The COVID-19 subvariant, which New York state health officials believe is significantly more contagious than the first descendant of the potent Omicron strain, now accounts for up to 73.3% of all viruses transmitted in the region, according to the new CDC circulate, which includes the Empire State data released on Tuesday.
Prevalence of BA.2.12.1, which health officials say appears to be at least 25% more transmissible than BA.2 (which is said to be 30% more contagious than its predecessor Omicron), has increased significantly faster in the agency’s New York area than nationally, as the latest weekly update shows.
The CDC puts it at (at least) 66.3% of COVID cases in the New York area, which for its purposes also includes New Jersey, Puerto Rico, and the British Virgin Islands, although BA.2.12.1’s share of the cases could be higher . In any case, this subvariant is locally the dominant strain, while the first Omicron variant, BA.2., has maintained its national dominance in recent weeks (56.4% of cases versus 42.6% for BA.2.12.1 ).
However, given the latest trends, BA.2.12.1 should assert its dominance in the United States before the end of this month.
CDC
The CDC updates its variant data weekly on Tuesdays.
Although no scientific evidence to date links BA.2.12.1 to more severe COVID-related illness or reduced vaccine efficacy at this time, the increased transmissibility seems clear. New York State, for example, is nearly half of the 79 U.S. counties classified by the CDC as having high risk of COVID-19 to the community.
None of the U.S. high-risk counties are in New York City, according to the CDC, but the five counties appear to be experiencing a kind of trickle-down effect. All counties except the Bronx, which has the second lowest full vaccination rate among the five, are now classified by the CDC as medium COVID alert areas.
The NYC Department of Health and Human Services variant tracker does not explicitly break out subvariant BA.2.12.1, but does point out that BA.2-linked subvariants are responsible for the overwhelming number of cases over the past month and a half or so. And the city’s COVID positivity rates are rising in line with increased transmission, data shows.
Many more BA.2.12.1 infections may go unreported. The proportion of positive COVID samples that have been genomically sequenced to isolate variants is a fraction of the total confirmed cases. The city completed this extensive work on just 4% of its cases in the most recent week of data, and the state sequenced fewer cumulatively (3.65% according to the CDC).
New York State
*New York City and Long Island are reported as one region because the vast majority of Long Island samples were sequenced in NYC labs and are reported in GISAID as NYC results.
In the Central New York region, which has had the highest case rates in the state since March, BA.2.12.1 was first detected in February and rose to 77% of sequences by April. The subvariant also accounted for more than half of the sequences in the Finger Lakes region and more than 25% of samples sequenced through April 20 in the state’s Capital, Mohawk Valley and Southern Tier regions.
All five of these regions have reinfection rates per 100,000 population above the national average, with Mohawk Valley being the highest among them (7.1). New York City’s reinfection rate remains below the moving state average (3.5 versus 4.6 reinfections per 100,000 people), but both numbers have risen recently.
New York’s reinfection data doesn’t account for vaccination, but the dashboard for breakthrough cases and hospitalizations does – and the story is similar there.
The rolling rate of new breakthrough cases per 100,000 population has increased every week since March 7, government data show. The weekly increases appear to have been most pronounced in late March, from 13 new breakthrough infections per 100,000 population in the week of March 21 to 34.2 in the week of April 25, the latest data available.
A look at the CDC’s COVID community level map shows the obvious impact.
New York’s hospitalization rate has also increased for fully vaccinated individuals, but to a much lesser extent. Hospitalizations are a delaying factor, so this jump didn’t happen until mid-April. The rolling hospitalization rate almost tripled from the week of April 11 (0.54) to the week of April 18 (1.48), although again several factors may be at play. State officials have not recently speculated as to the cause.
While much is still scientifically unknown about BA.2.12.1, health officials and experts pay close attention to the numbers.
New York City raised its COVID alert level to medium last week as cases across the five boroughs exceeded a rate of 200 per 100,000 people. It was the first time the health department had adjusted that level since the new system was introduced under the administration of Mayor Eric Adams earlier this year.
No new COVID protocol is currently being implemented in the city, but should the hospitalization rate exceed the CDC’s higher risk threshold of 10 per 100,000 and case rate of 200 per 100,000, indoor mask mandates could return citywide.
NYCDOH
Experts hope – and believe – that this will not be necessary.
While new case rates are rising, they remain well below the level they were during omicron’s peak surge in January. Most importantly, hospitalizations and deaths, the far more important metrics from a public health perspective, continue to decline.
In New York City, rolling COVID hospitalizations are up 7.5% over the past seven days compared to averages over the previous four weeks, which the city said is steady. The death rate continues to fall. Nationwide, 2,369 people have been hospitalized with COVID, more than double in the last month alone, according to Tuesday’s report. That total, however, is less than a fifth of where hospital admissions were during January’s surge.
And it’s eight times lower than the record 18,697 New Yorkers hospitalized with the virus in April 2020.
That’s why officials continue to urge caution about COVID protocol, but don’t panic.
“We’ve come a long way in the last two years, so let’s continue to use the tools we know help protect, treat and prevent serious illness from COVID-19,” Gov. Kathy Hochul said in a statement – as she herself is working to recover from last week’s diagnosis. “I know firsthand how testing can help stop the spread to our vulnerable loved ones, so let’s keep using this important tool. I also encourage every New Yorker to make sure you are fully vaccinated and up to date on your booster doses. And if you test positive, talk to your doctor about available treatments. This is how we will continue to get through the pandemic safely.”