True Spread of AY.4.2 Variant, Which Could Spread Faster, Unclear Due to Sequencing Issues

Current data on the spread of the AY.4.2 COVID-19 variant appears to be uncertain as scientists work to publish sequencing information.

AY.4.2, an offshoot of the Delta variant, has made headlines in recent weeks due to its rapid spread in the U.K. where it now accounts for around 12 percent of new sequenced samples.

It is identified by new main mutations in its spike protein: A222V and Y145H. While studies into AY.4.2 are still ongoing, some scientists have suggested it may be better at spreading than previous Delta versions.

The World Health Organization (WHO) acknowledged AY.4.2 in its weekly epidemiological report on October 26, noting that over 26,000 cases had been reported from 42 countries at that time.

Keeping track of the variant as it spreads is no simple task. There have been large fluctuations in the reported spread of AY.4.2, particularly in the United States.

On Monday last week, Newsweek reported that AY.4.2 had been detected in 32 states with 130 cases reported in the country overall.

This was according to data from GISAID—a highly regarded global variant tracking network that relies on scientists uploading COVID sequencing data—that was then visualised by Outbreak.Info.

Today, however, Outbreak.Info shows that there have been only 11 cases reported in the U.S. from a total of 10 states. GISAID data showed similar figures.

Explaining this data discrepancy, Jeffrey Barrett, a COVID-19 geneticist at the U.K.'s Wellcome Sanger Institute, said the global sequencing ecosystem is currently experiencing issues.

"It's a complicated scientific problem to update the sequence classification system, entirely maintained by academics," he told Newsweek. "And usually that kind of thing happens on a time scale of years, whereas now the whole world expects daily updates, and occasionally things break in a kind of obvious way like where the number of states changes day to day."

Part of the problem is to do with the Pango COVID classification system that has become widespread throughout the pandemic and is responsible for variant names like B.1.1.7 or B.1.351 that many people will now be familiar with.

As COVID-19 produces such a mind-boggling amount of information, lineages are sometimes reclassified which can lead to temporary fluctuations in the data.

"There have been a couple of fixes to how the lineages are being classified by Pango," an Outbreak.Info spokesperson told Newsweek.

While AY.4.2 does not have a new name, these changes could be the reason behind the data discrepancies.

In a statement to Newsweek, GISAID acknowledged "fluctuations" in data recently and said it was working with researchers at the Pango network to avoid them happening in future.

GISAID notes on its website: "As new lineages become more widespread, additional genetic markers emerge. Lineage definitions may be updated to allow researchers to track these separately and permit a more fine-grained picture of how a variant is circulating.

"When these updates occur, all genomes in EpiCoV undergo reclassification by Pango which can lead to temporary fluctuations in the tallies of variants. Over-interpretation of these changes in numbers should be avoided."

As of Wednesday morning there had been 29,537 total sequences of AY.4.2 reported worldwide, according to Outbreak.Info. The vast majority of AY.4.2 sequences are from the U.K.

A stock photo shows a lab worker holding a coronavirus test tube and a swab. Virus sequencing allows scientists to keep track of COVID variants. stefanamer/Getty