Covid-19: New South Africa variant triggers alarm bells in India

The Union Health Ministry ordered states and Union Territories to screen and test travellers from South Africa, Hong Kong, and Botswana, hours after South African authorities announced that they had detected a new novel coronavirus variant that had an unusual constellation of mutations.

India on alert
Health Secretary Rajesh Bhushan, in a communication to all states and Union Territories, said the National Centre for Disease Control (NCDC) had informed the Centre that multiple cases of a Covid-19 variant B.1.1529 had been reported in South Africa, Botswana, and Hong Kong.

This variant reportedly has significantly high levels of mutations and, thus, poses serious public health implications for India on the back of recently-relaxed visa restrictions and reopening of international travel, Bhushan said.

Bhushan said it was, therefore, imperative that international travellers travelling from or transiting through South Africa, Botswana, and Hong Kong were rigorously screened and tested.

The Union Health Ministry has also directed the states to closely track and tract the contacts of these international travellers.

All states will have to send samples from travellers testing positive to designated laboratories of the Indian SARS-CoV-2 Genomics Sequencing Consortium (INSACOG) that tracks and monitors variants of concern and variants of interest in the country. The states’ Covid-19 surveillance officers will have to coordinate with INSACOG labs and undertake test-track-treat to prevent the variant’s spread and the formation of case clusters.

Reaction in South Africa
South African scientists said the mutations in B.1.1529 were concerning as they could help the virus evade the body’s immune response and make it more transmissible, Reuters reported.

The World Health Organisation (WHO) currently designates four variants of concern — Beta (Pango lineage B.1.351), first detected in South Africa in May 2020; Alpha (B.1.1.7), first detected in the United Kingdom in September 2020; Delta (B.1.617.2), first detected in India in October 2020; and Gamma (P.1), first detected in Brazil in November 2020.

In a statement on Thursday, South Africa’s National Institute for Communicable Diseases (NICD) said 22 positive cases of the B.1.1.529 variant had been recorded in the country after genomic sequencing collaborations. Other NGS-SA laboratories were confirming more cases after sequencing results.

South African scientists told Reuters that early signs from laboratories indicated that the variant had rapidly grown in Gauteng, the most populated province, and might already be present in the country’s other eight provinces.

The NICD said despite limited data, experts were working with all established surveillance systems to understand the variant and what its potential implications.

South Africa Health Minister Joe Phaahla said they were hopeful of a longer break between waves — possibly it would hold off to late December or January, Bloomberg reported.

The strain has become dominant in South Africa with the country detecting nearly 100 cases as on Thursday. According to early RT-PCR results, 90% of 1,100 new cases in the province that includes Johannesburg on Wednesday were caused by the new variant, The Indian Express reported.

How different is this variant?
The spike protein of the B.1.1.529 variant has a high number of mutations that play a key role in the enabling virus’ entry into human cells. Vaccines also target these spike proteins. Researchers are trying to determine if it is more transmissible or lethal than previous ones.

Where it came from?
There is no certainty on how the variant emerged. A UCL Genetics Institute, London, scientist said the variant possibly evolved during a chronic infection in an immuno-compromised person — likely an untreated HIV/AIDS patient. South Africa has a whopping 8.2 million people with HIV infections, the highest in the world. The Beta variant identified in the country last year may have also come from an HIV-infected person.

Hong Kong, Botswana cases
The Hong Kong Special Administrative Region government announced two cases of the variant. The Regal Airport Hotel cases had similar genetic sequences and the viruses belonged to the B.1.1.529 lineage, it said in a release.

The sequences are similar to those found in Botswana and South Africa, supporting the idea that case 12,388 (a traveller from South Africa) was the index case.

The Hong Kong authorities added that there was a lack of scientific information on the public health significance of this lineage.

Botswana reported four B.1.1.529 cases in vaccinated travellers.

Botswana’s Presidential Covid-19 Task Force Coordinator Dr K Masupu said initial investigations suggest that the new variant had a high number of mutations compared with the locally predominant Delta variant.

It is still unclear what it means and is under investigation. New variants can potentially affect the severity of disease, but the variant’s real-world impact has not been established, he added.

International reaction
News of the variant sent markets into turmoil today. Travel-related stocks in Asia were the biggest losers as investors fear a negative impact on travel. The UK has issued a temporary ban on international flights from six African countries, while Australia refused to rule out tightening border rules for travellers from southern Africa.

The WHO will discuss the B.1.1.529 variant at a meeting today and decide if it would be designated as a variant of interest or concern. Governments will also take action on border controls once the Who decision is finalised.