In collaboration with the the Connecticut Department of Public Health, 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), and variants of concern that may emerge. See the CDC’s webpage for more information.

Variant B.1.1.7 (first detected in the UK)

Figure 1. Cumulative B.1.1.7 cases detected in Connecticut by week

Frequency of variant B.1.1.7 in Connecticut by county

Figure 2. Cumulative B.1.1.7 cases detected in Connecticut by county


  • 63 COVID-19 cases with the B.1.1.7 variant have been detected in Connecticut. They have been detected in the following counties.
    • New Haven County: 51 B.1.1.7 cases (we do most of our surveillance in this county)
    • Fairfield County: 5 B.1.1.7 cases
    • Litchfield County: 3 B.1.1.7 cases
    • Hartford County: 2 B.1.1.7 cases
    • Windham County: 1 B.1.1.7 case
  • Our sequence data can be visualized on our custom Nextstrain page and in Figure 3 below. Here is what it tells us:
    • There have been several distinct introductions into Connecticut from Europe and from other states, such as New York and New Jersey.
    • The Connecticut Department of Public Health has conducted follow-up contract tracing to minimize onward transmission from these cases. The close genetic relatedness of the B.1.1.7 sequences from many of the cases, however, suggests that there is established community transmission of the variant in several places across the state. 
  • So far we cannot determine the relative frequency of the B.1.1.7 variants among the cases of COVID-19 in Connecticut, but its frequency is rising. We are actively pursuing research in this area to inform public health measures.
  • Many labs are using the TaqPath PCR test to screen for potential B.1.1.7 cases using “spike gene target failure” (SGTF) results. We have found that many of the viruses that cause SGTF belong to a new viral lineage (B.1.375). This lineage was recently described by our team and collaborators and not directly related to B.1.1.7, but it has the same 69-70 deletion that leads to the SGTF result with the TaqPath assay. This lineage (B.1.375) is not known to enhance transmission or evade immune responses. Caution is recommended while interpreting TaqPath SGTF results: not all viruses with this characteristic are B.1.1.7 variants.

Figure 3. SARS-CoV-2 from lineage B.1.1.7. Colored in mint green are the viruses sequenced from Connecticut (click here to see full tree). Other red/pink B.1.1.7 samples came from other US states.

Variant B.1.351 (first detected in South Africa)

Figure 4. SARS-CoV-2 from lineage B.1.351. The sample from New York (green) was isolated from a resident of Fairfield county.

Variant P.1 (first detected in Brazil)

  • P.1 has not yet been detected in Connecticut, though it is possible that it has been introduced and is circulating.

Variants not yet of concern, but that we are monitoring

  • One of the primary reasons for why we are concerned with the B.1.351 and P.1 variants is that they contain the E484K mutation in the spike gene. This mutation has shown to decrease neutralization from antibodies elicited from natural infection and some vaccines. The mutation is also found on other SARS-CoV-2 variants, such as B.1.525, and B.1.526.
  • B.1.429, first detected in California, is another variant not yet of concern which we are monitoring, as it contains the L452R mutation in the spike gene.
  • 7 COVID-19 cases associated with B.1.429 have been detected in Connecticut. 2 more have been detected in New York. (Figure 5)

Figure 5. SARS-CoV-2 from lineage B.1.429. Colored on mint green are the viruses sequenced from Connecticut (click here to see original tree). Other red/pink B.1.429 samples came from other US states.

  • We have detected 8 COVID-19 cases in Connecticut associated with B.1.525 (Figure 6)
  • We have detected 11 COVID-19 cases from the related B.1.526 variant that also has the E484K mutation (Figure 7).
  • We are actively conducting research to determine the clinical importance of each of these variants.

Figure 6. SARS-CoV-2 from lineage B.1.525. Colored on mint green are the viruses sequenced from Connecticut (click here to see original tree). Other red/pink B.1.525 samples came from other US states.


Figure 7. SARS-CoV-2 from lineage B.1.526. Colored on mint green are the viruses sequenced from Connecticut (click here to see original tree). Genomes shown on darker green are B.1.526 samples from New York.


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.