What is a variant?
Viruses constantly change through a process called mutation. When a virus has one or more new mutations, it’s called a variant of the original virus. Since SARS-CoV-2, the virus that causes COVID-19, was discovered, there have been hundreds of variants identified and described. The original virus that was discovered in Wuhan has not been seen in the United States since the middle of 2020.
Are all variants important for public health?
Not necessarily. The World Health Organization (WHO) defines as the following:
- Variants of Concern: According to the WHO, a variant of concern contains changes that have resulted in one or more of the following: reduced efficacy of treatments or vaccine, increased disease severity, and increased spread from person to person.
- Variants of Interest: According to the WHO, a variant of interest contains changes that may result in reduced efficacy of treatments or vaccine, increased disease severity, and increased spread from person to person.
The CDC also uses the term Variants Being Monitored (VBM) as a general term for all variants of concern and variants of interest that are not the Delta variant.
Are variants determined for every positive COVID-19 test?
Not all positive COVID-19 tests proceed to sequencing for a variety of reasons. To determine which variant has infected an individual, a sample from that individual needs to be sequenced. Sequencing means performing additional techniques to determine the genetic makeup of the virus after initial detection.
Why is sequencing variants important?
Public health agencies track the number and geographic distribution in the population of variants that are designated as being of concern or of interest. This helps us to understand changes in the number of COVID-19 cases and hospitalizations and to plan for the future. For example, tracking a variant with high transmissibility, like the currently circulating Delta variant, can help hospitals prepare for a surge in cases.
The Wadsworth Center is currently sequencing COVID-19 virus specimens with a capacity up to approximately 100 per day. Specimens are selected at random from throughout the state to provide surveillance across all geographic locations and data analyzed across the entire sequence of the virus. The analyses include assessment for mutations that indicate variants of concern and variants of interest. Other laboratories in New York State are conducting similar work. These results from Wadsworth and other laboratories are uploaded into public databases, primarily GISAID. From this database, sequence data from all contributors can be downloaded and analyzed for a more complete picture of virus trends across the state and the distribution of variants from these analyses summarized over time.
Data as of May 25, 2022
The New York State Department of Health is monitoring the prevalence of SARS-CoV-2 variants, including the Omicron variant. The Department does this by studying data on sequences reported to two online databases of viral sequences: the GISAID repository and CDC’s national SARS-CoV-2 genomic surveillance program.
The World Health Organization (WHO) classified Omicron as a Variant of Concern on November 26, 2021. The Department of Health's Wadsworth Center Laboratory continues to actively monitor COVID-19 virus samples selected throughout the State to compare sequences and identify circulating and new variants, including Omicron. The Department also monitors all data submitted to public sequence databases by the many other sequencing laboratories throughout New York State and across the US, contributing to a robust and collaborative surveillance program for variant analysis. The Department will continue to communicate openly with New Yorkers as we closely follow WHO actions and work with our partners at the CDC. More information can be found at the CDC's Omicron Press Briefing and at the WHO's Update on Omicron.
The Omicron variant was first confirmed in New York State on December 2, 2021. During the winter Omicron wave that followed, the lineages BA.1 and BA.1.1 were most prevalent, and in February, a rapid growth of BA.2 began.
On April 13, 2022, the Department announced the emergence of two recently-identified Omicron subvariants in New York State, BA.2.12 and BA.2.12.1. Both subvariants are sub-lineages of BA.2, and at that time, were estimated to have a 23% – 27% growth advantage above the original BA.2 variant. BA.2.12.1 has been noted to be of higher concern, given additional mutations.
For samples of SARS-CoV-2 collected between May 8 -- May 21, 2022 from New York that are sequenced and uploaded into GISAID, 100% were the Omicron variant. During this time period 2.1% of Omicron sequences were lineage BA.1.1, 30.9% were BA.2, and 67.0% were BA.2.12.1.
Between May 15 and May 21, 2022 CDC’s program for HHS Region 2 (New York, New Jersey, Virgin Islands, Puerto Rico) estimated 100% of samples were the Omicron variant. During this time period 1.6% of Omicron sequences were lineage BA.1, 20.6% were BA.2, and 77.8% were BA.2.12.1.
Monitoring Omicron BA.2.12.1
For more information on the emergence of BA.2.12.1 in New York State, the graph below presents the percent of sequences in GISAID, with additional patient location information from laboratory databases, classified as BA.2.12.1 in each region over the past three months.
In the Central New York region, which has experienced the most elevated case rates in New York State since March 2022, BA.2.12.1 was first detected in February 2022 and rose to 77% of sequences by April 2022. Furthermore, in April BA.2.12.1 also represented >50% of sequences in the Finger Lakes region, and >25% of sequences in Capital Region, Mohawk Valley, and Southern Tier regions, based on sequences through April 20, 2022.
* New York City and Long Island are reported as one region because the vast majority of Long Island specimens were sequenced in New York City laboratories and are reflected in GISAID as New York City results.
Data Source Explanations
These data are pulled from the Global Initiative on Sharing Avian Influenza Data (GISAID) database, the world’s largest database for SARS-CoV-2 sequence data. The sequence data entered into GISAID may come from surveillance sequencing programs, more targeted cluster investigations, or other research.
From this database, we pulled only those sequences that were performed on samples from New York State, broken down by specific time frame of specimen collection. Because sequence uploads to the database can be delayed, data for the most recent time interval are based on a small number of specimens and should be interpreted with caution. When data are next abstracted, it is likely that the number of specimens for that interval will increase.
The CDC conducts general surveillance on a sample of SARS-CoV-2 specimens from around the United States. These samples are sent from commercial laboratories contracted with the CDC to sequence specimens from around the country, as well as public health labs in all US states and territories. The CDC presents these data nationally as well as broken down by HHS region.
From this database, we pulled HHS Region 2, which includes New York, New Jersey, the US Virgin Islands, and Puerto Rico. Because sequence uploads to the database can be delayed, results for the most recent time interval are based on a statistical projection from available specimens, and should be interpreted with caution. We additionally note that specimens from CDC’s program are uploaded into GISAID and thus the two data sources should not be considered fully-independent sources of information.
Why are there differences between the results from GISAID and CDC?
Sequencing is a time-intensive activity. Sequencing results obtained on a given day are typically based on specimens taken in the days and weeks prior. In a given most recent two-week period of sequence data from GISAID, the number of specimens may thus be lower and will typically come from the early portion of the period. As new results accrue over time, the results for this same period are expected to become more stable around the true variant proportions during the entire two weeks. To address these lags in information for the most recent weeks, CDC uses a statistical model called Nowcast to project variant proportions for more recent timeframes. This model is subject to assumptions and additional statistical uncertainty. The New York State GISAID data directly reflect sequences on specimens in a particular time period, with no statistical extrapolation. In the context of a rapidly-increasing variant, these factors may cause short-term differences between the data from both systems.
COVID-19 Variant Results
Variant prevalence across time
Estimates may differ slightly from graphs presented by CDC due to rounding.
- Centers for Disease Control and Prevention:
- World Health Organization: Tracking SARS-CoV-2 Variants
- Outbreak.info: New York, United States Mutation Report
- CoVariants: Variant: 21A (Delta)