In collaboration with the Connecticut Department of Public Health, Yale University, Jackson Laboratories, and diagnostic laboratories across the state, we are conducting surveillance for SARS-CoV-2 variants of the lineage B.1.1.7 (first detected in the UK), B.1.351 (first detected in South Africa), P.1 (first detected in Brazil), B.1.427/B.1.429 (first detected in California), and variants of concern that may emerge. See the CDC’s webpage for more information.

SARS-CoV-2 variants in Connecticut

VariantCategoryCumulative cases reported by the CDPH*Percent sequenced during previous week by Yale/JAX**Percent change from previous reportPhylogenetic tree view
B.1.1.7Variant of concern103360.5%+9.6%Nextstrain
B.1.1.7 w/ E484KVariant of concern30.5%+0.5%Nextstrain
B.1.351Variant of concern110.7%+0.2%Nextstrain
P.1Variant of concern90.7%-0.1%Nextstrain
B.1.429Variant of concern1201.7%+0.2%Nextstrain
B.1.427Variant of concern550.5%+0.5%Nextstrain
B.1.525Variant of interest100.0%-0.3%Nextstrain
B.1.526Variant of interest30814.1%-2.9%Nextstrain
B.1.526.1Variant of interest734.5%-1.5%Nextstrain
P.2Variant of interest70.0%0.0%Nextstrain
Non-VOC/VOINone211216.8%-6.2%Nextstrain
All lineages with E484KSubstitutions of Therapeutic Concern34112.9%-2.1%Nextstrain
All lineages with L452RSubstitutions of Therapeutic Concern1459.6%+1.6%Nextstrain

Table 1. Number and frequency of  sequence-confirmed cases detected per variant in Connecticut.

*Cumulative cases reported by the CDPH = the total cases for each variant that are confirmed by sequencing and reported by the Connecticut Department of Public Health.

**Percent sequenced during previous week from Yale/JAX =  percent of each variant of all samples (unbiased) from weekly sequencing conducted by Yale University and Jackson Laboratories for SARS-CoV-2 surveillance.

Variant of concern = A variant for which there is evidence of an increase in transmissibility, more severe disease (increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.
Variant of interest = A variant with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity.

Frequency of probable B.1.1.7 cases

Many labs are using the TaqPath PCR test to screen for potential B.1.1.7 cases using “spike gene target failure” (SGTF) results. Initially, we found that many of the viruses that cause SGTF belong to a new viral lineage (B.1.375 – not a variant of concern). However, now we find that >90% of SGTF results are from B.1.1.7, and thus we characterize samples that cause SGTF as probable B.1.1.7.

Figure 1: Overall test positivity (%) and presumed B.1.1.7 positivity (%) in tests performed by Yale-New Haven Hospital (primary catchment = New Haven County) and Jackson Labs (primary catchment = New Haven and Hartford Counties). Probable B.1.1.7 positivity defined as “spike gene target failure” (SGTF) frequency on the TaqPath SARS-CoV-2 diagnostic test.

SARS-CoV-2 sequencing in Connecticut

Genomic sequencing of COVID-19 cases is required to confirm the presence of SARS-CoV-2 variants. These efforts are ramping up across the country (see CDC National Genomic Surveillance Dashboard). The map in Figure 2 shows where we are primarily sequencing from in Connecticut. Since March 2020, 0.63% of Connecticut COVID-19 cases were sequenced, and Figure 3 shows how these efforts have changed throughout the pandemic.

Figure 2. Relative frequency of SARS-CoV-2 sequences generated by county in Connecticut in 2021.

Figure 3. COVID-19 cases sequenced in Connecticut per epidemiological week.  Note that there is a 2-3 week lag from cases identified to sequenced and posted on data repositories.

Genetic relatedness of SARS-CoV-2 genomes from Connecticut

We created a custom Nextstrain page to visualize the relatedness of sequenced COVID-19 cases in the state. Below shows an enlargement of the B.1.1.7 variant lineage. The full tree can be found on our Connecticut Nextstrain page.

Figure 4: Phylogenetic relationship among viruses from lineage B.1.1.7. Mint green represents viruses sequenced from Connecticut. For more details, click here.


For more information on the importance of these variants, including why we are conducting this surveillance, please refer to our Variant Surveillance About page.

The best response to the new variant is to rely on the disease control measures that are known to work to prevent the spread of COVID-19. State residents must follow the guidelines already in place set by the Connecticut Department of Health and the CDC.

Please direct all media inquiries to media@covidtrackerct.com.