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|
|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%|
Table 1. Number and frequency of sequenced cases per variant in Connecticut.
- *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.
- ***Delta numbers also include B.1.617.2 sublineages AY.1, AY.2, and AY.3.
- 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 of interest (VOI) = A variant with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity.
Figure 1. Estimated temporal frequencies of variants of concern (VOC) and variants of interest (VOI) in Connecticut identified through unbiased sequencing. Phylogenetic relationships of all VOC/VOIs in Connecticut can be visualized here.
Variant effective reproduction numbers (Rt)
Effective reproduction numbers (Rt) are estimates of the average number of secondary cases from a primary infection. Rt > 1 suggests that transmission is increasing, and Rt < 1 suggests that transmission is decreasing. We estimate Rt for each variant by combining the variant frequency estimates from our sequencing data with total daily reported COVID-19 cases from Connecticut. See our manuscript for more information about the methods.
Figure 2. Rt estimates for Alpha (B.1.1.7), Delta (B.1.617.2, AY.1, AY.2, and AY.3), Gamma (P.1), Other VOC/VOI (e.g. Beta, Iota, Epsilon), and Non-VOC/VOI (all lineages not currently listed as a VOC or VOI by the CDC). Estimated using a 3-week sliding window.
Frequency of probable B.1.1.7 cases
Figure 3. Overall test positivity (%) and presumed B.1.1.7 positivity (%) in tests performed by Yale-New Haven Hospital and Jackson Labs. Probable B.1.1.7 positivity defined as “spike gene target failure” (SGTF) frequency on the TaqPath SARS-CoV-2 diagnostic test.
SARS-CoV-2 mutations of interest
Figure 4. Estimated temporal frequency of all SARS-CoV-2 lineages in Connecticut containing the Spike E484K and N501Y mutations (dark orange) **potentially** associated with vaccine/immune evasion. These mutations commonly occur in Beta, Gamma, and some Alpha variants, as well as other emerging lineages. 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 variants by county
Figure 5. Proportion of variants of concern (VOC) and variants of interest (VOI) per county in Connecticut of all SARS-CoV-2 sequences identified through unbiased sequencing by Yale and JAX since April, 2021 (see map here).
Estimated temporal frequencies for all VOC/VOIs (Figure 1) and lineages with the E484K mutation (Figure 4) as shown above are broken down by some counties below.
SARS-CoV-2 variants by diagnostic lab
The majority of our unbiased sequencing is currently coming from the following diagnostic labs: Yale-New Haven Hospital, Jackson Laboratories, and Murphy Medical Associates. Other diagnostic labs will soon be included as the state expands their SARS-CoV-2 genomic surveillance program.
- Yale-New Haven Hospital: Tree, frequencies, and catchment area
- Jackson Laboratory: Tree, frequencies, and catchment area
- Murphy Medical Associates: Tree, frequencies, and catchment area
SARS-CoV-2 sequencing in Connecticut
Genomic sequencing of COVID-19 cases is required to confirm the presence of SARS-CoV-2 variants. These efforts are ramping up across the country (see CDC National Genomic Surveillance Dashboard).
Figure 6. 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 variant lineage. The full tree can be found on our Connecticut Nextstrain page.
Figure 7: 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.
- 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
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.
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