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Further Analysis of SARS-CoV-2 Genome Suggests It Is Stable

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Two teams of scientists in Italy have collaborated on a project that further analyzed the SARS-CoV-2 genome from locally acquired samples. The analysis of the samples via next-generation sequencing (NGS) reveals a specific level of genetic variability that implies the SARS-CoV-2 genome is stable.

The results are useful in the development of a safe and effective vaccine against SARS-CoV-2, as the more stable the virus's genome, the greater likelihood that a vaccine will be effective globally across populations.

Technology Networks
spoke with Professor Stefano Menzo, virologist, and Dr Valerio Onofri, geneticist, affiliates of the Department of Excellence of Biomedical Science and Public Health, Marche Polytechnic University in Ancona, to learn more about the findings.

Molly Campbell (MC): For our readers that may be unfamiliar, please can you explain how next-generation sequencing (NGS) is utilized to explore the genome of the SARS-CoV-2 virus?

Valerio Onofri (VO):
NGS is a high-throughput method to sequence DNA or RNA. Unlike the classic Sanger sequencing method, NGS provides millions to billions of short nucleotide sequence reads in just a few hours and at lower costs. This method is routinely used to find pathogenetic variants that cause inherited disease or cancer. It is also useful to discover the sequence of an unknown viral, prokaryote or eukaryote genome.

When a reference sequence becomes available, NGS labs can sequence a clinical or population sample, align the new sequence to the reference and annotate the differences to determine whether mutations have occurred. We are doing this work now to better understand the SARS-CoV-2 virus. The virus was first sequenced in December 2019 and in February 2020 in Wuhan, China where it originated. When the pandemic spread, many labs like ours began sequencing virus samples from local patients to detect variants and study their significance. NGS provides both fast whole genome sequencing and, thanks to sequencing redundancy, quasispecies analysis (analysis of both major and minor variants).

MC: Please can you tell us about The Ion AmpliSeq SARS-COV-2 Research Panel?

This panel was designed by Thermo Fisher Scientific to provide an efficient, high-throughput workflow for analyzing the entire SARS-CoV-2 genome on the Ion Torrent platform. Based on the targeted approach by amplicons method, it consists of about 250 PCR cycles to amplify the full SARS-COV-2 genome. Drawing on our expertise from routinely using this method for forensic and medical genetics, we helped Thermo Fisher validate the panel in virus isolates as well as throat/nasal swabs. It is now widely available for NGS-based research to better understand COVID-19.

MC: What have your analyses so far revealed about the genetic stability of the SARS-CoV-2 virus?

Stefano Menzo (SM):
So far, SARS-CoV-2 appears to be a relatively stable virus, meaning it does not display many variants in the quasispecies, compared to other known RNA viruses such as HCV or HIV.

MC: What does the SARS-
CoV-2 genome reveal about the evolutionary path of the coronavirus?

More sequencing of full-length genomes throughout the world will be necessary to better answer this question. For now, we can say the virus has started differentiating in the human population from a common ancestor at a slow/moderate pace.

MC: How can this data be utilized in the development of preventatives/ therapeutics against the COVID-19 outbreak?

Any vaccine will work best throughout the world if the virus is relatively confined geographically to limit the generation of escape mutants. The same is true for any antiviral treatment.

MC: What are your next steps in this research space?

We will continue to investigate the virus’s evolution by sequencing samples from patients with different clinical outcomes.

Professor Stefano Menzo, virologist, and Dr. Valerio Onofri, geneticist, affiliates of the Department of Excellence of Biomedical Science and Public Health, Marche Polytechnic University in Ancona, were speaking to Molly Campbell, Science Writer, Technology Networks.