CAPE TOWN – Scientists are concerned that antibodies that could detect SARS-CoV-2 in South Africa’s first wave will be less effective against a virus variant that first emerged here and is known as 501Y.V2.  What’s worse, they still don’t know if brand new COVID-19 vaccines will work against the variant – which is deemed to be 50% more transmissible than ones prevailing until now.

The uncertainty contrasts sharply with the more optimistic profile of vaccine efficacy against British variants that have spread widely across the world.

A small study of 50 blood samples from people previously infected with SARS-CoV-2 found that 90% had reduced immune response to the 501Y.V2 variant and almost half did not recognise it at all, South African scientists told reporters at a scientific briefing this week.

They stressed that there was no evidence yet that a vaccine would not be effective against the variant, but acknowledged that the lack of antibody sensitivity, known as ‘immune escape’, among people who had already recovered from COVID-19 in the first wave could suggest they might be vulnerable to re-infection with the new variant.

Professor Penny Moore, research chair of Virus-Dynamics at the University of the Witwatersrand and the National Institute of Communicable Diseases, conducted the research on blood samples of 50 people who had been previously infected.

Given that vaccines are also based on triggering similar antibody responses, they might also be less effective. But while the immune escape was “concerning”, Moore stressed that the dynamics of antibodies triggered by vaccines also could be different than natural antibody response.

“What we are doing now is taking blood from those people who mounted a response to the vaccine during vaccine trials and we are testing those antibodies against the viruses,” said Moore.

“That will give us a sense of whether the new variant is less sensitive to the antibodies that various vaccines elicit. But again, there are lots of caveats, because there are many vaccines, they all behave in a different way, and they all tickle the immune system to produce antibodies in a different way.”

‘Tweaking’ Vaccines a Possibility – But World May be Constantly Dealing with More & More Variants

Moore said that while it might be possible to “tweak” existing vaccines, slightly adjusting them to deal with the new variant, a new strategy might be necessary: “There is potential to do this [tweak the design] for some of the vaccines but in the future I think we will be consistently dealing with more and more of these variants.

“So we might need to be a little bit cleverer in how we design vaccines and look for other parts of the virus that cannot change so effectively and try to design vaccines to target these.”

‘Don’t Call It South African Variant’

Professor Salim Abdool Karim, co-chair of the South African health minister’s advisory committee on COVID-19, who led the briefing, appealed for the variant to be called by its scientific name, 501Y.V2, and “not the South African variant” just as COVID-19 “is not called the China virus”.

Variants have been identified in many parts of the world including the UK and Brazil, all with mutations to the spike protein that binds to the human cells.

Abdool Karim reported that the 501Y.V2 variant has 23 mutations including a 20% rotation in the spike protein which enables it to bind more strongly to human cells. Mathematical modelling predicts that it is 50% more infectious than its predecessor but not more severe.

In the Western Cape province, it took 107 days for 100,000 cases to develop, whereas in the second wave, it took only 54 days. However, hospitalisations for both waves were similar, indicating that the variant was not more severe.

Reinfection and The Variant

While there was a concern that the new variant could drive reinfections, Abdool Karim said “the data at this point does not point in that direction”.

Dr Koleka Mlisana, Executive Manager of Research at the National Health Laboratory Service (NHLS), said that an analysis of over 1.1 million positive tests found that by 6 January, there had been about 4000 reinfections.

“We have not seen a marked increase in reinfections since the variant, but bear in mind, we’re only talking about a month’s data so far, so this is an area that we need to look very closely,” said Mlisana.

Although national statistics are not yet available, the latest data for KwaZulu-Natal province found that the variant was present in 59 of the 61 genome sequences analysed.

501Y.V2 Variant Raises More Concern than UK-Identified Variant

While the variant identified in the United Kingdom has received a great deal of attention for driving a big surge of infections there, across Europe and elsewhere, scientists have been even more concerned about the 501Y.V2 – which makes more significant changes in the protein structure of the characteristic coronavirus spike, which new vaccines are targeting.

Pfizer/BioNTech has already published a number of studies on the variant identified in the UK late last year, (known as B.1.1.7).  One such pre-print study claimed the antibodies in the blood of vaccinated people still recognize the variant.  However, that study has already been hammered by online reviewers saying that the study sizes are far too small (16), and Pfizer’s interpretation of the data was overly optimistic.

Some Pharma Companies Already Preparing For Next Stage Variant Vaccines

While scientists try to assess the impacts of variants on existing vaccines, some pharma companies are already gearing up for a second generation of vaccine development to address them.

One example is the startup biotech firm, Gritstone Oncology, which will begin human testing for a “backstop” vaccine in the event that mutant strains do evade the current range of vaccines, STAT has reported.

Preclinical work on the vaccine was supported by the Bill and Melinda Gates Foundation. Though no data is publicly available yet, its Phase 1 clinical trial is due to begin shortly.

The firm’s CEO Andrew Allen told the outlet that “we all hope that this will not be necessary” and that he thinks “it’s prudent to have it developed as a backstop”.

It should also be noted, however, that if a virus variant were to escape the immune response generated by existing vaccines, updating the tool would take only a matter of months.

Image Credits: National Institute of Allergy and Infectious Diseases, NIH, Twitter: @WHO.