Everything we know about 501.V2, the new Covid-19 variant identified in SA

On Boxing Day last year, Prof Salim Abdool Karim, one of SA’s top infectious disease experts, set off to watch a cricket match. He arrived early and opened up his computer to check his e-mail. There was a message that would confirm his deepest fears of the latest variant of SARS-CoV-2 ripping through the country.

On Monday night, he and a team of leading scientists revealed in a webinar, hosted by the national ministry of health, what we know about the latest variant of the virus that causes Covid-19.

First, in-depth analysis in the laboratory has confirmed what was happening clinically and anecdotally: that the latest variant, known as 501.V2, spreads far more quickly than the one that brought us our first wave.

It spreads 50% more easily and quickly.

While this information affects the whole country, it is because of something happening in a microscopic world: amino acids that led to changing the shape of the protein on the virus had changed.

What this means is that “its ability to bind to a human cell is stronger because it rotates at 20 degrees” and can thus get deeper into the cells at that angle.

Said Abdool Karim: “Almost one out of three tests are now positive and that is higher than anything we saw in the first wave. This drastic change is being driven by a virus that biologically can attach to human cells more efficiently.”

He added: “The first wave reached a peak in the middle of July last year and then came down. The new variant emerged in the latter part of October, just as the second wave was building. It has now reached completely new heights, with more cases and deaths than anything we saw on any day during the first wave.”

Every province has been hit.

In the Western Cape, where it is now slowly easing, the second wave peak “was almost double that of the first wave’s”, and the pandemic was 50% quicker in hitting 100,000 cases in the province.

Of the research presented, however, not all was doom and gloom.

While hospital admissions and deaths have been higher, that is because of the skyrocketing infections: there is no evidence to suggest this variant causes more severe disease.

Scientists had suspected this, but data analysis has now confirmed it.

Also, according to Prof Mary-Ann Davies from the Western Cape health department, “the mortality rate across age groups in the first and second wave have been no different”.

She said the “probability of dying from Covid-19” remained the same in each age group in the first wave compared with that same age group in the second wave.

However, “while it is not causing more severe disease, the sheer numbers are putting huge pressure on hospitals and we may see an increase just because of those shortages of resources that occur when the numbers get higher”, she said.

According to Dr Richard Lessells, an infectious diseases expert at the KZN Research Innovation and Sequencing Platform: “Mutations are a change in the genetic code. As a virus passes from person to person and replicates in our bodies, you get errors in the genetic code — in other words, changes in the RNA code. Most are innocuous and cause no change in amino acids or virus protein, but some do cause such changes which in turn change the structure. Changes noted in the spike protein were of concern to us because that’s the part that latches onto receptors in cells in our bodies.”

We also don’t know yet if there is going to be yet another variant after this  and more after that.

—  Prof Koleka Mlisana, executive manager at the National Health Laboratory Service (NHLS)

Prof Koleka Mlisana, an executive manager at the National Health Laboratory Service (NHLS), said data also suggests infections from the first wave did not necessarily protect those who got it from getting it in the second wave, but more research is needed to determine if this is due to mutations and the different variants that result.

Using a “wealth of lab data from more than 6.7 million tests”, it came to light that some 4,000 people in SA were infected again after three months or more.

She added: “We also don’t know yet if there is going to be yet another variant after this  and more after that, but we want to use the information we have gleaned thus far to be better equipped to deal with new variants going forward.”