Coronavirus: Four warning signs indicating emergence of dangerous strains

RIO DE JANEIRO, BRAZIL – The UK was in lockdown in November 2020. No one could leave their homes except for essential activities, such as going for groceries. Gradually, infection rates began to drop in the country, except in Kent.

Despite strict rules against movement of people, Covid-19 continued to spread in that southeastern English county, quickly overwhelming hospitals with infected patients.

In South Africa, in October 2020, a new wave of Covid-19 suddenly began to sweep into the Eastern Cape province. The infection rate was much higher than in other areas of the country, where the number of cases was stabilizing after the first outbreak of Covid-19.

In Manaus, an unprecedented crisis reached its peak on January 15th, when crowded hospitals ran out of oxygen. The city, heavily hit by the first wave of covid19, was experiencing a new explosion of the disease.

In the three cases above, new and more contagious strains played an important role in the chaos caused by the surge in infections and hospitalizations. The trend is for other mutations to continue to emerge while the virus remains in circulation.

According to researchers interviewed by BBC News Brasil, four warning signs are particularly relevant in the monitoring of new strains. It is essential to stay alert to these signs in order to identify dangerous mutations as soon as possible in order to prevent strains from spreading and to mitigate the damage they can cause.

The main risks are that the virus will become more lethal, more contagious, and more resistant to vaccines and the human immune system.

One of the main warning signs for a possible new strain in the area is the occurrence of a sudden surge in hospitalizations and deaths by Covid-19.

In this case, researchers first check if there is a human explanation. For instance, if local governments relaxed social contact rules in the weeks leading up to the outbreak, or if the outbreak occurred shortly after a holiday period, such as Christmas or New Year.

If there is no reasonable explanation for a location suddenly experiencing a spike in infections, this is a warning sign of the possibility of a more contagious strain circulating in that location.

It was this sign that prompted scientists in South Africa to mobilize efforts to identify genetic changes in the coronavirus circulating in the Eastern Cape province.

While the whole country was experiencing a “plateau” of infections in early October 2020, almost three months after the peak of the first wave of Covid-19 there, the city of Nelson Mandela Bay was experiencing an exponential surge in hospitalizations.

In November, researchers at KwaZulu-Natal University in Durban, South Africa, sequenced the virus from infected people in the city and found it to be a variant with 20 mutations- a number considered high for Sars-CoV-2.

Soon, Covid-19 spread across the country again, triggering a new wave with a higher peak infection rate than the first. The high infection rate led scientists to suspect a more contagious strain of the virus.

They then identified two particularly worrying mutations that would later also be found in the strain detected in Manaus: the N501Y and E484K. Both are located in the spike of Sars-CoV-2, the protein that serves as the binding point between the coronavirus and human cells.

The N501Y renders the virus more contagious, while the E484K bypasses the action of neutralizing antibodies, which are placed between the spike and human cells to prevent the virus from binding.

The latter mutation is of particular concern to scientists because it appears to reduce the efficacy of vaccines and is suspected of facilitating reinfection by people who have already been infected by the original virus.

If an area begins to notice a surge in infections in people who say they have already contracted Covid-19 before, this is another warning factor for the potential presence of strains, particularly if the new infection has occurred within a short period of time.

A research conducted by the British government’s Public Health England agency found that most people who have already contracted Covid-19 (83%) have immunity for at least five months.

If a considerable number of people who have already become infected begin to test positive for Covid-19, it could be that a strain is in circulation capable of bypassing the antibodies produced by the immune system after a first infection.

Reinfection by a strain is one of the assumptions being researched to explain the surge in hospitalizations and deaths that occurred in January in Manaus, Amazonas. The city had already been heavily affected by the first wave of the disease. And a research study published in Science magazine on December 9th estimated that 76% of the population had already contracted Covid-19.

In theory, this number (if correct) would be a sufficient percentage to produce the so-called herd immunity, when a high number of people with antibodies is able to stop the spread of the disease because it struggles to find vulnerable people and loses strength. But in January, hospitals in the capital of Amazonas began to quickly fill to the point that the public health structure collapsed and dozens of people died from lack of oxygen.

An assumption for this new spike in Covid-19 cases is that part of them are reinfections by the P.1 strain, which was circulating in Manaus at the time.

Virologist Felipe Naveca, who was involved in sequencing this variant, explains that it is difficult to confirm massive cases of reinfection, because it is necessary for the patient to undergo two Covid-19 tests with positive testing within 90 days, in addition to the sequencing of two different strains of the virus.

“Often this is not possible because the person seeks the healthcare system at the end of infection. But I believe there are several cases of reinfection. We have some waiting confirmation,” said the researcher, who is part of the Instituto Leônidas & Maria Deane (ILMD/FioCruz).

Another sign of potential emergence of a variant is a consistent change in the symptoms of those who test positive for Covid-19 or a significant increase in severe cases of the disease.

These factors would suggest the presence of mutations that interact differently with human cells, causing reactions that differ from those caused by the original coronavirus strain.

For now, there is no conclusive evidence that the variants found in Manaus, South Africa, and the UK cause different symptoms or are more aggressive.

But because they are more transmissible, they can rapidly increase the number of people infected, causing overcrowding in hospitals and more deaths.

Furthermore, by ensuring a more effective “fit” of virus particles into the human cell and bypassing the action of antibodies, the N501Y and E484K mutations ultimately produce higher viral loads in infected individuals.

“Studies show that these strains enable the virus to bind to the cell more effectively, more solidly. And that a larger amount of virus can adhere to each cell. So we have a higher rate of viral reproduction in the body,” explains virologist Julian Tang, from the University of Leicester in the UK.

Preliminary research released by the British government on January 22nd estimated that the strain found in Kent (UK) may be up to 30% deadlier than the original virus.

According to the study, among 1,000 60-year-old people infected by the old variant, 10 are likely to die. With the strain identified in Kent, this number rises to 13 in 1,000.

Finally, another sign to be observed is the eventual accelerated infection of people in age groups that were not heavily affected by the original strain of the coronavirus.

That is, if more children and adolescents begin to become infected or present more severe cases of Covid-19, this would be an indication of a strain with mutations capable of improving the binding between the virus’ spike protein and the receptors in the cells of young people.

Studies suggest that children are less severely affected by the coronavirus because they have fewer receptors in the lungs capable of recognizing and binding to the spike protein.

As yet, there are no conclusive studies on the impact of the strains on children. But the British government has already stated that there is evidence of increased transmission of the UK strain among children. This would help explain how quickly this strain has spread throughout the country, becoming the dominant virus in England.

As a result of the suspicion that the virus is infecting more children and young people, Prime Minister Boris Johnson has ordered the closure of schools in England until at least March 8th. Reopening will depend on vaccination rates among the most vulnerable population.

While the virus is circulating with significant transmission rates, there is a risk of new variants emerging, points out microbiologist Ana Paula Fernandes, a researcher at the Center for Technology in Vaccines and Diagnostics at the Federal University of Minas Gerais (UFMG).

“The more people infected in a population, the greater the chance of strains emerging,” says Fernandes, who is also coordinator of the national diagnostics network, which links different universities and research institutes in Brazil to tackle the pandemic. “Without containment measures and without broad vaccine coverage, a strain may emerge that will completely bypass vaccines. That is a concern.”

Among Fernandes and FioCruz virologist Felipe Naveca’s recommendations to reduce transmission are the wearing of professional masks, such as N95, indoors, trying to circulate only outdoors or in ventilated environments, opening car windows, particularly if one is in a cab or an Uber, avoiding going to bars, restaurants, and other places of leisure that gather people indoors, wearing masks also outdoors, washing hands constantly, and using hand sanitizer.

Source: BBC News Brasil