key: cord-0960330-ta1rn82u authors: Velasco, John Mark; Chinnawirotpisan, Piyawan; Valderama, Maria Theresa; Joonlasak, Khajohn; Manasatienkij, Wudtichai; Huang, Angkana; Diones, Paula Corazon; Navarro, Fatima Claire; Vila, Vicente; Tabinas, Henry; Chua, Domingo; Fernandez, Stefan; Jones, Anthony; Klungthong, Chonticha title: Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines date: 2021-07-15 journal: Microbiol Resour Announc DOI: 10.1128/mra.00498-21 sha: 772a6e3a100c677c4cd04f4b68cb2208109f9ceb doc_id: 960330 cord_uid: ta1rn82u Here, we report the complete genome sequences of 11 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants from the Philippines. Lineage analysis showed 3 B.1.1.7 and 8 B.1.351 sequences. One B.1.1.7 sequence contained two additional mutations, F318N and V320F, with V320F located in the receptor binding domain of the S1 subunit. , reduced neutralizing titers, reduced vaccine efficacy (15) (16) (17) (18) (19) (20) (21) , and significantly higher adjusted odds ratio for hospitalization and intensive care admission (22) . We compared the S gene mutations in our sequences with 542,800 B.1.1.7 and 14,359 B.1.351 GISAID sequences accessed on 8 May 2021 using outbreak.info (23) , and one of our B.1.1.7 sequences (MZ068158) contained two unique mutations, F318N and V320F. The F318N mutation was located in an unknown function region between the N-terminal domain and the receptor binding domain, while the V320F mutation was located in the receptor binding domain in the S1 subunit. The surge of COVID-19 cases starting in early March 2021 (24) in the NCR may be explained by the circulation of these variants in addition to the relaxation of quarantine measures, increased mobility of the population, and lower compliance with health standards. Informed consent was obtained from the patients for SARS-CoV-2 real-time RT-PCR (rRT-PCR) testing and sequencing. The sample collection was considered a public health effort and did not require an institutional review boardapproved human use protocol. Data availability. The SARS-CoV-2 genome sequences from the Philippines were deposited in the GenBank database (accession no. MZ068151 to MZ068161). The raw reads have been deposited in the NCBI Sequence Read Archive (SRA accession no. SRR14460618 to SRR14460628). The BioProject accession number is PRJNA726840. The BioSample accession numbers are SAMN18976036 to SAMN18976046. China Novel Coronavirus Investigating and Research Team. 2020. A novel coronavirus from patients with pneumonia in China PGC SARS-CoV-2 bulletin no. 6: first case of the new variant under lineage B.1.1.7 detected in the Philippines Philippine genomic biosurveillance detects SARS-CoV-2 UK variant Sustained biosurveillance efforts detect 6 B.1.351 cases, 30 B.1.1.7 cases, and 2 cases with mutations of interest Continuing biosurveillance detects additional B.1.1.7 and B.1.351 cases and P.1. variant case COVID-19 ARTIC v3 Illumina library construction and sequencing protocol V.4. Wellcome Sanger Institute 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 Region sequencing laboratories, 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 The COVID-19 Genomics UK (COG-UK) consortium. 2021. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States The CITIID-NIHR BioResource COVID-19 Collaboration, The COVID-19 Genomics UK (COG-UK) Consortium. 2021 Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies 2021. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants Efficacy of the ChAdOx1 nCoV-19 Covid-19 vaccine against the B.1.351 variant Covid-19: Novavax vaccine efficacy is 86% against UK variant and 60% against South African variant BNT162b2 mRNA COVID-19 vaccine induces antibodies of broader cross-reactivity than natural infection but recognition of mutant viruses is up to 10-fold reduced New SARS-CoV-2 variants-clinical, public health, and vaccine implications Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies COVID study groups. 2021. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries An interactive Web-based dashboard to track COVID-19 in real time We acknowledge the Department of Research and Training, the Department of Pathology and Laboratory Medicine, and the Hospital Infection Control Committee of the V. Luna Medical Center (Quezon City, Philippines) for support with the specimen collection. The 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 our private views and are not to be construed as official or as reflecting the true views of the Department of the Army or the Department of Defense. The investigators have adhered to the policies for the protection of human subjects as prescribed in AR 70-25.This study was funded by the Armed Forces Health Surveillance Division and its Global Emerging Infections Surveillance Branch, USA, under grant no. P0103_21_AF (COVID-19 Supplemental: AFRIMS Virology Regional COVID-19 Surveillance and Characterization Program) and P0084_21_AF (Respiratory Work Plan) for fiscal year (FY) 2021. We declare no competing interests.