RITM releases first 17 sets of SARS-CoV-2 genome sequences from PH cases through Third Generation Sequencing Technology

The Department of Health-Research Institute for Tropical Medicine (DOH-RITM), in collaboration with experts from the University of Glasgow, Scotland, UK, has released a total of 17 viral genome sequences of the SARS-CoV-2 from the Philippines, using Third Generation Sequencing technology. Selected samples from COVID-19 cases from January, March, and June 2020 were released through the Global Initiative on Sharing All Influenza Data or GISAID Initiative, an open-access database that enables rapid sharing of sequencing data to contribute to the global response to epidemics and pandemics.

Whole genome sequencing of SARS-CoV-2 specimens from the Philippines can provide the data necessary to uncover patterns of virus circulation in the country.  Sequence data can reveal the distribution of SARS-COV-2 lineages and estimate when these were introduced/imported in the country. Sequences can also complement contact tracing and identify cases that belong to the same transmission clusters and trace sources of infection.  Particular characteristics in the sequences may also provide essential information for the development of diagnostic tests, therapeutics, and vaccines, all of which will further aid in the pandemic response.

RITM used the MinION sequencing platform and the ARTIC Network sequencing and bioinformatics protocols to generate the SARS-CoV-2 genomes from the Philippines. Third-generation sequencing with long-reads such as the MinION sequencing platform from Oxford Nanopore Technologies (ONT), has enabled researchers from countries affected by COVID-19 to rapidly generate and publish thousands of SARS-CoV-2 genomes as part of their research and public health response. This was the first time that the technology was used in the Philippines for SARS-CoV-2 genome sequencing.

SARS-CoV 2 strains circulating in the Philippines

SARS-CoV-2 has two major lineages that both originated in China, A and B, with at least 6 sub-lineages in each major lineage.  Lineages are defined by mutations in the SARS-CoV-2 genome sequence.  Five lineages were identified in the Philippine sequences: A, B, B.1, B.1.1, and B.6.  Lineages A and B were the original strains from China.  Lineages B.1 and B.1.1 are associated with the outbreaks in Italy and other European countries. Lineage B.6 was also detected in India, UK, North America, Australia, and Singapore.  Sequences were from samples collected in Luzon (NCR, Ilocos Sur, Rizal, and Laguna) and one sequence from Bohol.  Most cases did not have a history of travel outside the Philippines. The local transmission of different lineages and strains may have been imported from multiple introductions of different lineages into the country.  While it is also possible that the virus may have accumulated mutations through transmission within the country, the relatively slow mutation rate of SARS-CoV-2 may not drive the circulation of very varied lineages in the country.  It is more likely that these lineages were imported from other countries.

The first three SARS-CoV-2 strains detected in the Philippines were from different lineages, A and B. The sequence of the first case belonged to Lineage A and the sequences from the next two cases belonged to Lineage B.  These first three cases were travelers from Wuhan, Hubei, China, implying separate introductions of different SARS-CoV-2 lineages in January.

Almost all sequences from samples collected in March belonged to Lineage B.6.  Only two of the cases had traveled from Japan and South Korea while the rest of the cases had no recent history of travel outside the country at the time of sample collection.

D614G mutation detected in SARS-CoV-2 samples from the Philippines

The sequences from the most recent samples collected in June belonged to Lineage B.1 and B.1.1, which were the lineages that spread across Europe.  The sequence that belonged to Lineage B.1.1 also had the D614G mutation on the spike protein gene previously linked to increased transmission efficiency.  This same mutation was also detected in seven more samples collected in June and July in NCR and Laguna, sequenced using Sanger or first-generation sequencing. This SARS-CoV-2 variant with the D614G mutation is suspected to have surpassed previous strains in prevalence not only in Europe and the United States but in other places around the globe.

Several studies have already shown that the D614G mutation in the spike gene enables SARS-CoV-2 to produce more virus particles in vitro compared to strains without the said mutation (Korber et al.,2020; Hu et al., 2020, Lorenzo-Redondo et al., 2020; Ozono et al., 2020; Wagner et al., 2020). However, more studies need to be performed to determine the impact of this mutation in transmission, disease severity and consequently to therapeutics and vaccines currently under development.

Collecting more samples and establishing more sequences from the COVID-19 cases in the country will provide clearer insight as to how the virus is spreading within the local communities, and help health authorities have a better understanding of what mitigation and control measures are necessary.  The SARS-CoV-2 viral genome sequencing is part of an ongoing research study at RITM funded by DOH and in collaboration with the University of Glasgow. The project will continue to sequence more samples in 2020.  The Institute also hopes to further capacitate subnational laboratories and enable them to adapt the technology for SARS-CoV-2 sequencing and, in the future, for rapid characterization of future novel diseases with unknown causes.

The viral genomes that have been sequenced so far by RITM and PGC represent a very small picture of SARS-CoV-2 transmission in the country.  The sequencing results, however, suggest that from January to July 2020, there were multiple introductions of different SARS-CoV-2 lineages and strains in the country.  These imported strains then started transmission clusters that further spread the infection within the country.  While it is critical to mitigate transmission within the country to prevent further spread of the virus, there is also a need to strengthen surveillance and control measures at our country’s ports of entry.  Previous epidemics and pandemics have shown that mutations in pathogen genomes may generate new viral strains that cause more severe disease or to spread more easily from person to person.  By limiting the introduction of new strains into the country, we may not only help reduce the spread of infections, but also prevent new potentially, more virulent and/or infectious strains from coming into the country.


Hu, J., He, C.-L., Gao, Q.-Z., Zhang, G.-J., Cao, X.-X., Long, Q.-X., Deng, H.-J., Huang, L.-Y., Chen, J., Wang, K., et al., (2020). The D614G mutation of SARS-CoV02 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera. Bio-Rxviv, 2020.06.20.161323.

Korber, B., Fischer, W.M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E.E., 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.

Lorenzo-Redondo, R., Nam, H.H., Roberts, S.C., Simons, L.M., Jennings, L/ J., Qi, C., Achenbach, C.J. Hauser, A.R., Ison, M. G., Hulquist, J.F. and Ozer, E.A. (2020). A Unique Clade of SARS-CoV-2 Viruses is associated with Lower viral loads in patient upper airways. medRxiv, 2020.05.19.20107144.

Ozono, S., Zhang, Y., Ode, H., Seng, T.T., Imai, K., Miyoshi, K., Kishigami, S., Ueno, T., Iwatani, T., Suzuki, T., et al (2020). Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry. bioRxiv, 2020.06.15.151779.

Wagner, C., Roychoudhury, P., Hadfield, J., Hodcroft, E.B., Lee, J., Moncla, L.H., Muller, N.F. Behrenes, C., Huang, M.-L., Mathias, P., et al (2020). Comparing viral load and clinical outcomes in Washington State acrpss D614G mutation in spike protein of SARS-CoV-2 http://github.com/blab/ncov-D614G.