SARS-CoV-2 variants in Connecticut

Pango Lineage	WHO Label	Category	Cumulative cases reported by the CDPH*	Percent sequenced during previous week by Yale/JAX**	Percent change from previous report
B.1.1.7	Alpha	Variant of concern	3191	56.5%	-10.7%
B.1.351	Beta	Variant of concern	38	2.2%	2.2%
P.1	Gamma	Variant of concern	123	10.9%	2.7%
B.1.429 / B.1.427	Epsilon	Variant of concern	200	0.0%	0.0%
B.1.525	Eta	Variant of interest	19	0.0%	0.0%
B.1.526	Iota	Variant of interest	1006	10.9%	2.7%
B.1.526.1		Variant of interest	253	2.2%	-1.1%
P.2	Zeta	Variant of interest	9	0.0%	0.0%
B.1.617		Variant of interest	0	0.0%	0.0%
B.1.617.1	Kappa	Variant of interest	3	0.0%	0.0%
B.1.617.2	Delta	Variant of concern	32	6.5%	3.2%
B.1.617.3		Variant of interest	0	0.0%	0.0%
Non-VOC/VOI	NA	None	2805	10.9%	1.1%
All lineages with E484K	NA	Substitutions of therapeutic concern	1004	25.4%	8.9%
All lineages with L452R	NA	Substitutions of therapeutic concern	527	11.9%	6.1%

Table 1. Number and frequency of  sequence-confirmed cases detected per variant in Connecticut.

• *Cumulative cases reported by the CDPH = the total cases for each variant that are confirmed by sequencing and reported by the Connecticut Department of Public Health. 
• **Percent sequenced during previous week from Yale/JAX =  percent of each variant of all samples (unbiased) from weekly sequencing conducted by Yale University and Jackson Laboratories for 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 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.
• As of 5/12/2021, CDC updated the list of VOI to include both B.1.526 and B.1.526.1 separately. In previous reports, all B.1.526 sublineages (B.1.526, B.1.526.1, B.1.526.2) were included in this report as B.1.526. CDC also included as VOI the lineages detected in India: B.1.617, B.1.617.1, B.1.617.2, and B.1.617.3.

Figure 1. Estimated temporal frequencies of variants of concern (VOC) and variants of interest (VOI) in Connecticut identified through unbiased sequencing by Yale and JAX.A breakdown of lineage B.1.526 into sublineages B.1.526.1 and B.1.526.2 can be found here. Phylogenetic relationships of all VOC/VOIs in Connecticut can be visualized here.

Frequency of probable B.1.1.7 cases

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 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, and thus we characterize samples that cause SGTF as probable B.1.1.7.

Figure 2. Overall test positivity (%) and presumed B.1.1.7 positivity (%) in tests performed by Yale-New Haven Hospital (primary catchment = New Haven and Fairfield Counties) and Jackson Labs (primary catchment = New Haven and Hartford Counties). 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 3. Estimated temporal frequency of all SARS-CoV-2 lineages containing the Spike E484K mutation **potentially** associated with vaccine/immune evasion in Connecticut identified through unbiased sequencing by Yale and JAX. Phylogenetic relationships of all lineages with the Spike E484K mutation 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
• N501Y/T: Tree and frequencies
• P681H: Tree and frequencies

SARS-CoV-2 variants by county

Figure 4. 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 2) as shown above are broken down by some counties below.

• New Haven: VOC/VOIs | E484K 
• Fairfield: VOC/VOIs | E484K
• Hartford: VOC/VOIs | E484K

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). The map in Figure 5 shows where we are primarily sequencing from in Connecticut. Figure 6 shows how these efforts have changed throughout the pandemic.

Figure 5. Relative frequency of SARS-CoV-2 sequences generated by county in Connecticut in 2021.

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.1.1.7 variant lineage. The full tree can be found on our Connecticut Nextstrain page.

Figure 7: Phylogenetic relationship among viruses from lineage B.1.1.7. Mint green represents viruses sequenced from Connecticut. For more details, click here.

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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

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Please direct all media inquiries to media@covidtrackerct.com.