Omicron BA.2 sub-variant spreading in New York City

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The BA.2 omicron COVID-19 sub-variant is spreading in New York City. 

According to New York State health department data, BA.2 is doubling in proportion statewide every two weeks and represents about one in 10 sequenced cases. 

“Between February 27 and March 5, 2022 CDC’s program for HHS Region 2 (New York, New Jersey, Virgin Islands, Puerto Rico) estimated 100% of samples were the omicron variant, compared to 100% in the previous one-week period. During this time period, 82.7% of omicron sequences were lineage BA.1.1.529, and 17.3% were BA.2,” the state reported. 


The Centers for Disease Control and Prevention (CDC) shows the trend in similar data for New York and New Jersey.

This comes as COVID-19 cases have fallen in the Big Apple and around the nation since the winter’s surge. COVID-19 risk is considered low in most of New York state and the city.

Gothamist has reported that city wastewater surveillance is revealing an increase in coronavirus readings over recent weeks. 

People walk though Times Square during the coronavirus disease (COVID-19) pandemic in the Manhattan borough of New York City, New York, U.S., November 10, 2021.
(REUTERS/Carlo Allegri)

One estimate suggests BA.2 – nicknamed the “stealth” variant – is about 30% more contagious than BA.1.

The sublineage has been found to have a higher growth rate compared to BA.1, though the World Health Organization (WHO) reported last week that BA.1.1 remains predominant.

In a weekly update, the agency said an analysis of GISAID data exhibits a growth rate advantage of BA.2 over the BA.1 lineage, “with a pooled mean transmission advantage of 56% under the assumption of an unchanged generation time.”

In a February statement, the WHO explained that BA.2 differs from BA.1 in its genetic sequence, including some amino acid differences in the spike protein and other proteins. 


“BA.2 Studies have shown that BA.2 has a growth advantage over BA.1. Studies are ongoing to understand the reasons for this growth advantage, but initial data suggest that BA.2 appears inherently more transmissible than BA.1, which currently remains the most common omicron sublineage reported.  This difference in transmissibility appears to be much smaller than, for example, the difference between BA.1 and delta. Further, although BA.2 sequences are increasing in proportion relative to other omicron sublineages (BA.1 and BA.1.1), there is still a reported decline in overall cases globally,” it wrote. 

Studies are also evaluating the risk of reinfection with BA.2 compared to BA.1. 

The WHO highlighted that, for patients in the United Kingdom, there was no difference in the risk of hospitalization from original omicron for those infected with BA.2. 

Additionally, in a release, it noted that real-world data on clinical severity from South Africa, the United Kingdom and Denmark indicated there was “no reported difference in severity” for the variants of concern.

Throughout the omicron surge, vaccines have continued to be highly effective against hospitalization.

“In terms of early studies, we have not seen any studies that suggest it’s more severe, nor have we seen studies that suggests that it will evade our vaccines any more so than omicron has already – and, in fact, that our vaccines will work just like it has with omicron,” CDC Director Dr. Rochelle Walensky said at a February White House COVID-19 response team briefing.

However, while omicron variants are milder than delta, a CDC study shows that they’re three to five times deadlier than pre-delta variants.