Variants SARS-CoV-2 B.1.1.7 were detected for the first time in Connecticut on January 6th, 2021.
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.
- So far 17 COVID-19 cases with the B.1.1.7 variant have been detected in Connecticut. Our group has sequenced 13 of these (all in New Haven County, where we do most of our surveillance), including the first two cases in the state on January 6th, 2021. The other four have been reported by The Jackson Labs (3, 1 sequence not yet available due to low coverage) and Quest Diagnostics (1). Our sequence data can be visualized on our custom Nextstrain page and in the Figure below.
- Most of the B.1.1.7 cases in Connecticut are results of independent introductions into the state, and are associated with genomes collected in other states in the Northeast, such as New York and New Jersey.
- The Connecticut Department of Public Health have conducted follow-up contract tracing to minimize onward transmission from these cases. However, we expect that there is community transmission of B.1.1.7 in Connecticut.
- 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.
- We also sequenced B.1.1.7 cases from other states: 2 from New York, 13 from New Jersey, and 10 from Illinois.
- 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 a 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.
- 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.
- We have not yet detected variants from the lineages B.1.351 (first detected in South Africa) or P.1 (first detected in Brazil) in Connecticut.
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 since January 6th, 2021 (click here to see original tree). Other red/pink B.1.1.7 samples came from other US states.
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.
Please direct all media inquiries to media@covidtrackerct.com.
Table 1. List of TaqPath Spike Gene Target Failure (SGTF) Samples sequenced by our lab at YSPH.
| # | ID | GISAID # | Collection Date | State | Lineage |
|---|---|---|---|---|---|
| 1 | USA/IL-Yale-S025/2021 | EPI_ISL_847829 | 2021-01-03 | Illinois | B.1 |
| 2 | USA/IL-Yale-S144/2021 | EPI_ISL_861760 | 2021-01-14 | Illinois | B.1 |
| 3 | USA/CT-Yale-S220/2021 | EPI_ISL_912167 | 2021-01-22 | Connecticut | B.1 |
| 4 | USA/CT-Yale-S047/2021 | EPI_ISL_861764 | 2021-01-05 | Connecticut | B.1.1.107 |
| 5 | USA/CT-Yale-S125/2021 | EPI_ISL_861768 | 2021-01-12 | Connecticut | B.1.1.107 |
| 6 | USA/CT-Yale-S154/2021 | EPI_ISL_861767 | 2021-01-18 | Connecticut | B.1.1.107 |
| 7 | USA/CT-Yale-S048/2021 | EPI_ISL_861734 | 2021-01-05 | Connecticut | B.1.1.220 |
| 8 | USA/CT-Yale-S124/2021 | EPI_ISL_861770 | 2021-01-12 | Connecticut | B.1.1.220 |
| 9 | USA/CT-Yale-S126/2021 | EPI_ISL_861745 | 2021-01-12 | Connecticut | B.1.1.220 |
| 10 | USA/IL-Yale-S024/2020 | 2021-12-01 | Illinois | B.1.1.282 | |
| 11 | USA/NJ-Yale-S122/2021 | EPI_ISL_861763 | 2021-01-07 | New Jersey | B.1.1.50 |
| 12 | USA/CT-Yale-S018/2021 | EPI_ISL_779153 | 2021-01-02 | Connecticut | B.1.1.7 |
| 13 | USA/CT-Yale-S019/2021 | EPI_ISL_779154 | 2021-01-04 | Connecticut | B.1.1.7 |
| 14 | USA/CT-Yale-S153/2021 | EPI_ISL_861736 | 2021-01-18 | Connecticut | B.1.1.7 |
| 15 | USA/IL-Yale-S112/2021 | EPI_ISL_861739 | 2021-01-06 | Illinois | B.1.1.7 |
| 16 | USA/IL-Yale-S115/2021 | EPI_ISL_861762 | 2021-01-07 | Illinois | B.1.1.7 |
| 17 | USA/IL-Yale-S116/2021 | EPI_ISL_861740 | 2021-01-07 | Illinois | B.1.1.7 |
| 18 | USA/IL-Yale-S120/2021 | EPI_ISL_861748 | 2021-01-08 | Illinois | B.1.1.7 |
| 19 | USA/IL-Yale-S121/2021 | EPI_ISL_861766 | 2021-01-08 | Illinois | B.1.1.7 |
| 20 | USA/IL-Yale-S140/2021 | EPI_ISL_861769 | 2021-01-14 | Illinois | B.1.1.7 |
| 21 | USA/IL-Yale-S146/2021 | EPI_ISL_861737 | 2021-01-15 | Illinois | B.1.1.7 |
| 22 | USA/IL-Yale-S147/2021 | EPI_ISL_861754 | 2021-01-15 | Illinois | B.1.1.7 |
| 23 | USA/NJ-Yale-S114/2021 | EPI_ISL_861743 | 2021-01-06 | New Jersey | B.1.1.7 |
| 24 | USA/NJ-Yale-S132/2021 | EPI_ISL_861732 | 2021-01-09 | New Jersey | B.1.1.7 |
| 25 | USA/NJ-Yale-S133/2021 | EPI_ISL_861761 | 2021-01-09 | New Jersey | B.1.1.7 |
| 26 | USA/NJ-Yale-S141/2021 | EPI_ISL_861741 | 2021-01-14 | New Jersey | B.1.1.7 |
| 27 | USA/NJ-Yale-S142/2021 | EPI_ISL_861757 | 2021-01-14 | New Jersey | B.1.1.7 |
| 28 | USA/NJ-Yale-S143/2021 | EPI_ISL_861759 | 2021-01-14 | New Jersey | B.1.1.7 |
| 29 | USA/NY-Yale-S107/2021 | EPI_ISL_861758 | 2021-01-08 | New York | B.1.1.7 |
| 30 | USA/CT-Yale-S131/2021 | EPI_ISL_912160 | 2021-01-16 | Connecticut | B.1.1.7 |
| 31 | USA/NY-Yale-S224/2021 | EPI_ISL_912169 | 2021-01-06 | New York | B.1.1.7 |
| 32 | USA/IL-Yale-S229/2021 | EPI_ISL_912170 | 2021-01-02 | Illinois | B.1.1.7 |
| 33 | USA/NJ-Yale-S230/2021 | EPI_ISL_912171 | 2021-01-18 | New Jersey | B.1.1.7 |
| 34 | USA/NJ-Yale-S233/2021 | EPI_ISL_912172 | 2021-01-19 | New Jersey | B.1.1.7 |
| 35 | USA/NJ-Yale-S234/2021 | EPI_ISL_912173 | 2021-01-19 | New Jersey | B.1.1.7 |
| 36 | USA/NJ-Yale-S235/2021 | EPI_ISL_912174 | 2021-01-18 | New Jersey | B.1.1.7 |
| 37 | USA/NJ-Yale-S239/2021 | EPI_ISL_912175 | 2021-01-21 | New Jersey | B.1.1.7 |
| 38 | USA/NJ-Yale-S241/2021 | EPI_ISL_912176 | 2021-01-21 | New Jersey | B.1.1.7 |
| 39 | USA/NJ-Yale-S242/2021 | EPI_ISL_912177 | 2021-01-23 | New Jersey | B.1.1.7 |
| 40 | USA/IL-Yale-S247/2021 | EPI_ISL_912178 | 2021-01-25 | Illinois | B.1.1.7 |
| 41 | USA/CT-Yale-S249/2021 | EPI_ISL_912179 | 2021-01-26 | Connecticut | B.1.1.7 |
| 42 | USA/CT-Yale-S250/2021 | EPI_ISL_912180 | 2021-01-26 | Connecticut | B.1.1.7 |
| 43 | USA/CT-Yale-S252/2021 | EPI_ISL_912181 | 2021-01-27 | Connecticut | B.1.1.7 |
| 44 | USA/CT-Yale-S253/2021 | EPI_ISL_912182 | 2021-01-27 | Connecticut | B.1.1.7 |
| 45 | USA/CT-Yale-S254/2021 | EPI_ISL_912183 | 2021-01-27 | Connecticut | B.1.1.7 |
| 46 | USA/CT-Yale-S255/2021 | EPI_ISL_912184 | 2021-01-27 | Connecticut | B.1.1.7 |
| 47 | USA/CT-Yale-S256/2021 | EPI_ISL_912185 | 2021-01-05 | Connecticut | B.1.1.7 |
| 48 | USA/CT-Yale-S105/2021 | 2021-01-11 | Connecticut | B.1.1.7 | |
| 49 | USA/CT-Yale-S106/2021 | 2021-01-11 | Connecticut | B.1.1.7 | |
| 50 | USA/IL-Yale-S109/2021 | EPI_ISL_861744 | 2021-01-04 | Illinois | B.1.2 |
| 51 | USA/IL-Yale-S110/2021 | EPI_ISL_861742 | 2021-01-04 | Illinois | B.1.2 |
| 52 | USA/IL-Yale-S123/2021 | EPI_ISL_861765 | 2021-01-07 | Illinois | B.1.2 |
| 53 | USA/NJ-Yale-S020/2020 | EPI_ISL_847840 | 2020-12-24 | New Jersey | B.1.2 |
| 54 | USA/AR-Yale-S193/2021 | 2020-12-31 | Arkansas | B.1.2 | |
| 55 | USA/AZ-Yale-S023/2020 | EPI_ISL_847836 | 2020-12-30 | Arizona | B.1.375 |
| 56 | USA/CT-Yale-665/2020 | EPI_ISL_752606 | 2020-12-13 | Connecticut | B.1.375 |
| 57 | USA/CT-Yale-S001/2020 | EPI_ISL_779137 | 2020-12-28 | Connecticut | B.1.375 |
| 58 | USA/CT-Yale-S002/2020 | EPI_ISL_779138 | 2020-12-31 | Connecticut | B.1.375 |
| 59 | USA/CT-Yale-S003/2020 | EPI_ISL_779139 | 2020-12-29 | Connecticut | B.1.375 |
| 60 | USA/CT-Yale-S004/2020 | EPI_ISL_779140 | 2020-12-31 | Connecticut | B.1.375 |
| 61 | USA/CT-Yale-S005/2020 | EPI_ISL_779141 | 2020-12-28 | Connecticut | B.1.375 |
| 62 | USA/CT-Yale-S006/2020 | EPI_ISL_779142 | 2020-12-28 | Connecticut | B.1.375 |
| 63 | USA/CT-Yale-S007/2020 | EPI_ISL_779143 | 2020-12-28 | Connecticut | B.1.375 |
| 64 | USA/CT-Yale-S008/2020 | EPI_ISL_779144 | 2020-12-28 | Connecticut | B.1.375 |
| 65 | USA/CT-Yale-S009/2020 | EPI_ISL_779145 | 2020-12-28 | Connecticut | B.1.375 |
| 66 | USA/CT-Yale-S010/2020 | EPI_ISL_779146 | 2020-12-28 | Connecticut | B.1.375 |
| 67 | USA/CT-Yale-S011/2020 | EPI_ISL_779147 | 2020-12-29 | Connecticut | B.1.375 |
| 68 | USA/CT-Yale-S012/2020 | EPI_ISL_779148 | 2020-12-29 | Connecticut | B.1.375 |
| 69 | USA/CT-Yale-S014/2020 | EPI_ISL_779149 | 2020-12-30 | Connecticut | B.1.375 |
| 70 | USA/CT-Yale-S015/2020 | EPI_ISL_779150 | 2020-12-29 | Connecticut | B.1.375 |
| 71 | USA/CT-Yale-S016/2021 | EPI_ISL_779151 | 2021-01-01 | Connecticut | B.1.375 |
| 72 | USA/CT-Yale-S017/2020 | EPI_ISL_779152 | 2020-12-29 | Connecticut | B.1.375 |
| 73 | USA/CT-Yale-S046/2020 | EPI_ISL_792557 | 2020-12-15 | Connecticut | B.1.375 |
| 74 | USA/CT-Yale-S100/2021 | EPI_ISL_861752 | 2021-01-05 | Connecticut | B.1.375 |
| 75 | USA/CT-Yale-S101/2021 | EPI_ISL_861750 | 2021-01-03 | Connecticut | B.1.375 |
| 76 | USA/CT-Yale-S102/2021 | EPI_ISL_861753 | 2021-01-05 | Connecticut | B.1.375 |
| 77 | USA/CT-Yale-S103/2021 | EPI_ISL_861771 | 2021-01-03 | Connecticut | B.1.375 |
| 78 | USA/IL-Yale-S118/2021 | EPI_ISL_861733 | 2021-01-08 | Illinois | B.1.375 |
| 79 | USA/IL-Yale-S119/2021 | EPI_ISL_861755 | 2021-01-08 | Illinois | B.1.375 |
| 80 | USA/IL-Yale-S135/2021 | EPI_ISL_861749 | 2021-01-11 | Illinois | B.1.375 |
| 81 | USA/IL-Yale-S137/2021 | EPI_ISL_861735 | 2021-01-12 | Illinois | B.1.375 |
| 82 | USA/IL-Yale-S139/2021 | EPI_ISL_861738 | 2021-01-13 | Illinois | B.1.375 |
| 83 | USA/IL-Yale-S148/2021 | EPI_ISL_861756 | 2021-01-15 | Illinois | B.1.375 |
| 84 | USA/IL-Yale-S149/2021 | EPI_ISL_861751 | 2021-01-16 | Illinois | B.1.375 |
| 85 | USA/IL-Yale-S150/2021 | EPI_ISL_861772 | 2021-01-16 | Illinois | B.1.375 |
| 86 | USA/MA-Yale-S111/2021 | EPI_ISL_861747 | 2021-01-05 | Massachusetts | B.1.375 |
| 87 | USA/NJ-Yale-S145/2021 | EPI_ISL_861746 | 2021-01-15 | New Jersey | B.1.375 |
| 88 | USA/NY-Yale-S021/2020 | EPI_ISL_847830 | 2020-12-27 | New York | B.1.375 |
| 89 | USA/TN-Yale-S049/2021 | EPI_ISL_847835 | 2021-01-05 | Tennessee | B.1.375 |
| 90 | USA/TX-Yale-S022/2020 | EPI_ISL_847839 | 2020-12-29 | Texas | B.1.375 |
| 91 | USA/IL-Yale-S151/2021 | EPI_ISL_912161 | 2021-01-17 | Illinois | B.1.375 |
| 92 | USA/CT-Yale-S197/2021 | EPI_ISL_912163 | 2021-01-04 | Connecticut | B.1.375 |
| 93 | USA/CT-Yale-S198/2021 | EPI_ISL_912164 | 2021-01-04 | Connecticut | B.1.375 |
| 94 | USA/CT-Yale-S199/2020 | EPI_ISL_912165 | 2020-12-29 | Connecticut | B.1.375 |
| 95 | USA/NC-Yale-S206/2021 | EPI_ISL_912166 | 2021-01-11 | North Carolina | B.1.375 |
| 96 | USA/CT-Yale-S221/2021 | EPI_ISL_912168 | 2021-01-15 | Connecticut | B.1.517 |
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