NOTE: REPORT FOR SARS-CoV-2 VARIANT SURVEILLANCE INITIATIVE
HAS NOW MOVED TO A NEW DASHBOARD.
In collaboration with the Connecticut Department of Public Health, the Centers for Disease Control and Prevention, Yale University, Jackson Laboratories, and diagnostic laboratories across the state, we are conducting surveillance for SARS-CoV-2 variants. See the CDC’s webpage for more information.
SARS-CoV-2 variants in Connecticut
| Pango Lineage | WHO Label | CDC Classification | Cumulative sequenced cases* | Percent and total sequenced from past 3 weeks** | Percent change from previous report |
|---|---|---|---|---|---|
| B1.1.529/BA.1* | Omicron BA.1* | VOC | 12294 | 0% | 0.0% |
| BA.2 | Omicron BA.2* | VOC | 4962 | 19.9% (55) | -2.1% |
| BA.2.12.1 | Omicron BA.2.12.1* | VOC | 3117 | 64.9% (179) | -1.2% |
| BA.3 | Omicron BA.3* | VOC | 0 | 0.0% (0) | 0.0% |
| BA.4 | Omicron BA.4* | VOC | 68 | 6.2% (17) | 1.9% |
| BA.5 | Omicron BA.5* | VOC | 96 | 9.1% (25) | 1.5% |
| XE | Omicron XE* | VOC | 4 | 0.0% | 0.0% |
| XQ | Omicron XQ* | VOC | 1 | 0.0% | 0.0% |
| B.1.617.2/AY.*# | Delta | VOC | 17516 | 0.0% | 0.0% |
| B.1.1.7 | Alpha | VBM | 3525 | 0.0% | 0.0% |
| B.1.351 | Beta | VBM | 42 | 0.0% | 0.0% |
| P.1 | Gamma | VBM | 227 | 0.0% | 0.0% |
| B.1.427/429 | Epsilon | VBM | 214 | 0.0% | 0.0% |
| B.1.525 | Eta | VBM | 21 | 0.0% | 0.0% |
| B.1.526 | Iota | VBM | 1594 | 0.0% | 0.0% |
| B.1.617.1 | Kappa | VBM | 7 | 0.0% | 0.0% |
| B.1.621 | Mu | VBM | 120 | 0.0% | 0.0% |
| P.2 | Zeta | VBM | 9 | 0.0% | 0.0% |
| C.37 | Lambda | None | 21 | 0.0% | 0.0% |
| Non-VOC/VOI | NA | None | 2841 | 0.0% | 0.0% |
- *Cumulative sequenced cases = the total cases for each variant that are confirmed by sequencing and reported by the Connecticut Department of Public Health.
- **Percent sequenced from past 3 weeks = samples collected within three weeks of the report date and sequenced by a collaborating lab for unbiased SARS-CoV-2 surveillance.
- Variant of concern (VOC) = A variant for which there is evidence of an increase in transmissibility, more severe disease (increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.
- Variant being monitored (VBM) = A variant for which there are data indicating a potential or clear impact on approved or authorized medical countermeasures or that has been associated with more severe disease or increased transmission but are no longer detected or are circulating at very low levels in the United States, and as such, do not pose a significant and imminent risk to public health in the United States.
Omicron variant tracking through SGTF rates
“S-gene target failures” (SGTFs) are features of a specific PCR assay (TaqPath) that fails to detect the “S-gene target failures” (SGTFs) are features of a specific PCR assay (TaqPath) that fails to detect the spike gene of variants with a specific deletion. Most Omicron BA.1 sequences have this deletion and most Delta and Omicron BA.2 sequences do not, so tracking SGTFs is a proxy for BA.1. Sequencing is required to confirm. The data presented here are from the Yale New Haven Hospital Clinical Virology Lab, which mostly represents outpatient testing from southern Connecticut (Fairfield, New Haven, and New London Counties). They do not represent the trends for all of Connecticut.
SARS-CoV-2 variant trends in Connecticut
Variant frequencies in Connecticut from June 2021 to present. Browse the data yourself here.
Variant frequencies in Connecticut from June 2021 to present. Browse the data yourself here
Lineage frequencies in Connecticut from June 2021 to present. Browse the data yourself here.
SARS-CoV-2 mutations of interest
Temporal frequencies of SARS-CoV-2 mutations in the Spike protein at amino acid positions 484 and 501 in Connecticut. Viruses containing the Spike E484K and N501Y mutations are **potentially** associated with vaccine/immune evasion. See our manuscript for more details. Phylogenetic relationships of all lineages with the Spike E484K and N501Y mutations in Connecticut can be visualized here.
Other mutations of interest in the spike gene:
- L18F: Tree and frequencies
- K417N/T: Tree and frequencies
- L452R: Tree and frequencies
- S477N: Tree and frequencies
- E484K: Tree and frequencies
- N501Y/T: Tree and frequencies
- P681H: Tree and frequencies
SARS-CoV-2 sequencing in Connecticut
COVID-19 cases sequenced in Connecticut per epidemiological week. Note that there is a 2-3 week lag from cases identified to sequenced and posted on data repositories.
Genetic relatedness of SARS-CoV-2 genomes from Connecticut
We created a custom Nextstrain page to visualize the relatedness of sequenced COVID-19 cases in the state. Below shows an enlargement of the B.1.617.2 clade. The full tree can be found on our Connecticut Nextstrain page.
Phylogenetic relationship among viruses from lineage B.1.617.2. Mint green represents viruses sequenced from Connecticut. 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.
Resources
- CDC: SARS-CoV-2 classifications
- CDC: COVID-19 cases caused by variants
- CDC: National Genomic Surveillance
- Connecticut DPH: COVID-19 resources
- Jackson Laboratory: COVID-19 variant data
- Jackson Laboratory: Coronavirus Information
- Yale University: COVID-19 information
- Grubaugh Lab: Lab website
- Nextstrain code: Github
Acknowledgement
The data were retrieved from GISAID. We gratefully acknowledge the Authors form Originating and Submitting laboratories of sequence data on which the analysis is based.
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 SARS-CoV-2. State residents must follow the guidelines already in place set by the Connecticut Department of Public Health and the CDC.
Please direct all media inquiries to media@covidtrackerct.com.