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.
Table 1. Number of genomes detected per variant in Connecticut.
Note: VOC = variants with increased transmissibility and/or virulence, supported by epidemiological or clinical evidence. VOI = variants that share genetic traits also present in VOCs, but without clear evidence of being of concern.
Variant B.1.1.7 (first detected in the UK)
Figure 1: B.1.1.7 genomes detected in Connecticut by week
Figure 2: B.1.1.7 genomes detected in Connecticut by county
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 have 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.
Figure 3: TaqPath SARS-CoV-2 positivity and “spike gene target failure” (SGTF) frequency from tests performed by Yale New Haven Hospital.
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: 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
Figure 5: Phylogenetic relationship among viruses from lineage B.1.351. For more details, click here.
P.1 has not yet been detected in Connecticut, though it is possible that it has been introduced and is circulating.
Variants of interest that we are monitoring
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. See Table 1 for B.1.429 cases in Connecticut.
Figure 6: Phylogenetic relationship among viruses from the lineage B.1.429 For more details, click here.
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. We are actively conducting research to determine the clinical importance of each of these variants. See Table 1 for B.1.525 and B.1.526 cases in Connecticut.
Figure 7: Phylogenetic relationship among viruses from lineage B.1.525. For more details, click here.
Figure 8: 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.
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