC v3 Illumina library construction and sequencing protocol V.4. Wellcome Sanger Institute Fast and accurate short read alignment with Burrows-Wheeler Transform An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools Full-length transcriptome assembly from RNA-Seq data without a reference genome A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology The WHO European Region sequencing laboratories and GISAID EpiCoV group. 2020. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region MAFFT multiple sequence alignment software version 7: improvements in performance and usability IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies FigTree, a graphical viewer of phylogenetic trees MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets RITM releases first 17 sets of SARS-CoV-2 genome sequences from PH cases through third generation sequencing technology Philippine Genome Center reports detection of the D614G variant of SARS-CoV-2 virus in the Philippines Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus Over 124,000 overseas Filipinos flown home amid COVID-19 pandemic-DFA. Philippine Daily Inquirer We acknowledge the support of the Department of Research and Training, the Department of Pathology and Laboratories, and the Hospital Infection Control Committee of the V. Luna Medical Center (Quezon City, Philippines) for support with specimen collection. Informed consent was obtained from the patients for SARS-CoV-2 testing. Sample collection was considered a public health effort and did not require an institutional review board (IRB)-approved human use protocol. The memorandum for Public Health Testing Support for the COVID-19 Global Health Emergency was issued by the Walter Reed Army Institute of Research (WRAIR). This memorandum authorizes WRAIR to participate in the public health response for the COVID-19 Global Health Emergency within the boundaries set herein and designates that these activities are not considered a human subject research activity in accordance with 32 CFR 219, DoDI 3216.02, or WRAIR Commander's IRB policy no. 02 (Determinations).This study was funded by the Armed Forces Health Surveillance Branch (AFHSB) and its Global Emerging Infections Surveillance (GEIS) Section, USA, under grant no. P0128_20_AF_13 for fiscal year (FY) 2020. Material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The opinions or assertions contained herein are the private views of the authors and are not to be construed as official or as reflecting true views of the Department of the Army or the Department of Defense. The investigators have adhered to the policies for protection of human subjects as prescribed in AR 70-25.We declare no competing interests.