Covid-19 variants and mutations in South Africa: The worst is yet to come, experts warn
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Johannesburg - South Africa could have as many as 30 coronavirus mutations and now health experts fear patients with advanced HIV could become “a factory of variants for the whole world."
This week, the country reported 9,149 new cases and government is urged to step up efforts with experts saying the speed of the rollout could determine how severe the third wave proves to be.
To add to the Covid-19 woes, scientists recently detected potentially dangerous coronavirus mutations in a woman with advanced HIV. The 36-year-old woman carried the coronavirus for 216 days, and during the said period, the virus collected more than 30 mutations. The case was published as a preprint in the medical journal medRxiv this month.
After the woman tested positive for Covid-19 in September last year, the virus gathered 13 mutations to spike protein and 19 other genetic shifts that might change the behaviour of the virus. But scientists are unclear if the woman passed on these mutations to others.
However, they added that it is possibly not a coincidence that most of the new variants have surfaced from areas such as KwaZulu Natal, where one in four adults is HIV positive. Although there is limited evidence to indicate that HIV-infected people are more susceptible to contracting Covid-19 and developing grave medical consequences, researchers are of the opinion that if more such cases come to light, it will not bode well.
Covid-19 expert Professor Salim Abdool Karim warned that the real current rate of infections is probably twice what is being reported and that the latest data is actually a reflection of what happened well over a week ago.
“It is going to increase, and we know this from our first and second waves that the virus will grow in one or two provinces, initially. From then, it cedes to other provinces. So we should be expecting that in the next two weeks, cases would rapidly rise,” said Karim.
Professor Shabir Madhi, a vaccinologist at Wits University, is already predicting that Gauteng, in particular, will experience its highest number of Covid-19 cases during the third wave.
“Despite a high percentage of the population likely having been infected during the course of the first two waves in Gauteng, the trajectory of the current resurgence is on track to exceed the number of cases that occurred in either of the first two waves,” Madhi told the Saturday Star.
The country’s National Institute for Communicable Diseases (NICD) said the increase in cases has brought the national seven-day moving average incidence (5,959 cases) which exceeds the new wave threshold as defined by the government’s Ministerial Advisory Committee (MAC). MAC defines the new wave seven-day moving average threshold as 30% of the peak incidence of the previous wave.
The country has now reported a total of 1,722,08 cases, with the 9,149 new cases representing a 15.7% positivity rate based on tests completed. A further 100 related deaths have been reported, bringing total fatalities to 57,410 to date.
There was an increase of 844 admissions in the past 24 hours and 127 additional in-hospital deaths reported in the past 24 hours. The majority of new cases today are from the Gauteng province (61%), followed by the Western Cape (10%) province.
Madhi says despite Gauteng’s high number of cases, the province is yet to hit its peak.
“It's likely that we are yet to peak in Gauteng, which is likely to occur over the course of the next two or three weeks. Based on past experience, it is likely that the current surge will then start subsiding and taper off by late July.”
Madhi added that while some provinces have only entered into their third wave recently, Gauteng has been in its third wave for some time now. “We have been in a third wave in Gauteng for the past three weeks- since the positivity rate of tested cases went above 10%. Using a threshold of one-third of the peak of the past waves as a measure of the start of a resurgence does not make epidemiological sense, as subsequent resurgences can be less severe, but still constitute a wave.”
Asked what factors will influence how South Africa’s third wave plays out, Madhi said: “The struggling roll out of Covid-19 vaccines to high-risk groups poses the greatest challenge since, if we had protected the high-risk groups against severe disease and death, we would be better placed to weather this wave which was predictable.
The failure of the timeous roll out of the Covid-19 vaccine programme now places the burden of weathering the third wave on the shoulders of the public, who need to be more responsible in adhering to masking and avoiding indoor gatherings in particular. The main driver of transmission is indoor gatherings in poorly ventilated spaces, more so when people are not wearing face masks,” said Madhi.
He has even called for more restrictions on public gatherings, including places of worship, and indoor dining, etc. There are also growing calls for schools across the country to close to curb the spread of the virus.
Despite an increase in cases, Madhi doesn’t expect the country to move into a stricter level of lockdown.
South Africa is currently on an adjusted level 2 lockdown.