key: cord-0977153-f6l8m3c5
authors: Velasco, J. S.; Chinnawirotpisan, P.; Joonlasak, K.; Manasatienkij, W.; Huang, A.; Valderama, M.. T.; Diones, P. C.; Leonardia, S.; Timbol, M. L.; Navarro, F. C.; Villa, V.; Tabinas, H.; Chua, D.; Fernandez, S.; Jones, A.; Klungthong, C.
title: Coding Complete Genome Sequences of Twenty-three SARS-CoV-2 Strains Isolated in the Philippines
date: 2020-09-29
journal: nan
DOI: 10.1101/2020.09.29.20203695
sha: 64e6a6bc7ddecc688eb54b0fda99dc910e6ea194
doc_id: 977153
cord_uid: f6l8m3c5

Here, we report the coding complete genome sequences of 23 severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) strains from the Philippines. Sequences were obtained from nasopharyngeal and oropharyngeal swabs from COVID-19 positive patients. Mutation analysis showed the presence of the D614G mutation in the spike protein in 22 of 23 genomes.

2(SARS-CoV-2) strains from the Philippines. Sequences were obtained from nasopharyngeal and oropharyngeal 27 swabs from COVID-19 positive patients. Mutation analysis showed the presence of the D614G mutation in the spike 28 protein in 22 of 23 genomes. 29 30 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belonging to the family Coronaviridae and genus 31

Betacoronavirus is the causative agent of . In the Philippines, the first confirmed SARS-CoV-2 case was 32 reported on 30 January 2020(2) and as of 31 Aug 2020, more than 200,000 cases had been reported(3). Here, we 33 announce the coding complete genome sequences of 23 SARS-CoV-2 strains collected from 3 April-18 July 2020 from 34 COVID-19 RT-PCR positive Filipino patients(4). Viral RNA was extracted from nasopharyngeal/oropharyngeal swabs 35

using QIAamp viral RNA Mini kit (Qiagen) and used as template for amplicon sequencing using ARTIC SARS-CoV-2 V3 36 primers(4). DNA libraries were constructed and multiplexed using Illumina DNA prep, and then pooled before sequencing. 37

Sequencing was performed on MiSeq using the MiSeq reagent kit V 2(Illumina). Reference mapping was performed by 38 BWA-MEM aligner using Wuhan-Hu-1 genome sequence(GenBank Accession number NC_045512.2) as the reference 39 sequence(5). Primer regions trimming and call variants (Q ≥25) were performed using iVAR v.1.2.2(6) and samtools 40 (7), respectively. Consensus sequences were generated by iVAR v.1.2.2(6) (Q ≥25 and depth of coverage ≥10). Gaps, 41 deletion, and ambiguous bases were identified and confirmed by genome-guided assembly with the reference 42 sequence(NC_045512.2) using Trinity v2.8.5(8) and Sanger sequencing. Lineage and clade were determined using 43

Pangolin v.2.0.4(9), GISAID clade nomenclature(10), and phylogenetic analysis (11, 12, 13) . We used MEGA 7.0(14) 44 to examine nucleotide and amino acid substitutions. All tools were run with default parameters. Raw reads yielded a 45 total of 8.4 gigabases (94% of the clusters with Phred quality score (Q)≥30). The length of reads obtained were 35-251 46 nucleotides and the range of number of reads obtained per library was 0.87 -1.48 million reads. Consensus sequences 47 lengths were similar to the Wuhan-Hu-1 strain(NC_045512.2) with mean coverage ranging from 2,361X to 7,177X. 48 filipinos-flown-home-amid-covid-19-pandemic-dfa.

All rights reserved. No reuse allowed without permission. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this this version posted September 29, 2020. . All rights reserved. No reuse allowed without permission.

preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this this version posted September 29, 2020. . https://doi.org/10.1101/2020.09.29.20203695 doi: medRxiv preprint

China Novel Coronavirus I, Research T. 2020. A Novel Coronavirus from 88 Patients with Pneumonia in China

Correction to: First COVID-19 92 infections in the Philippines: a case report

Fast and accurate short read alignment with Burrows-Wheeler Transform

An amplicon-based sequencing framework for accurately measuring intrahost virus 102 diversity using PrimalSeq and iVar

The 105 sequence alignment/map format and SAMtools

Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. 109

A dynamic 111 nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology (online 112 ahead of print

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European 115

MAFFT multiple sequence alignment software version 7: improvements in 118 performance and usability

All rights reserved. No reuse allowed without permission. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this this version posted September 29, 2020. . https://doi.org/10.1101/2020.09.29.20203695 doi: medRxiv preprint