SARS-CoV-2 Gene Variants Provide Clues to Coronavirus’ Epidemiology

Two teams of infectious disease researchers in Italy say they have further analyzed the SARS-CoV-2 genome from samples acquired locally to generate early data that reveal a level of genetic variability suggesting the rapidly spreading virus’s genome is stable. The findings, developed using a new next-generation sequencing (NGS) research assay from Thermo Fisher Scientific, increase the likelihood that future coronavirus vaccines can have a higher rate of effectiveness and could help the global scientific community’s effort to better understand the epidemiology and spread of COVID-19.

The two independent research teams from “Lazzaro Spallanzani” National Institute for Infectious Diseases (IRCCS) in Rome and the Forensic Division of the Department of Biomedical Sciences and Public Health (DSBSP) at Ancona University Hospital sequenced multiple samples and identified the presence of gene variants when compared against the original Wuhan coronavirus reference genome. Viruses that mutate rapidly over short periods of time make it challenging to develop effective vaccines that protect people against infection. The low number of variants discovered in the Italian samples two months after the virus was first sequenced in China suggests that SARS-CoV-2, which has infected more than an estimated 64,000 people in Italy and 380,000 globally, is a relatively slow-mutating pathogen. Both teams in Italy carried out the sequencing work with Thermo Fisher’s new Ion AmpliSeq SARS-COV-2 Research Panel, which features a 24-hour, end-to-end workflow.

“The ability to very quickly run multiple samples and accurately decipher key changes in the virus’s genetic code will be crucial for the global scientific community to stay ahead of SARS-CoV-2 and to develop strategies against it that, ultimately, can be leveraged to help resolve the pandemic,” said Dr. Maria Rosaria Capobianchi, head of the Virology Department, Lazzaro Spallanzani National Institute for Infectious Diseases, which was the first research center in Europe to generate whole genome sequencing data of the coronavirus using Thermo Fisher’s Ion Torrent NGS platform. “Viral genomes are dynamic and these preliminary data need further analysis to determine the biological significance of the gene variants and to investigate the evolutionary path of the coronavirus.”

Professor Stefano Menzo, head of Virology at Ancona University Hospital, said: “Had we investigated other viruses we might have expected up to dozens of new mutations after so many infectious cycles in patients. Our initial data show that this is a very stable RNA virus, with only five novel variants. A virus with a stable genome is good news for vaccine development because it indicates that the effectiveness of vaccines could be more consistent, possibly over many years.”

The scientists now plan to further analyze the data with Thermo Fisher’s new Ion SARS-CoV-2 analysis solution for variant annotation and consensus sequencing assembly to better understand the impact on disease severity, mode of transmission, and phylogenetic studies. The Ion AmpliSeq SARS-COV-2 Research Panel is a targeted NGS solution that analyzes the entire SARS-CoV-2 genome. It provides an efficient, high-throughput end-to-end workflow for monitoring genomic evolution, which is critical during a rapidly developing pandemic. The panel is optimized to run on the Ion GeneStudio S5 Systems.

Panel Optimization for Genexus System Underway 

To further expedite NGS analysis of SARS-CoV-2 and to help meet growing customer demand, Thermo Fisher has begun to optimize the Ion AmpliSeq SARS-COV-2 Research Panel for the Ion Torrent Genexus System. Launched in November 2019, the company’s newest sequencing platform automates the entire targeted NGS workflow and can deliver specimen to report economically in as little as 14 hours. Optimization and validation of the research panel on the Genexus System is now underway in collaboration with Thermo Fisher customers.

“Thermo Fisher’s immediate response to first develop a PCR SARS-CoV-2 diagnostic assay and now a next-generation sequencing research solution to help customers investigate coronavirus is at the core of our mission,” said Peter Silvester, senior vice president and president of Life Sciences Solutions at Thermo Fisher Scientific. “We share the global community’s heightened concern during this unprecedented public health crisis and, for this reason, we are continuing to maximize our efforts to provide our laboratory partners, infectious disease researchers and vaccine developers with the most advanced tools in support of their very important work.”