Genomic sequencing performed by The Jackson Laboratory
JJAX’s COVID-19 testing laboratory in Connecticut, which has already processed more than 1.5 million samples using its PCR test for SARS-CoV-2 virus, is working to greatly expand genomic surveillance for Connecticut residents.
Breakdown of number of each variant sequenced by week. The “Other” category includes SARS-COV-2 variants not classified as variants of concern (VOC) or variants of interest (VOI) by the WHO.
Top graph shows total counts of each variant sequenced since the beginning of our project. Bottom graph has totals from the most recent week.
The data are organized by the month that the sample was collected, starting from the first full month in January 2021. It is important to note that not all samples positive for SARS-CoV-2 are sequenced. Many samples were selected for sequencing based on pre-screening for potential variants of concern based on targeted genotyping assays. Since not all samples are sequenced, the information presented is incomplete and does not represent all potential COVID-19 cases caused by variant strains
The SARS-CoV-2 virus has an RNA genome that is about 30,000 nucleotides long and encodes eleven genes. Genomic surveillance involves sequencing the complete genome from many isolates to understand how strains circulating in the community differ from one another.
SARS-CoV-2, like all viruses, evolves over time through the accumulation of mutations – changes in the genome sequence. Some mutations change the sequence of the encoded proteins, resulting in viruses that are more contagious, are resistant to antibody therapy, or reduce vaccine-induced protection. “Strain”, “variant” and “lineage” are often used interchangeably to indicate a group of viruses that share a set of mutations.
For more discussion of these terms, see these articles in Forbes and JAMA (may require subscription).
Identifying variants and new viral strains is a critical first step in understanding how SARS-CoV-2 is evolving in response to existing therapies, vaccines and tests. This information helps inform public health officials and aids in the development of public health responses to limit the spread of the virus as quickly as possible.