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 interest identified by the CDC. See the CDC’s webpage for more information.

SARS-CoV-2 variants in Connecticut

VariantCountry first reportedCategoryCumulative cases reported by the CDPH*Percent sequenced during previous week by Yale/JAX**Percent change from previous report
B.1.1.7UKVariant of concern253264.3%6.1%
B.1.1.7 w/ E484KUKVariant of concern30.0%0.0%
B.1.351South AfricaVariant of concern280.3%-1.2%
P.1BrazilVariant of concern772.7%-0.7%
B.1.429USA (California)Variant of concern1240.0%0.0%
B.1.427USA (California)Variant of concern700.0%0.0%
B.1.525USA (New York)Variant of interest150.3%0.3%
B.1.526USA (New York)Variant of interest88522.5%7.2%
B.1.526.1USA (New York)Variant of interest1953.2%-3.1%
P.2BrazilVariant of interest70.0%0.0%
B.1.617IndiaVariant of interest00.0%0.0%
B.1.617.1IndiaVariant of interest00.0%0.0%
B.1.617.2IndiaVariant of interest10.0%-0.4%
B.1.617.3IndiaVariant of interest00.0%0.0%
Non-VOC/VOINANone25576.7%-8.6%
All lineages with E484KNASubstitutions of therapeutic concern79622.8%7.2%
All lineages with L452RNASubstitutions of therapeutic concern4122.6%-3.4%

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.

Figure 1. Estimated temporal frequencies of variants of concern (VOC) and variants of interest (VOI) in Connecticut identified through unbiased sequencing by Yale and JAX. White space indicates that there isn’t enough sequencing data to estimate which variants are present. Phylogenetic relationships of all VOC/VOIs in Connecticut can be visualized here.

Figure 2. Estimated temporal frequency of all SARS-CoV-2 lineages containing the Spike E484K mutation **potentially** associated with vaccine/immune evasion in Connecticut identified through unbiased sequencing by Yale and JAX. White space indicates that there isn’t enough sequencing data to estimate which variants are present. Phylogenetic relationships of all lineages with the Spike E484K mutation in Connecticut can be visualized here.

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 3 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 variants by county

Figure 4. Proportion of variants of concern (VOC) and variants of interest (VOI) per county in Connecticut of all SARS-CoV-2 sequences identified through unbiased sequencing by Yale and JAX since February, 2021. 

Estimated temporal frequencies for all VOC/VOIs (Figure 1) and lineages with the E484K mutation (Figure 2) as shown above are broken down by some counties below.

SARS-CoV-2 variants by diagnostic lab

The majority of our unbiased sequencing is currently coming from the following diagnostic labs: Yale-New Haven Hospital, Jackson Laboratories, and Murphy Medical Associates. Other diagnostic labs will soon be included as the state expands their SARS-CoV-2 genomic surveillance program.

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. Figure 3 shows how these efforts have changed throughout the pandemic.

Figure 5. Relative frequency of SARS-CoV-2 sequences generated by county in Connecticut in 2021.

Figure 6. 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 7: 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.

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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.