Covid-19 Variants

COVID-19 Variants: Based on Genetic Sequencing of All Positive COVID-19 Tests MUSC Conducts – Red and Yellow are Variants of Concern

Updated: September 23rd 2021

  • A team from the MUSC Molecular Pathology Laboratory are doing genetic sequencing of all positive COVID-19 testing samples for all COVID-19 tests that MUSC conducts to identify COVID-19 variants. The study team includes Drs. Julie Hirschhorn, Dariusz Pytel, James Madory, Frederick Nolte, Scott Curry, Bailey Glen and laboratory technologist Jaclyn Dunne.
  • MUSC is sequencing all COVID-19 positives samples collected at MUSC for PCR based-tested by Cepheid and Abbott testing systems.  
  • This graphic shows the distribution of variants of COVID-19 grouped by month.
  • Those shown in red/orange shades are “variants of concern” and in green shades are “variants of interest”, as classified by the CDC. The lambda variant has been classified by the World Health Organization (WHO) as a VOI, but has yet to be classified by the CDC as a VOI or VOC.
  • Some variants can have an impact on how easily the virus passes from an infected individual to another individual (transmission rate), response to the monoclonal antibody treatments is reduced for some variants, and increased disease severity.
  • The nomenclature of the variants can be confusing because different organizations use different names for the same variants. The table below identifies the label given by the various organizations.

  • The Alpha variant has a 50% increased transmission rate 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.
  • The 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.
  • The Gamma variant has a reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment.
  • The Delta variant has been shown to have an increased transmission rate. Outcome, treatment, and vaccine response data is in the early stages of study.
  • 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 2 and 4 weeks.
  • Sequencing is performed using the Illumina NextSeq550Dx platform using the Illumina COVIDSeq reagents.