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.
In the context of vaccine design and diagnostic assays, it is important to track and study the mutations of the virus as it spreads around the world. Epidemiologists likewise study the random mutations occurring in circulating viruses to inform containment measures.
Coronaviruses including the SARS-CoV-2 are characterized by the presence of spikes surrounding the virus core. These spikes enable the virus to attach to human cells through the ACE2 receptor. Since the spike protein mediates the entry of the coronavirus into host cells, insights into mutations affecting this region is important to understand its infectivity as well as its antigenicity.
The Global Initiative on Sharing All Influenza Data (GISAID) records show that among the most frequently observed amino acid replacements from high quality genomes deposited in its database, the D614G mutation at the spike protein is the most common, with 16,254 occurrences reported as of July 14, 20201. In the D614G variant of the virus, the “D” amino acid aspartate at position 614 of the spike protein has mutated to the “G” amino acid glycine. The G614 variant of SARS-CoV-2 has been reported to have become the dominant strain of the virus in circulation around the world2.
As part of the validation study of the locally developed SARS-CoV-2 RT-PCR kit, the Philippine Genome Center has done whole genome as well as targeted sequencing of the SARS-CoV-2 virus in the Philippines. Among COVID-19 positive samples from the Philippine General Hospital collected last March 2020 during the early stages of the pandemic in the Philippines, 13 local isolates that were sequenced show the wild type or the original D614 genotype. Six (6) of these were sequenced to near completion and are now deposited in GISAID. In addition, seven (7) samples deposited by the RITM in GISAID also show the D614 wild type strain. All in all, a total of 20 Philippine isolates collected in March 2020 with available sequences spanning the spike protein region show the D614 genotype.
In contrast to the coronavirus collected in March, we now report the detection of the D614 variant among nine (9) randomly selected COVID-19 positive samples collected in Quezon City in July. In the month of June, both the D614 as well as the G614 have been detected in a small sample of positive cases. Although this information confirms the presence of G614 in the Philippines, we note that all the samples tested were from Quezon City and may not represent the mutational landscape for the whole country.
Data from an in vitro study suggest that viruses with the D614G mutation appear to have higher levels of viral RNA and higher titers of pseudo viruses2. Together with the observation that G614 is now the dominant viral state, the authors claim that the said mutation can increase the viral rate of transmission2. However, there is still no definitive evidence showing that carriers of the G614 variant are actually more transmissible than those with D614, and the mutation does not appear to substantially affect clinical outcomes as well3. Nevertheless, considering the presently wide geographic spread of G614, continuous monitoring of the said mutation – and other frequently observed mutations for that matter – must be done in order to better understand the evolutionary trajectory of SARS-CoV-2 to inform containment, diagnostic, and therapeutic strategies.
The resequencing and detection of SARS-CoV-2 positive samples have been supported in part by the DOST-PCHRD and the Philippine General Hospital through its Director, Dr. Gap Legaspi.
2Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, et al. (2020). Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell 182. Available online 3 July 2020.
3Grubaugh DN, Hanage WP, and Rassmusen AL. (2020). Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Cell. doi: 10.1016/j.cell.2020.06.040.