CAS alumni co-author paper on SARS-CoV-2 mutations
- Ian Lemuel Virtucio
- Oct 3, 2020
- 3 min read
Two alumni from the University of the Philippines College of Arts and Sciences (CAS) — and currently students of the College of Medicine MD-PhD in Molecular Medicine program — co-authored a paper that evaluated the mutation characteristics of the genome and translated proteins of SARS-CoV-2, the causative agent of COVID-19.
Karol Ann Baldo and Christian Luke Badua from Batch 2019 BS Biochemistry and BS Biology programs, respectively, initially conducted the study entitled “Genomic and Proteomic Mutation Landscapes of SARS-CoV-2” as a Special Project in Biochem 205 under their adviser, Dr. Paul Mark Medina. It was published in the Journal of Medical Virology last September 24.
The team used publicly available genome data in NCBI GenBank and in GISAID EpicCoV grouped according to three geographic areas (China, USA, and ‘Others’ countries) in two time points (December 2019-March 2020; December 2019-May 2020). Within these two time points, the study characterized regions of the viral genomes which are prone to mutations (hotspots), and those with relatively low prevalence (coldspots).
Mutations in such hotspots were found to increase (some up to four times) for within a particular landmass (USA or China) and even among separated land regions (Others). Additionally, phylogenetic (evolutionary history) analyses of SARS-CoV-2 genes and proteins showed three major clades and one minor clade. A clade is a grouping that includes a common ancestor and all of its lineal descendants.
It was emphasized that the mutations might have given the virus a more elusive conformation from treatment by remdesivir, which is currently at phase 3 of COVID-19 clinical trials, thus challenging its effectiveness for future use among varying geographical areas.
In a Messenger chat interview, Baldo shared to The Aurum News Team that over the two time points, “the genomes and proteomes of SARS-CoV-2 remains to be consensus (...haven’t significantly changed or deviated from the reference or original viral sequence), hence its general population is expected have similar interaction with the currently developing tools for treatment and vaccines, maybe by the next year”.
Moreover, Baldo claims that it is necessary to “do continuous analysis of [drugs for treatment] and vaccines’ effectivity attributed to the innate instability of the genome of SARS-CoV-2, as an RNA virus such as that of Influenza. There are multiple factors that may be considered, including patient susceptibility and comorbidities, and the exposure and spread to a region of a variant that has potentially deleterious effects to drug susceptibility.”
Their findings further conclude that the mutation landscape in SAR-CoV-2 genome and proteome should be characterized in order to optimize the effectiveness of diagnostic tools and treatment options for COVID-19, since a number of research have already been in progress in the development of a vaccine.
Significance in the Philippine geographical unit
According to Baldo, “[the data] suggests that increasing occurrence of prominent and impactful mutations may also occur in the Philippines, across its landmasses and between its islands, especially that of mutations that may increase the infectivity of the virus (e.g. D614G in the receptor binding domain of the S protein)”.
Two SARS-COV-2 samples from the Philippines were included in the analysis applications and “that drug susceptibility could be derived in-silico study”.
Viral mutations do happen
Last August 18, the Philippine Genome Center (PGC) and the Research Institute for Tropical Medicine (RITM) detected the G614 variant of SARS-CoV-2 in a small sample of positive cases in Quezon City. This more infective variant has almost replaced the original D614 virus in most of Europe and the Americas, but the PGC assures that this may not represent the mutational landscape for the whole country.
In medical microbiology, viral genome mutations are common as a result of genetic selection, and arise through unrepaired errors during replication. Scientists say that the human pathogen had already undergone thousands of mutations since it emerged in Wuhan, China — majority of which have no effect or have vanished in lineages. Mutations can be deleterious, neutral, or occasionally favorable.
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