Two new omicron variants JN.1 and HV.1 under scrutiny in US

EG.5 and HV.1 responsible for over 45% infections according to latest CDC update

The Centres for Disease Control and Prevention (CDC), part of the United States Department of Health and Human Services, flagged a new mutation of COVID-19’s omicron variant BA.2.86, called JN.1, in a report last week.

With limited information, they said they cannot comment on whether it will spread more widely as they are still determining its characteristics. 

The variant has been in circulation in 11 countries, namely the United Kingdom, Iceland, Portugal, Spain, and the Netherlands. JN.1 was first detected in September 2023 in the United States. The variant is not yet a cause for worry and currently represents only 0.1 per cent of SARS-CoV-2 viruses in the US, whereas 99 per cent belong to the XBB group of the Omicron variant.

Read more: Consider updating COVID-19 vaccine composition to include omicron: WHO to authorities

As BA.2.86, its ancestor had more than 30 mutations, it was feared to have a growth advantage. However, this sub-variant just contains an extra spike mutation, namely L455S, which is suspected to be able to evade immunity just as much.

On the key difference, L455S mainly escapes Class 1 neutralising antibodies, which made up for the weakness of BA.2.86, Chinese scientist Yunlong Richard Cao said on X, formerly known as Twitter.

“Reassuringly, BA.2.86 was not more resistant to human sera than the currently dominant XBB.1.5 and EG.5.1, indicating that the new subvariant would not have a growth advantage in this regard. Importantly, sera from patients who had XBB breakthrough infection exhibited robust neutralising activity against all viruses tested, suggesting that upcoming XBB.1.5 monovalent vaccines could confer added protection,” researchers at the Columbia University Vagelos College of Physicians and Surgeons wrote in their paper published in Nature journal.

BA.2.86, the previous variant, did not spread efficiently, similarly, the JN.1 variant may not take off, Amesh Adalja, a senior scholar at the Johns Hopkins University Center for Health Security, told Down to Earth (DTE). 

Read more: The ‘kraken’ COVID variant XBB.1.5 is rising quickly in the US — here’s what it could mean for the UK

Before this latest sub-variant arrived on the scene, another variant had taken over the US towards the end of the summer season. Thereafter, August, September, and October saw a surplus of hospital admissions.

HV.1, a derivative of EG.5, accounts for 25.2 per cent of all circulating variants in the country, surpassing the presence of EG.5 responsible for 21 per cent of all infections in the country. 

EG.5 was first found in the country in April. Together, both EG.5 and HV.1 are responsible for over 45 per cent of infections according to the latest CDC update between October 15 and October 28.

Dr Dan Barouch, at Beth Israel Deaconess Medical Center in Boston, told newspaper The New York Times that one of the few additional mutations in HV.1 has likely given it an edge over EG.5, increasing its transmissibility and boosting its ability to escape immunity

Without data on how well the new vaccines perform against HV.1, he doesn’t believe it will be substantially different from their efficacy against EG.5.

“New variants of SARS-CoV-2 are expected to continue to emerge. Some variants will emerge and disappear, while others will emerge and continue to spread and may replace previous variants,” the CDC said.

Adalja told DTE that there is always going to be a dominant variant that is going to be most transmissible: one that is on top, one that is rising. It will always be this way within an endemic respiratory virus. Unless there is a significant behavior change, wherein the virus starts causing more severe disease, the general public need not be notified of every variant change.

Between September 18 and October 15, the highest numbers of hospitalisations were reported in the US (68,409), Mexico (6,214), and Greece (3,793), according to the World Health Organization (WHO)’s epidemiological update on October 27, 2023.

Read more: Lifecycle of COVID-19: Yet another omicron sub-variant has countries on high alert

However, reported cases do not accurately represent infection rates due to the reduction in testing and reporting globally. Between September 25 and October 22, only 40 per cent (93 of 234) of countries reported at least one case to WHO.

About 24,265 SARS-CoV-2 genetic sequences were shared between September 25 and October 22 with the Global Initiative on Sharing All Influenza Data, a global database of genomic sequences.

The WHO is monitoring three variants of interest: XBB.1.5, XBB.1.16, and EG.5. There are six variants under monitoring: BA.2.86, DV.7, XBB, XBB.1.9.1, XBB.1.9.2 and XBB.2.3

Globally, EG.5 represents 45.8 per cent of sequences and has been reported by 87 countries, the update said. As of October 22, 2023, over 771 million confirmed cases and over six million deaths have been reported globally.

As many countries integrate COVID-19 reporting into respiratory disease surveillance, WHO plans to continue monitoring the COVID-19 data on morbidity and the impact on health systems. 

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