The Importance of SARS-CoV-2 Genotyping in Clinical Care Settings

As the SARS-CoV-2 virus continues to evolve, variants of concern (VOC) have the potential to increase transmissibility and decrease the effectiveness of COVID-19 vaccines. For this reason, clinicians around the world have begun genotyping SARS-CoV-2 variants. The Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM) formed a joint committee to review the potential role of genotyping SARS-CoV-2 in clinical care settings, regulatory considerations of such programs, and emerging issues. This review was published in Clinical Infectious Diseases.

SARS-CoV-2 is an RNA virus with a genome of approximately 30 kilobases. The mutation rate of this virus is significantly decreased compared with other RNA viruses, such as HIV or influenza. The mutation rate of SARS-CoV-2 is approximately 1 mutation per genome per 2 weeks, which corresponds with 2 generations of host infection.

As of the summer of 2021, less than2 million SARS-CoV-2 genomes have been sequenced. Despite these data, there has been few instances in which information about SARS-CoV-2 variants has altered or benefited patient care.

The World Health Organization (WHO) and the United States Centers for Disease Control and Prevention (CDC) define SARS-CoV-2 variants of interest (VOI) as mutations which change the receptor binding, neutralization activity, therapeutic effect, or diagnostics.  They define SARS-CoV-2 VOC as mutations which increase both the transmissibility and severity of the disease.

Some frontline laboratories have begun to use allele-specific reverse transcription quantitative polymerase chain reaction (RT-qPCR) genotyping to identify SARS-CoV-2 VOI and VOC. The use of RT-qPCR also mitigates the demand for whole-genome sequencing, requires less viral RNA than other methods to generate similar results, and allows multiple mutations to be analyzed simultaneously. The researchers noted, however, that RT-qPCR testing may not be effective in identifying the correct lineage of the virus. In addition, continuous updates to the design of RT-qPCR assays are needed as new SARS-CoV-2 variants continue to emerge.

Whole-genome sequencing of SARS-CoV-2 typically uses an amplicon tiling approach. Multiple companies have developed specific protocols for SARS-CoV-2 in response to demand, with a greater than 99% recovery rate of the SARS-CoV-2 genome. This strategy is more costly and time consuming but likely more accurate than RT-qPCR genoytyping. The researchers noted that clinicians using this approach should share consensus SARS-CoV-2 genomes with the Global Initiative on Sharing All Influenza Data (GISAID) and/or with GenBank databases.

The researchers noted that no assays have been authorized by the Food and Drug Administration (FDA) for SARS-CoV-2 genotyping. In addition, any assay developed for clinical practice in the US needs to be validated in a high complexity laboratory in accordance with regulations defined in the Clinical Laboratory Improvement Amendments.

The researchers recommended that clinicians report SARS-CoV-2 VOI and VOC to the WHO; the updated list of known VOI and VOC can be found here.  They also noted that clinicians should report SARS-CoV-2 coding mutations, especially those from the spike protein. Reporting coding mutations is standard practice for other viruses and also allows for the analysis of specific mutations as new genotypic-phenotypic data emerge.

Although much of these data have not been applied in clinical practice, SARS-CoV-2 variants which alter the effectiveness of monoclonal antibody treatments have been identified. For example, SARS-CoV-2 variants that contain L452R or E484K   mutations have been found to decrease susceptibility to bamlanivimab. In addition, decreased susceptibility to etesevimab has been found among variants which contained K417T or K417N mutations. Of note, the US government temporarily halted the distribution of these antibodies to multiple states due to the increased prevalence of these VOC.

Although whole-genome sequencing may be effective in detecting single-source infectious outbreaks in healthcare facilities, sufficient phylogenetic analysis is required to discern between a cluster of infections from a common lineage and those with a rare lineage from an instance of nosocomial transmission. Additional evidence of healthcare-associated transmission may be needed to alter or expedite prevention strategies in clinical practice.

Data on SARS-CoV-2 VOC may also aid in cohorting patients on the basis of viral genotype, especially for those hospitalized at older facilities with limited single-bed rooms. In clinical settings with an increased SARS-CoV-2 transmission risk, as well as in communities with multiple VOC co-circulating, infected patients with the same VOC should be roomed together to decrease the risk for recurrent infection .

SARS-CoV-2 genotyping has been critical for monitoring the COVID-19 pandemic and identifying causes of diagnostic or therapeutic failure. In an era in which genotyping has become standard care for other diseases, such as some cancers, the COVID-19 pandemic has demonstrated that tracking specific SARS-CoV-2 variants may be clinically beneficial. To routinely assess viral variants at scale, increase turnaround time, and decrease healthcare costs, cooperation is needed between private laboratories and public health facilities, as well as consensus protocols for genotyping SARS-CoV-2 variants.

Disclosure: Multiple authors declared affiliations with industry. Please see the original reference for a full list of disclosures.

Reference

Greninger AL, Bard JD, Colgrove RC, et al. Clinical and infection prevention applications of SARS-CoV-2 genotyping: an IDSA/ASM consensus review document. Clin Infect Dis. 2021;ciab761. doi:10.1093/cid/ciab761