New Covid subvariants BA.4, BA.5 detected in South Africa

Amid the emergence of Omicron subvariant XE in India, two new sublineages BA.4 and BA.5 have been detected in South Africa, Botswana, Belgium, Germany, Denmark and the UK, health officials have said. Initial examination shows the share of these new sublineages is increasing in South Africa, though no spike in cases has been reported so far.

"Early indications show that these new sublineages are increasing as a share of genomically confirmed cases in SA. No cause for alarm as no major spike in cases, admissions or deaths in SA," Tulio de Oliveira, Director of Centre for Epidemic Response & innovation, South Africa, has said.

The World Health Organisation (WHO) has also said that it's monitoring several descendent lineages of the Omicron variant, including new sublineages like BA.4 and BA.5. It said the Omicron variant remains the dominant variant circulating globally.

"Among the Omicron descendent lineages, the relative proportion of BA.2 has increased to 93.6%, while BA.1.1 accounts for 4.8% and BA.1 and BA.3 account for <0.1% of all Omicron lineages," the global health body said in its weekly epidemiological update.

The WHO has said the SARS-CoV-2 virus continues to evolve, and given its high level of transmission, further variants, including recombinants, will continue to emerge. Omicron's two subvariants BA.1 and BA.2 have caused recent waves in Europe and parts of Asia. Health officials in South Africa are also studying the prevalence of BA.1 and BA.3.

In a series of tweets, Oliveira said BA.4 and BA.5 have led to a rise in sequenced cases in South Africa since early March, studies conducted by the National Health Laboratory Service (NHLS) and the Network for Genomic Surveillance South Africa (NGS-SA) showed.

But there's good news. "The good news is that BA.4 and BA.5 (like BA.1) can be identified by a proxy marker of SGTF using the Thermo Fisher qPCR assay," Oliveira said, explaining that there’s less chance they could have high transmission.

Despite the increase in the percentage of genomes, BA.4 and BA.5 are not causing a spike in infections in South Africa. "The same is seem for hospitalisation and deaths, which SA is at a record low," the top infectious diseases expert said.

She also said that BA.4 and BA.5 sublineages share a similar spike profile as BA.2, "except for additional mutations: 69-70del, L452R, F486V". L452R was present in Delta, Kappa & Epsilon variants, while F486V is an uncommon RBD mutation, she said.

She has attributed the complex immunity landscape in South Africa, with high population immunity, as the probable reason for low infections, hospitalisation, and deaths since the Delta and Omicron BA.1 wave.

From the initial examination, the experts have said that further evolution of Omicron and identification of additional Omicron sublineages is entirely expected.

She has said BA.5 has many shared mutations with the other Omicron lineages but with some differences like the impact of differences on virus phenotype. Oliveira said it's too early to understand the overall impact of BA.4 and BA.5. But, she said, there's no cause for alarm like in the case of BA.2, which caused a wave but not a major spike in cases, admissions or deaths in the country.

To counter its impact, vaccination is the key, which can protect against severe disease, hospitalisation and death from all known variants, she maintained.

Besides, the WHO has said it’s also tracking the recombinant variants, both Delta and Omicron. The recombinant was first detected in the United Kingdom on 19 January and around 600 sequences have been reported in the country. Early estimates show XE is 10% more transmissible than Omicron BA.2; however, this finding requires further confirmation.

Globally, the WHO has said there was an uptick in Covid cases in the first half of March 2022, but the number of new cases decreased later, with a 16% decline during the week of 28 March through 3 April 2022 as compared to the previous week. As of 3 April 2022, just over 489 million cases and over 6 million deaths have been reported globally.

Meanwhile, India's first confirmed case of Omicron XE has been detected in Mumbai. The patient, who is a 67-year-old man, had travelled to Gujarat's Vadodara from Mumbai. He suffered from a mild fever on March 12. The genome sequencing of his samples showed the confirmed case of Omicron XE.