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), 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.

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

Note: Variant of concern = variants with increased transmissibility, immune evasion, and/or virulence, supported by epidemiological or clinical evidence. Variant of interest = variants that share genetic traits also present in variants of concern, but without clear evidence of increased transmissibility, immune evasion, and/or virulence.

Variant B.1.1.7 (first detected in the UK)

Distribution and frequency of confirmed B.1.1.7 cases

Variants can only be confirmed through sequencing. This process takes more time and effort than diagnostic testing, so confirmed cases will be severely under-reported and will have a 2-3 week lag.

Figure 1: B.1.1.7 sequence-confirmed cases detected in Connecticut by week

Frequency of variant B.1.1.7 in Connecticut by county

Figure 2: B.1.1.7 sequence-confirmed cases detected in Connecticut by county

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.

Genetic relatedness of B.1.1.7 cases

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.

Figure 4: Phylogenetic relationship among viruses from lineage B.1.1.7. Green and mint green represent viruses collected in New York and Connecticut, respectively. For more details, click here.

Other variants of concern

B.1.351

The B.1.351 variant has been detected in Connecticut. It was first identified in New York on Feb 11th in a Fairfield County resident. See Table 1 for confirmed B.1.351 cases in Connecticut.

Figure 5: Phylogenetic relationship among viruses from lineage B.1.351. For more details, click here.

P.1

The P.1 variant has been detected in Connecticut. It was first reported on March 17th, 2021 (sample taken on March 3rd) from a New Haven County resident. See Table 1 for confirmed P.1 cases in Connecticut.

Figure 6: Phylogenetic relationship among viruses from the lineage P.1. For more details, click here.

B.1.427 and B.1.429

B.1.427 and B.1.429 were first detected in California, and the CDC recently classified these related lineages as variants of concern. They were first detected in Connecticut in early December, 2020. See Table 1 for confirmed B.1.427 and B.1.429 cases in Connecticut.

Figure 7: Phylogenetic relationship among viruses from the lineage B.1.429 For more details, click here.

Variants of interest that we are monitoring

B.1.525/B.1.526/R.1

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, B.1.526, and R.1, which are all found in Connecticut. We are actively conducting research to determine the clinical importance of each of these variants. See Table 1 for confirmed B.1.525, B.1.526, and R.1 cases in Connecticut.

Figure 8: Phylogenetic relationship among viruses from  lineage B.1.525.  For more details, click here.

Figure 9: Phylogenetic relationship among viruses from lineage B.1.526. 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.