In collaboration with the Connecticut Department of Public Health, the Centers for Disease Control and Prevention, Yale University, Jackson Laboratories, and diagnostic laboratories across the state, we are conducting surveillance for SARS-CoV-2 variants. See the CDC’s webpage for more information.

SARS-CoV-2 variants in Connecticut

Pango LineageWHO LabelCDC ClassificationCumulative cases reported by the CDPH*Percent sequenced during previous week by Yale/JAX/CDC**Percent change from previous report
B.1.1.7AlphaVariant of concern332327.3%8.3%
B.1.351BetaVariant of concern400.0%0.0%
P.1GammaVariant of concern1760.0%-4.8%
B.1.617.2***DeltaVariant of concern8763.6%11.2%
B.1.427 / B.1.429EpsilonVariant of interest2100.0%0.0%
P.2ZetaVariant of interest90.0%0.0%
B.1.525EtaVariant of interest210.0%0.0%
B.1.526IotaVariant of interest18056.1%1.3%
B.1.617.1KappaVariant of interest20.0%0.0%
All lineages with E484KNASubstitutions of Therapeutic Concern10913.2%-11.1%
All lineages with L452RNASubstitutions of Therapeutic Concern59471.0%28.1%

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/CDC =  percent of each variant of all samples (unbiased) from weekly sequencing conducted by Yale University, Jackson Laboratories, and the Centers for Disease Control and Prevention for SARS-CoV-2 surveillance. The data may not represent all sequenced cases from the previous week.
  • ***Delta numbers also include B.1.617.2 sublineages AY.1, AY.2, and AY.3.
  • Variant of concern (VOC) = 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 (VOI) = 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, JAX, and the CDC. Phylogenetic relationships of all VOC/VOIs in Connecticut can be visualized here.

Variant effective reproduction numbers (Rt)

Effective reproduction numbers (Rt) are estimates of the average number of secondary cases from a primary infection. Rt > 1 suggests that transmission is increasing, and Rt < 1 suggests that transmission is decreasing. We estimate Rt for each variant by combining the variant frequency estimates from our sequencing data with total daily reported COVID-19 cases from Connecticut. See our manuscript for more information about the methods.

Figure 2. Rt estimates for Alpha (B.1.1.7), Delta (B.1.617.2, AY.1, AY.2, and AY.3), Gamma (P.1), Other VOC/VOI (e.g. Beta, Iota, Epsilon), and Non-VOC/VOI (all lineages not currently listed as a VOC or VOI by the CDC). Estimated using a 3-week sliding window.

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. Close to 100% of SGTF results are confirmed to be 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 and Fairfield Counties) 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 Mutations of interest

Figure 4. 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, JAX, and the CDC. Phylogenetic relationships of all lineages with the Spike E484K mutation in Connecticut can be visualized here.

Other mutations of interest in the spike gene:

SARS-CoV-2 variants by county

Figure 5. 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 April, 2021 (see map here). 

Estimated temporal frequencies for all VOC/VOIs (Figure 1) and lineages with the E484K mutation (Figure 4) 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).

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.1.617.2 variant lineage. The full tree can be found on our Connecticut Nextstrain page.

Figure 7: Phylogenetic relationship among viruses from lineage B.1.617.2. 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 SARS-CoV-2. State residents must follow the guidelines already in place set by the Connecticut Department of Public Health and the CDC.

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