High Performance Computing and Data Science Workflow in Julia

HPC and Data Science Workflow in Julia #PGCTalks Date: July 16, 2021, Friday, 4:30-6:00pm This webinar is open to the public and registration is free. Abstract Julia is specifically designed from the start of its conception as a language for high-performance computation but at the same time highly interactive. To achieve this, Julia is one […]

Detection and Genome Sequencing of SARS-CoV-2 Variants Belonging to the B.1.1.7 Lineage in the Philippines

Coronavirus disease 2019 (COVID-19) is an infectious disease that has gained pandemic status from the World Health Organization, with millions of cases and deaths recorded worldwide. This global health crisis is caused by the virus referred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of the genus Betacoronavirus (Coronaviridae), together with the causative agents of the first SARS outbreak in 2003 and the Middle East respiratory syndrome (MERS) in 2012.

PGC SARS-CoV-2 Bulletin No. 7: Detection and characterization of a new SARS-CoV-2 lineage P.3, with spike protein mutations E484K, N501Y, P681H and LGV 141-143 deletion, from samples sequenced through the intensified UP-PGC, UP-NIH and DOH biosurveillance program

A close examination of the mutation profile of the P.3 viruses revealed that apart from E484K and N501Y, they also share other spike protein mutations that are likely to have functional significance (Figure 2). This includes the P681H mutation, also found in lineage B.1.1.7 viruses, as well as a three-amino acid deletion at positions 141 to 143 (LGV141_143del).

PGC SARS-CoV-2 Bulletin No. 6: First case of the new variant under Lineage B.1.1.7 detected in the Philippines

Through the biosurveillance efforts of the UP – Philippine Genome Center (PGC), in coordination with the Department of Health (DOH) – Epidemiology Bureau and the Inter-Agency Task Force (IATF) Task Force on COVID-19 Variants,  we report the first confirmed case of the SARS-CoV-2 B.1.1.7 lineage, more commonly known as the UK variant, in the Philippines. An announcement of this finding can be found in an official DOH press release dated January 13, 2021.

PGC SARS-CoV-2 Bulletin No. 5: New Variants from UK and South Africa NOT detected in 305 local viral samples

Recently, new SARS-CoV-2 variants were detected in the United Kingdom and South Africa with multiple spike protein mutations that may cause substantial changes in certain properties of the virus. These observations spurred biosurveillance efforts in different countries, with some countries outside of the UK and South Africa already reporting the presence of these new variants within their territories. The data presented in this report is part of our own continuing biosurveillance efforts to track the entry of these new variants in the country, as well as other viral mutations that may be of concern locally.

PGC SARS-CoV-2 Bulletin No. 4: Newly reported variant in the United Kingdom has yet to be observed locally

In a report posted at the Global Initiative for Sharing All Influenza Data (GISAID) website, the UK variant is said to harbor multiple spike protein mutations within a single sample, including a combination of the following: H69del, V70del(69), Y145del(143), N501Y, A570D, D614G, P681H(674), T716I, S982A, and D1118H (GISAID, 2020). While the discovery of this new UK variant appears to be concerning, the report cautions that the detailed effects of these mutations remain to be fully determined.

PGC SARS-CoV-2 Bulletin No. 3: 23 newly reported SARS-CoV-2 genome sequences from the Philippines support PGC’s previously hypothesized viral entry routes and waves of transmission

A group of researchers from the U.S. Army Medical Directorate–Armed Forces Research Institute of Medical Sciences, the University of the Philippines Manila, and the V. Luna Medical Center recently reported 23 new SARS-CoV-2 genome sequences from the Philippines, all of which were from cases of local transmission (Velasco et al., 2020). Among these samples, one was collected in early April while the rest were obtained in the months of June and July.

PGC SARS-CoV-2 Bulletin No.2: Three Possible Routes of SARS-CoV-2 infection in the Philippines

Majority of the Philippine submissions (18 of 23) were collected in the month of March, wherein except for one sample which clustered with isolates from Shanghai, China, all others were observed to group into clades linked to the outbreak in the cruise ship, M/V Diamond Princess, moored in Yokohama, Japan in early February 2020. Later that month, passengers and crew members of this cruise ship representing various nationalities including Filipinos, Indians, and Australians were repatriated to their home countries.

PGC SARS-CoV-2 Bulletin No.1: Philippine Genome Center Reports Detection of the D614G Variant of SARS-CoV-2 Virus in the Philippines

COVID-19 or the Coronavirus Disease 2019 is caused by SARS-CoV-2 virus, the genome of which is a single-stranded positive sense RNA that is about 30,000 bases long. It contains 11 genes and several regions have been known to be immunogenic, including different parts of the Spike (S) protein, the Nucleocapsid (N) protein, as well as the Membrane (M) and Envelope (E) proteins, which have therefore been targeted for vaccine development.