About: ANALYSIS OF SARS-COV-2 GENOME SEQUENCES FROM THE PHILIPPINES: GENETIC SURVEILLANCE AND TRANSMISSION DYNAMICS

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About: ANALYSIS OF SARS-COV-2 GENOME SEQUENCES FROM THE PHILIPPINES: GENETIC SURVEILLANCE AND TRANSMISSION DYNAMICS Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	ANALYSIS OF SARS-COV-2 GENOME SEQUENCES FROM THE PHILIPPINES: GENETIC SURVEILLANCE AND TRANSMISSION DYNAMICS
Creator	Tan, Christina Velasco, John Aaron, Julius Acosta, Shaira Alejandria, Marissa Ann, Joy Araiza, Mae Arevalo, Geraldine Bascos, Neil Cutiongco-De La Paz, Eva Dela Tonga, Angelo Demot, Bernard Destura, Raul Dizon, Joshua Dollete, Maribell Dungca, Theresa Fabilloren, D Gabriel, Arielle Galarion, H Gaza, L Geganzo, Genavia, Shana Jowina, Ma King, El Lapid, Carlo Llames, Hannah Maralit, Benedict Mejia, Morado, D Nipales, Jarvin Pangilinan, Coleen Punayan, Kris Rose, Shebna Salamat, Sonia Salinas, Melanie Saloma, Cynthia Sanchez, Alessandra Schwem, E Tablizo, Francis Yap, Jan
source	MedRxiv
abstract	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.
has issue date	2020-08-25(xsd:dateTime)
bibo:doi	10.1101/2020.08.22.20180034
has license	medrxiv
sha1sum (hex)	8a978b1a8df6f7a328b0b19f2123a2d46a8985ea
schema:url	https://doi.org/10.1101/2020.08.22.20180034
resource representing a document's title	ANALYSIS OF SARS-COV-2 GENOME SEQUENCES FROM THE PHILIPPINES: GENETIC SURVEILLANCE AND TRANSMISSION DYNAMICS
resource representing a document's body	covid:8a978b1a8df6f7a328b0b19f2123a2d46a8985ea#body_text
is schema:about of	named entity 'Health' named entity 'Manila' named entity 'preprint' named entity 'mutation' named entity 'preprint' named entity 'N-terminal' named entity 'RdRp' named entity 'preprint' named entity 'preprint' named entity 'comorbid conditions' named entity 'preprint' named entity 'protein stability' named entity 'medRxiv' named entity 'phylogenetic positions' named entity 'preprint' named entity 'sequence similarity' named entity 'virulent strain' named entity 'phylogenomic' named entity 'amino acid sequence' named entity 'preprint' named entity 'protein' named entity 'quarantine' named entity 'amino acid replacement' named entity 'nucleic acid' named entity 'Philippines' named entity 'preprint' named entity 'genome' named entity 'mutation' named entity 'genome' named entity 'SARS-COV-2' named entity 'SARS-CoV-2' named entity 'co-morbidities' named entity 'gene' named entity 'peer review' named entity 'gene' named entity 'glycoprotein' named entity 'binding affinity' named entity 'China' named entity 'medRxiv' named entity 'preprint' named entity 'preprint' named entity 'Asia' named entity 'CC-BY-ND' named entity 'GISAID' named entity 'amino acid' named entity 'preprint'

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