Avian Flu Diary: NY State DOH Statement on Omicron Subvariants BA 2.12 and BA.2.12.1

BA.2 surge - Credit CDC Nowcast

#16,696

Over the past 36 hours the internet has been abuzz over the press release (below) from the New York State Department of Health describing two new Omicron BA.2 sub-lineages - BA.2.12 and BA.2.12.1 - that are rapidly gaining ground in that state.

According to early analyses, both appear to have a transmissibility advantage over BA.2 of 23%-27%, with BA.2.12.1 slightly ahead of BA.2.12. At this time there is no evidence that either produce more severe illness than BA.2.

These transmission advantages are substantial, and suggest these emerging sub-lineages may contribute to yet another surge of the virus in the weeks and months ahead. Assuming of course, that something even more `biologically fit' doesn't emerge in the meantime.

While it will certainly dismay anyone banking on the idea that BA.2 was the last gasp of the pandemic, the continual emergence of new subvariants (and recombinants) is fully expected. Luckily, most will be mere flashes in the pan, and fade into obscurity.

A few, however, may bring with them traits that allow them to thrive. Identifying those - particularly early in the game - can be difficult.

For now, these BA.2 sublineages appear to have a substantial evolutionary advantage over BA.2, and so they are certainly worthy of our attention. Whether they will drive the next phase of the pandemic - or will be knocked off by a new contender - remains to be seen.

The press release from the NYS DOH follows, after which I'll have a brief postscript.

New York State Department of Health Announces Emergence of Recently Identified, Highly Contagious Omicron Subvariants in New York and Urges Continued Vigilance Against COVID-19
Department's Wadsworth Center Identifies Two Sub-lineages of BA.2—BA.2.12 and BA.2.12.1—Potentially Contributing to Increased Transmission Reported in Central New York and Surrounding Regions
Department Reminds All New Yorkers to Get Fully Vaccinated/Boosted, Consider Wearing a Mask in Public Indoor Spaces, Test Following Exposure/Symptoms, Seek Treatment/Stay Home if COVID-Positive and Consult with Healthcare Provider Regarding Treatments
In Collaboration with Laboratories Statewide, the Department Remains on Forefront of Global Effort to Monitor, Track, and Sequence Variants
ALBANY, N.Y. (April 13, 2022) The New York State Department of Health today announced the emergence of two Omicron subvariants in New York State, BA.2.12 and BA.2.12.1. Both variants are sub-lineages of BA.2, which now accounts for 80.6% of COVID-19 infections in New York. The subvariants have been estimated to have a 23% – 27% growth advantage above the original BA.2 variant. Over the past few weeks, the Department has been investigating higher than average infection rates in Central New York. Based on newly available data in the public database, GISAID, as well as additional data submitted directly to the Wadsworth Center from sequencing laboratories in New York, State health officials have determined that these highly contagious new variants are likely contributing to the rising cases.

For the month of March, BA.2.12 and BA.2.12.1 rose to collectively comprise more than 70% prevalence in Central New York and more than 20% prevalence in the neighboring Finger Lakes region. Data for April indicate that levels in Central New York are now above 90%. The Department's findings are the first reported instances of significant community spread due to the new subvariants in the United States. At this time, there is no evidence of increased disease severity by these subvariants, though the Department is closely monitoring for any changes.
"We are alerting the public to two Omicron subvariants, newly emerged and rapidly spreading in upstate New York, so New Yorkers can act swiftly," said State Health Commissioner Dr. Mary T. Bassett. "While these subvariants are new, the tools to combat them are not. These tools will work if we each use them: get fully vaccinated and boosted, test following exposure, symptoms, or travel, consider wearing a mask in public indoor spaces, and consult with your healthcare provider about treatment if you test positive. I thank the Department's scientists for leading this effort and those contributing to this work throughout New York and around the world."
The new subvariants were found through the robust surveillance infrastructure and testing network led by the Department's Wadsworth Center in collaboration with laboratories statewide. In addition to sequencing COVID-19 virus samples selected throughout New York State, the Wadsworth Center monitors all data submitted to public databases by many other sequencing laboratories throughout New York and across the country. Results are uploaded into public databases, primarily GISAID, and studied for a more complete view of virus trends and the distribution of variants from these analyses summarized over time. To expand the State's detection capabilities even further, the Department is accelerating early warning monitoring systems such as wastewater surveillance programming.
In light of today's news and elevated cases statewide, State health officials urge New Yorkers to continue to take precautions to limit the spread of COVID-19. The Department recommends all New Yorkers:
Get fully vaccinated and boosted when eligible.
Consider wearing a mask in public indoor spaces, regardless of vaccination status.
Test following exposure, symptoms, or travel.
If COVID-positive, stay home and consult with a healthcare provider about treatments.
Improve air ventilation or gather outdoors to reduce transmission and the risk of severe disease over the upcoming Easter and Passover holidays.
The New York State Department of Health reminds all New Yorkers that COVID-19 remains a public health risk to individuals of all ages. Short-term side effects of COVID-19 may include flu-like symptoms, fatigue, trouble breathing, fever or chills, muscle and body aches, and more. Severe symptoms can lead to serious illness and hospitalization. New Yorkers who are not vaccinated or up to date with vaccinations are at increased risk of developing severe disease.New Yorkers can schedule their free COVID-19 vaccine, booster, or additional dose by visiting the State's Am I Eligible website or vaccines.gov to find a nearby location.
The Department is closely monitoring the situation and will continue to communicate openly with New Yorkers. More about the Department's work to monitor, track, and sequence COVID-19 variants is here.
New Yorkers are encouraged to check COVID-19 case rates and new hospital admissions in their communities here. New Yorkers should stay updated on COVID-19 testing options here and treatment options here.

With millions of people infected each day - and some of those coinfected with more than one variant - the ability of the SARS-CoV-2 virus to reinvent itself is showing no signs of abating. This week we are focused on BA.2.12.1, but next week it could easily be BA.7, BA.8, or even a non-Omicron variant.

While we hopefully won't see the return of a more virulent COVID, that is far from guaranteed.

Although I'm as tired of this pandemic as the next guy, I'm still wearing a face mask in public, have been fully vaccinated (and boosted), and will likely take the 4th booster in the weeks ahead.