New Covid variant JN.1 now in South Africa but risk low, say health officials

The World Health Organization (WHO) has classified a highly mutated descendant of Omicron as a new variant of interest – and cases are spreading fast globally.

JN.1 cases were originally counted and tracked as part of BA.2.86 cases, but it has taken off in “multiple countries”, according to the WHO, which said this week that the new variant now represents the vast majority of BA.2.86 cases.

The risk to public health remains low, though, according to the WHO in its risk evaluation.

“Considering the available, yet limited evidence, the additional public health risk posed by JN.1 is currently evaluated as low at the global level. It is anticipated that this variant may cause an increase in SARS-CoV-2 cases amid a surge of infections of other viral and bacterial infections, especially in countries entering the winter season,” the risk evaluation continued. 

Detailing the reasons for its decision to declare JN.1 as a separate variant of concern, the WHO said there had been a rapid increase in JN.1 – this growth factor is one of the outstanding characteristics of the variant, as are mutations that indicate its ability to escape immunity.

Read more in Daily Maverick: Highly mutated Covid variant found globally, but the pandemic in ‘a different phase’

There have been only two published studies on symptoms associated with JN.1 infections. One was done in Belgium on patients older than 65. The study reported no significant difference in symptoms from other Omicron variants and specifically from BA.2.86. 

A Singapore study reported a lower risk of hospitalisation and severity.

Globally, there has been a rapid increase in the proportion of JN.1 reported, with its prevalence at 27.1% at the end of 2023 – a substantial rise from October and November last year.

Dr Sibongile Walaza from the National Institute for Communicable Diseases said SARS-CoV-2 continues to circulate in South Africa and it is expected that variants will continue to emerge. 

“With currently available data, albeit limited, there is no reason for concern. The WHO has assessed the overall risk as low as the limited evidence on JN.1 does not suggest additional public health risks relative to the other currently circulating Omicron descendent lineages,” Walaza continued. 

She said they had not received any reports of increased severity (hospitalisations or deaths) associated with this variant.

“With high immunity levels (exposure and/or vaccine) in the communities, there is currently no indication of increased severity from this variant as compared to other circulating variants. 

“Individuals at risk of severe disease (elderly, immune compromised) are recommended to receive vaccine and booster doses as per guidelines.

“It is unlikely that JN.1 will present differently from what we’ve been experiencing recently, ie mild [symptoms]. Regular hand-washing, protecting coughs and sneezes, and staying away from people who may be at high risk of severe disease remain recommended when sick with any respiratory illness.”

She said only limited data on the clinical presentation of cases with JN.1 was available.

“However, similar to other Covid-19 variants, symptoms may differ based on a person’s overall health and their immunity,” Walaza said.

The latest report from South African teams tracking SARS-CoV-2 viruses published on 5 January states that 11 samples of the JN.1 variant were found in the Western Cape and one in Gauteng.

The percentage of samples that tested as JN.1 increased from 3% in November to 16% in December. DM