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.
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.
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.
The Philippine Genome Center (PGC) thru its Core Facility for Bioinformatics (CFB) releases today to the global community through the GISAID database six (6) genomes of the SARS-CoV-2 sequences from Philippine samples taken in Metro Manila between 26 to 28 March 2020.
The Philippine Genome Center is facilitating a Bioinformatics Internship Program for incoming and current Grade 11 students of the University of the Philippines Integrated School (UPIS) slated on June 8-19, 2020.
The 2020 Bioinformatics Conference aims to bring together researchers, students, and professionals from the field of genomics and bioinformatics. Themed “#BioInfoPH: Overcoming Challenges, Building Opportunities”—the conference intends to surface the complexities of conducting bioinformatics and genomics research in the Philippines and therein address these challenges through the conference forum.
Student applicants must be undergraduate or graduate students in good academic standing, enrolled in a science or engineering course at an accredited college or university in the Philippines. Young professional applicants must have a BS degree in a science or engineering field, and be a researcher and/or faculty member employed at a research or higher education institution in the Philippines.
The program extends to four (4) batches which will be held throughout 2019-2020. The training of the first batch will run from June 17-July 26 , 2019.
This skill building workshop aims to freely integrate available molecular data from global repositories that are pertinent to locally circulating pathogens and apply it to research areas of interest for both the Biological Threat Reduction Program of the US government thru the Defense Threat Reduction Agency.
For a very long time, most bioinformatic tools for handling genome data have been geared toward haploid (or diploid but nearly homozygous) organisms such as humans, bacteria and laboratory strains of model species. As a result, these tools often perform very badly on highly heterozygous diploid or polyploid organisms, which is the case of many non-model and/or marine species.