SARS-CoV-2, the virus which causes COVID-19 illnesses, has recorded a lot of mutations since its first discovery late in December in Wuhan, Hubei Province, China. A new variant of the virus, D614G, seems to be sweeping the globe and has not been reported to be present in the Philippines. As news agencies and frontliners worry how this new strain will affect public health, scientists race to know more about it through genetic sequencing.

In the 13th “Stop COVID Deaths: Clinical Management Updates” webinar series entitled “Genetic Sequencing Research: Mutation of SARSCov2 (Implications for Clinical Management and Vaccine Development)” held on July 17, 2020, the Philippine Genome Center (PGC) Executive Director Dr. Cynthia P. Saloma discussed this topic by sharing part of the results of a field validation study of the GenAmplifyTM nCOV rRT-PCR Detection Kit. 

The GenAmplifyTM nCoV rRT-PCR kit, the first locally developed kit for COVID-19, is the work of PGC Deputy Executive Director Dr. Raul Destura and researchers at the UP Manila National Institutes of Health. The kit underwent three weeks of field validation before it was approved for use by the Food and Drug Administration on 3 April 2020.
 
In the field validation, the team led by Dr. Marissa Alejandria collected nasal and oro-pharyngeal swabs from 380 volunteer patients at the Philippine General Hospital. Another set of patients came from The Medical City to complete the 500 volunteers in the study. Using the GenAmplifyTM rRT-PCR kit, samples with the SARS-CoV-2 genes were rapidly identified. These underwent Capillary Sequencing at the PGC which confirmed the presence of the target gene(s) being detected in the virus. Afterwards, samples also underwent viral metagenomics sequencing through NGS (Next Generation Sequencing) to look for SARS viral sequences as well as those of co-infecting pathogens. 

Dr. Saloma shared the profile of six COVID-19 patients— all came from Metro Manila with no travel history outside the country. Two had direct contact with an infected person, one got it by caring for a relative, and SARS-CoV-2 mutations… while the other patient (a doctor) got it from his wife who was exposed to a confirmed case. The clinical presentation of the patients ranged from moderate to severe. Four patients had severe COVID-19 pneumonia. Two needed mechanical ventilation. Of the six patients, four recovered with some manifesting prolonged viral shedding.

Interspersed in the discussion of the study were the history of COVID-19 in the Philippines and in the world, especially the quarantine of the M/V Diamond Princess cruise ship in Yokohama, Japan, which had 440 Filipino crew members and five passengers repatriated to the Philippines on February 25 and 26; the importance of China’s early release of SARS-CoV-2 data which allowed many institutions to develop diagnostic tests and design recombinant vaccines; and, quick lessons on genomic sequencing and its importance in understanding the virus origin, mutations, and how it evolves as it spreads worldwide. 

Other take-aways from the forum were the following:
• The six samples showed community transmission.
• From further studies of the early samples done by the PGC and other institutions like the Research Institute of Tropical Medicine, the scientists hypothesized that the virus most likely came from people who worked or stayed at the M/V Diamond Princess cruise ship. (The Filipino crew members were repatriated to the Philippines on Feb. 25-26 and were quarantined in Clark for 14 days. March 22-28 was the period of sample collection from the six PGH patients.) 
• Close to half a million Filipinos are seafarers, which makes the process of repatriation and quarantine in our seaports and airports a challenge to avert COVID-19 transmission to the local population.
• The results are from a very small sample of SARS-CoV-2 transmission in the country. There is need to sequence a lot more samples in the country, particularly those from earlier months, if we want to have a clearer and bigger picture of the geographic spread of COVID-19 in our country. 
• Based on the capillary sequencing done by PGC from the March, June, and July samples, the D614G variant, where the amino acid aspartate in position 614 in the Spike region of the virus has mutated into glycine, has been common in Europe since March. It was detected locally in three of 5 samples collected in June and it comprised all the nine samples collected in July. Worldwide, it was found that the D614G is increasing and there are in vitro studies which suggest that it is more infectious than the original Wuhan strain. However, the mutation does not seem to affect the disease’s severity and there are no proofs as yet that this variant is more transmissible. 

Dr. Saloma identified the future directions of the PGC: (1) genomic epidemiological monitoring of COVID-19 in the Philippines; (2) biosurveillance of SARS-CoV-2 infection in the country to see if the virus is mutating and in which region, and if the mutations occur in regions used to design vaccines being developed around the world; and, (3) creation of the Philippine Virome Database.

The PGC, established in 2009, is a multidisciplinary research center within the UP System which specializes in genomics and bioinformatics. Their paper is now available as a preprint at medRxiv.

Fedelynn Jemena | Published in Healthscape Special COVID-19 Issue No. 15