Covid-19 Variants

COVID-19 Variants: Based on Genetic Sequencing of All Positive COVID-19 Tests MUSC Conducts

Updated: January 19th 2022

  • The graphic above shows the distribution of variants of COVID-19 in January of 2022.  
  • MUSC is sequencing COVID-19 positives samples collected at MUSC for PCR based-tested by Cepheid and Abbott testing systems that meet the requirement of having a diagnostic PCR threshold crossing number of less than 30 Ct.  
  • The CDC has created a classification system for SARS-CoV-2 variants that can be rapidly updated as new variants emerge in the United States. There are currently no variants of interest or high consequence identified in the United States.
  • • Variants of Concern (VOC)
    • Variants of Interest (VOI)
    • Variants Being monitored (VBM)
    • Variants of High Consequence (VOHC)
  • The World Health Organization (WHO) also has a classification system, but the variants classified as variants of concern can differ from those classified as variants of concern by the CDC. The difference in classification is because the CDC is classifying variants based on their presence in the United States and the WHO is basing classifications on the world population.
  • A variant of concern is defined by the CDC as a variant with evidence of increased transmission (spread from person to person), more severe disease (such as increased hospitalizations or deaths), reduced effectiveness of vaccines or COVID treatments (such as monoclonal antibodies), or diagnostic detection failures. According to the CDC, current variants of concern include Delta and Omicron.
  • Variants of Concern all have a couple of things in common:
    1. More mutations
    2. Many of these mutations occur in the Spike protein of SARS-CoV-2. The spike protein is critical for the virus to enter human cells, can affect our own immune system’s ability to recognize the virus, and can assist with the evasion of antibody treatment.
  • Variants being monitored (VBM) are defined by the CDC when the data indicates there is a potential or clear impact an approved or authorized medical countermeasures or have been associated with increased transmission or more severe disease, but are no longer in circulation in the United States population.
  • It is important to monitor the variants in circulation to also ensure that current diagnostic and antigen assays can detect the new variants identified in the population.
  • The nomenclature of the SARS-CoV-2 variants can be confusing because different organizations use different names for the same variants. The table below identifies how the different variants are named across the major organizations.

  • The Delta variant has a 50% increase transmission rate compared to the Alpha variant. Outcome, treatment, and vaccine response data is in the early stages of study. The majority of cases identified recently in South Carolina are the Omicron variant.
  • All of the AY lineages shown above are sub-lineages of Delta.
  • The Omicron variant was identified as a VOC by the WHO on November 26, 2021. This decision was based on the increased number of mutations present in the Spike Protein of SARS-CoV-2. The scientific community is hard at work trying to understand the characteristics of the omicron variant. Under study currently is how easily the variant spreads person to person compared to other variants, whether it causes more severe disease, to what extent the virus may evade the vaccine, and if natural immunity from previously having COVID-19 offers protection from reinfection by omicron.
  • The Alpha variant has a 50% increased transmission rate compared to the earlier strains of SARS-CoV-2 meaning that it can more easily pass from an infected person to another individual. There is also data to suggest that the severity of disease is greater with this variant strain.
  • Beta variant has a 50% increase transmission rate and has been shown to have a reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment.
  • Gamma variant has a reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment.
  • The Lambda variant was first sequenced in Peru in December of 2020. According to the (GISAID website), there are 705 documented cases of the Lambda variant in the United States (as of 7/15/2021). We have identified a single case collected at the end of April 2021.
  • More information on each variant is available from the CDC website (click below). This includes information on where each variant originated from, when it was first detected, and what its attributes are (Center for Disease Control and Prevention Website).
  • The time from specimen collection to sequence data reporting ranges between 1 and 4 weeks, depending on the number of positive cases identified at MUSC. When there are more positive cases, the frequency of sequencing runs is increased. 
  • Sequencing is performed using the Illumina NextSeq550Dx platform using the Illumina COVIDSeq RUO reagents.
  • The COVID-19 Sequencing Team at MUSC includes Drs. Julie Hirschhorn, Dariusz Pytel, Scott Curry, Bailey Glen, and James Madory. Previous team members include Frederick Nolte and Jaclyn Dunne.