SARS-CoV-2 variants in circulation in Connecticut
We are conducting surveillance for variants of the lineage B.1.1.7 (first detected in the UK), B.1.351 (first detected in South Africa), and other variants of concern, following preliminary data showing that these new SARS-CoV-2 variants may have higher potential of transmission.
- We have so far detected four COVID-19 cases with the B.1.1.7 variant in Connecticut (so far all in New Haven County, where we do most of our surveillance), with the first two cases reported on January 6th, 2021.
- The first B.1.1.7 cases in Connecticut were unrelated to each other and both were associated with travel (Ireland [Yale-S018] and New York State [Yale-S019]).
- The second two B.1.1.7 cases (Yale-S105 & Yale-S106) detected last week were household members of a case from January 6th (Yale-S019). See Figure 1.
- We also detected a B.1.1.7 case in Westchester County, NY (Yale-S107). This may be important as there were a lot of introductions from New York into Connecticut during the early pandemic.
- So far we cannot determine the relative frequency of the B.1.1.7 variants among the cases of COVID-19 in Connecticut, but it is still expected to be very rare. We are actively pursuing research in this area to inform public health measures.
- Since mid-December we sequenced 37 SARS-CoV-2 cases from Connecticut suspected of the B.1.1.7 variant by the TaqPath PCR test (SGTF, “spike gene target failure”) (see Table 1). Our sequence data can be visualized on our custom Nextstrain page.
- We have not yet detected variants from lineage (B.1.351), first detected in South Africa.
- Among the sequenced samples, 27 out of 37 (73%) of the SARS-CoV-2 genomes belong to a new viral lineage (B.1.375) recently described by our team and collaborators, not directly related to B.1.1.7, but also showing a 69-70 deletion that leads to the spike gene target failure with the TaqPath assay.
- Caution is recommended while interpreting TaqPath spike gene target failures: not all viruses with this characteristic are B.1.1.7 variants.
- Given that international and domestic travel is still occurring in the US, SARS-CoV-2 continues to be transmitted, and new variants will continue to emerge and spread across the country.
Figure 1. Variants from lineage B.1.1.7. Colored on mint green are Connecticut variants identified by our group at Yale School of Public Health on January 6th, 2021 (click here to see original tree).
Table 1. List of TaqPath Spike Gene Target Failure (SGTF) Samples sequenced by our lab at YSPH.
|ID||Collection Date||State||Lineage||GISAID #|
For more information on the importance of this variant, 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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