Scientists explain SARS-CoV-2 mutations, genomics in latest webinar

| Written by Fred Dabu

Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel. [https://www.youtube.com/watch?v=PfwDc3mBKew[
Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel.

 

Reports on mutations of the SARS-CoV-2 virus, mainly on D614G which affects the spike protein on the virus’ surface, have led the public to ask whether these changes make the virus that causes the COVID-19 disease more infectious, lethal, or on the other hand, benign and less transmissible.

As the official count went beyond 61,000 (as of July 16) confirmed COVID-19 cases in the Philippines, more participants are joining the community of health educators, learners and practitioners following the UP Webinar Series “STOP COVID DEATHS: Clinical Management Updates”.

Dr. Cynthia P. Saloma, Executive Director of the UP Philippine Genome Center and Professor of Molecular Biology and Biotechnology at UP Diliman, talked about “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” during the 13th episode of the webinar series held on July 17. This episode is now accessible on the YouTube channel of TVUP. This webinar had 1,500 registered participants, the highest number for the series.

Available information shows that globally, there are multiple mutations, and not just three, the resource speaker explained in the webinar. According to Dr. Saloma, even the Philippine isolates have genetic sequences that are unique. “Our analysis shows that they are benign. At this point in time, the data suggest that they are harmless mutations. The information is important for us to track the source of infection and transmissibility,” she explained.  She added that more research needs to be done to help scientists and policymakers understand how these mutations affect existing health interventions and efforts leading to the development of vaccines.

 

Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel. [https://www.youtube.com/watch?v=PfwDc3mBKew[
Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel.

 

Dr. Saloma’s webinar presentation revolved around the importance of genomic information, how genomics and genome sequencing of the virus can inform decision-making, testing and management of the disease, and what steps should be taken in the future.  She showed the sequence variants in isolates or samples collected here in the Philippines from March to July to determine SARS-Cov-2 circulating viruses and come up with transmission analysis. She explained that virus mutations can have implications on vaccine design, testing, and treatment.

Saloma said “China’s release of the SARS-Cov-2 data in January allowed many institutions around the world to develop tests, diagnose the virus, and for vaccine developers to design vaccines based on sequence alone, and for structural modeling studies. . . .  Worldwide, we have a publicly available shared database wherein researchers from all over the world can deposit their sequences.”

 

Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel. [https://www.youtube.com/watch?v=PfwDc3mBKew[
Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel.

 

“With whole genome sequencing, we can track sequence variations, and disprove conspiracy theories that say the SARS-Cov-2 is a bioweapon. The data in the field suggest that it wasn’t developed as a bioweapon and that it evolved naturally,” Saloma explained.

“It is important for epidemiologists to study the random mutations in the SARS-Cov-2 genetic code to inform containment measures, to analyze the similarities between the different viruses, and to allow scientists to build a genetic tree,” she added.

Saloma went on to discuss how technology helps researchers understand virus spread. “We can organize samples in the tree according to the date they were taken. This helps us visualize how the virus spread over time. Geographical movement is interpreted based on the location of the samples. It is important that we have very good record-keeping and contact tracing. It helps us analyze how the transmissions take place,” she said.

 

Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel. [https://www.youtube.com/watch?v=PfwDc3mBKew[
Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel.

 

Saloma shared valuable information yet to be published. “The data presented are part of the results of the field validation study of the GenAmplify nCov RT-PCR detection kit of Dr. Raul Destura, with the study funded by PCHRD DOST, and the project leader was Dr. Marissa Alejandria,” she said.

“Majority of the analysis was done during the month of April, with samples collected during the last week of March (about 380 cases). Within this period, the number of cases grew from 2,311 (April 1) to 8,488 (April 30),” added Saloma.

 

Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel. [https://www.youtube.com/watch?v=PfwDc3mBKew[
Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel. 

 

Saloma further said that “numerous mutations have already been identified across the viral genome of SARS-CoV-2 from different countries. . . .  Many of the variations that we observed in the six Philippine isolates are not really alarming. These should not cause alarm. We are still tracking the mutations happening in the country.”

Included in Saloma’s discussion were updates on major COVID-19 vaccine development programs around the world.

 

Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel. [https://www.youtube.com/watch?v=PfwDc3mBKew[
Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel.
Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel. [https://www.youtube.com/watch?v=PfwDc3mBKew[
Screenshot from the webinar “Genetic Sequencing Research: Mutation of SARS-Cov-2 (Implications for Clinical Management and Vaccine Development)” aired on July 17, with replay available on the TVUP YouTube channel.

 

To verify information on the source of the virus variants circulating in the Philippines, Saloma discussed how “Next Generation Sequencing (NGS) data can help shed light on cases of community infections, traceability of the virus, and travel history of patients, among others. It can also be used to track worldwide SARS-CoV-2 sequence variations, and mutations of the virus through time with phylodynamic analysis.”

“So far, SARS-CoV-2 viruses circulating in the Philippines seem not to vary that much with the Original Wuhan Isolate,” Saloma said.  She discussed a hypothesis formed from the Nextstrain global dataset and subsampling tree showing the path of transmission of the SARS-CoV-2 virus in the Philippines that was from China to India until it reached the country. She added, however, an Asia-focused subsampling tree showed the transmission route to be from China to Japan to India to the Philippines. She said that this variation was due to the time of collection and focus of the samples.

These hypotheses were related to the phylogenetic tree showing the Philippine samples clustered in B, C, and D. In cluster B, the samples shown as coming from Japan came from Filipino and Indian seafarers on the Diamond Princess cruise ship and were taken in late February. In cluster C & D, they were shown as coming from Shanghai, China in mid-February. “Based on this tree, we can say that the samples we had in March came from the transmissions from the Diamond Princess cruise ship” that was boarded at Yokohama, Japan and not from India, Saloma said.

“For the community transmission (samples from PGH, dated March 22-28), possibly there was transmission from the seafarers to the community.  Based on the clustering of samples, we hypothesize that there are at least two sources of the viral transmission in the country: China (mainly from Shanghai) and Japan (from the Diamond Princess). This is only a small proportion of the transmission, we need to sequence more samples, particularly the earlier cases, if possible, to provide us a comprehensive picture of the geographic spread of the SARS-CoV-2 in the country,” Saloma clarified.

Saloma concluded her presentation by highlighting the need for advancing: genomic epidemiological monitoring of COVID-19 in the Philippines; biosurveillance of SARS-CoV-2 infections in the country to track mutations and aid in developing vaccines; and, the creation of the Philippine virome database, as these will greatly help Filipinos to understand transmission of the virus, assist in designing therapies and vaccines, track the virus, and prepare for future pandemics.

Guest speakers for this episode included: Dr. Grace Javier Alfonso, Executive Director of TVUP and UP Professor Emeritus, and Dr. Eva Maria Cutiongco de la Paz, Executive Director of UP-NIH and Director of the Health Program of the Philippine Genome Center, who both shared their appreciation to the growing community of scholars and practitioners who are participating in the webinar series.

Hosted by Dr. Raymond Francis R. Sarmiento, Director of the UP-NIH National Telehealth Center, and Dr. Susan Pineda Mercado, Special Envoy of the President for Global Health Initiatives, this webinar series is organized by the University of the Philippines in partnership with the Philippine Health Insurance Corporation (PhilHealth) and the UP Manila NIH National Telehealth Center. The series aims to share the best available knowledge and practices to more people in order to help improve the Filipino people’s understanding and management of COVID patients and other aspects of the health crisis in general.

The UP-PhilHealth webinar series will take on a new twist this coming Friday, July 31, 12:00 n.n, with the “STOP COVID DEATHS: VIRTUAL GRAND ROUNDS”, the very first online medicine grand rounds in the Philippines. The 15th installment in the UP “STOP COVID DEATHS” webinar series will focus on “Doctor as Patient: The Journey of Dr. Rody Sy”, Professor Emeritus of the UP College of Medicine and a National Academy of Science and Technology Academician.

Register here: bit.ly/StopCOVIDDeathsWebinar15.

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