As the world continues its fight against the SARS-CoV-2 crisis, the emergence of many new variants of the virus within the past several months has caused great concern, with questions being raised about their transmissibility, severity of the disease, and potential resistance to therapeutics and vaccines. The United Kingdom (UK) variant (501Y.V1 of B.1.1.7 lineage) and South African variant (501Y.V2 of B.1.351 lineage) have been detected in the US, and both variants have been shown to share the same N501Y mutation in the spike (S) gene that is associated with significantly increased transmissibility, which could further strain an already burdened health care system. The same N501Y mutation is also present in new variants that are currently emerging [1-3].
With ongoing uncontrolled transmission of SARS-CoV-2 around the world, sequence-based surveillance is necessary to identify, address, and track emerging variants of SARS-CoV-2. Scientists have feared many variants could be evolving in the US, and a recently concluded surveillance study in Columbus, Ohio, has confirmed those suspicions . Two new variants have been identified through surveillance efforts.
In this study conducted at The Ohio State University, researchers examined a set of 222 nasopharyngeal samples from April 2020 to January 2021 for surveillance purposes. Briefly, viral RNA was first extracted and purified, and then reverse-transcribed to cDNA, and a PCR-based test for SARS-CoV-2 was performed. For variant detection and analysis, next-generation sequencing (NGS) was performed, and the sequences were monitored for changes over time to identify mutations that emerged. This entire workflow was conducted using products developed by Thermo Fisher .
Through this study, researchers found two SARS-CoV-2 variants that emerged in December 2020 in Ohio, which likely evolved from a different viral backbone that was dominant in Columbus during the early months of the crisis. The first variant, COH.20G/677H, detected in late December 2020, was derived from a SARS-CoV-2 population with a 20C/20G clade backbone and was found to have single mutations in the S, N, and M genes. These mutations were more frequent by the week, surging from 10 percent to 60 percent of samples in three weeks, strongly suggesting increased transmissibility of this variant .
The second variant, COH.20G/501Y, was identified in only one sample. This variant was found to share the same N501Y mutation within the receptor binding domain of the S gene that is thought to increase the transmissibility of the UK (20I/501Y.V1) and South African (20H/501Y.V2) variants, but did not share the same changes in the consensus sequences as reported for these two variants, potentially indicating an independent acquisition of this variant (COH.20G/501Y) in the 20G clade branch. It is also known that the 20H/501Y.V2 variant was regularly present in Columbus samples during the early months of the crisis, suggesting this variant to be highly transmissible .
It is worth noting that these two variants were identified in a relatively small sample size, and it is likely there could be other variants that are yet to be identified, which could potentially explain the recent surge in cases in the US.
As we continue the fight against SARS-CoV-2 and set our sights toward recovery, global surveillance of the virus is necessary in order to get ahead of the mutations that can otherwise cause further setbacks. Thermo Fisher is here to aid you every step of the way—from large-scale testing to surveillance of new mutations and variants through targeted NGS. Whether your lab is conducting genetic surveillance of emerging viral mutations or are conducting SARS-CoV-2 detection and need to verify mutations, it is challenging to quickly assess which solution is right for your lab. Please fill out the form so that a technical specialist can contact you.
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- Horby P, Huntley C, Davies N et al. (2021) NERVTAG note on B.1.1.7 severity. SAGE meeting report.
- Centers for Disease Control and Prevention (2021) Science brief: Emerging SARS-CoV-2 variants. https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html
- Tu H, Avenarius MR, Kubatko L et al. (2021) Distinct patterns of emergence of SARS-CoV-2 spike variants including N501Y in clinical samples in Columbus Ohio. bioRxiv doi: https://doi.org/10.1101/2021.01.12.426407