Covid-19 and Variants of Concern
Since its first occurrence in 2019, COVID-19 has been spreading globally infecting close to 165 million people and having killed more than 3.4 million people as of May19, 2021. The CDC has recommended self-protection measures such as wearing mask, keeping social distance, and washing hands often, and recently getting vaccinated. Although the infection control has improved in the US due to rapid and large population of adult vaccination, new variants of concern (VoC) have increased the transmission rate, the level of hospitalization, and death rate in different countries. Some of the VoCs may also escape the immune system response causing reinfections or not responsive to Vaccinations. These VoCs include B.1.1.7 (first identified in UK), B.1.351 (first identified in South Africa), B.1.1.28/P.1 (first identified in Brazil), B.1.427 and B.1.429 (first identified in Southern California), and most recently B.1.617 (first identified in India). A comprehensive report is worth reading to get better understanding of the SARS-CoV-2 variants.
Why Is It Important to Detect the VoC?
Detecting VoC is critical for controlling the spread of the dangerous variants. Detection of the new variants provides upfront information about their transmission speed and effects causing severity of the disease. Detection of the existing VoCs helps the tracking and surveillance of the virus spread in different countries and communities, and evaluation of the effect of vaccination. The information collected through detection effort is important for public health authorities to warn the public of the potential danger and enhance the public health and social measures to slow down the virus spread.
For variant detection, the United Kingdom is leading the sequencing effort and has 5 to 10% positive cases sequenced for the virus genome. The US CDC invested $200 million in sequencing investment and the U.S. government plans to spend $1.75 billion in the sequencing effort. Other countries have also closely monitored the virus genomic changes.
Methods Used for VoC Detection
Many genomic methods can be used for genotyping or detection of VoCs, including screening of known VoCs (SNP genotyping, RT-PCR, or CRISPR) or Sequencing ( Sanger sequencing and whole genome sequencing, WGS). The screening methods are powerful tools to find a known variant in a population, but they can’t be used to find emerging variants that could become VoC later. The sequencing methods, however, can be used to identify new variants as well as monitoring the existing VoCs by providing the exact sequence nature.
Sanger Sequencing as a Tool for Variant Identification
Sanger sequencing is an important tool for identification of both existing and new variants, providing tracking and surveillance information better than the screening methods. With a universal primer, the Sanger sequencing can cover the gene of the spike protein of the SARS-CoV-2 virus to identify any new or existing variants with point mutations or small indels in the spiking gene.
In comparison with WGS, Sanger sequencing is more cost-effective and can be done in more laboratories as genetic analyzers are common instrument in genomic or molecular diagnostics labs. However, Sanger sequencing does not replace WGS, as WGS can find emerging variants much faster because of the high throughput nature. But because WGS takes longer time, needs more bioinformatics expertise, and has other disadvantages as well, detection of known variants in a small population may be more efficient using Sanger sequencing.