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30 mutations: a patient with HIV was ill with COVID for 7 months

An HIV-infected woman from South Africa has been ill with COVID-19 for 233 days, during which time SARS-CoV-2 has accumulated more than 30 mutations in her body. There are about 10 million people with HIV worldwide who are unaware of their status or unable to suppress the infection with drugs — and doctors fear that if they become infected with COVID-19, they will become a source of new, more deadly strains of SARS-CoV-2.

South African researchers from the University of Kwazulu-Natal have documented a case of COVID-19 lasting more than six months in a patient with HIV. They described it in detail in an article published on the medRxiv preprint service.

A 36-year-old woman felt unwell in September 2020 and tested positive for SARS-CoV-2. The disease lasted seven months, during which the virus strain acquired more than 30 new mutations.

In South Africa, there are about 7.5 million people living with HIV, including children. In the world — almost 40 million. The majority of HIV carriers have access to treatment, but about a quarter do not receive the necessary care. If the infection is not contained with the help of antiretroviral therapy, the disease weakens the immune system, which causes frequent and long-term infections.

The patient learned about her diagnosis back in 2006. The viral load was reduced to a minimum thanks to ART. However, the woman had extremely low levels of CD4+ T cells, which help the body to produce antibodies, and CD8+ T cells to destroy cells affected by the coronavirus.

In September 2020, the patient suffered from cough, sore throat, and shortness of breath for 12 days. After doctors found out that she had COVID-19, the woman received oxygen therapy for nine days. Then she was discharged. However, even after discharge, tests continued to show a positive result for SARS-CoV-2 for 216 days.

The researchers found that the virus received 32 genetic changes, 13 of which were related to the protein spike that the virus needs to enter cells and infect them. Other mutations were similar to those previously found in SARS-CoV-2 strains from the UK and South Africa.

Six months after the start of observations, doctors replaced some drugs in her therapy regimen. This allowed to boost the immune system and get rid of the infection. On the 233rd day of the illness, the test for SARS-CoV-2 finally turned out to be negative. The patient became a participant in a study on the impact of HIV on the course of COVID-19.

In total, doctors are monitoring 300 HIV carriers infected with COVID-19.

It is too early to say whether the case of this woman is unique, the authors of the work note. It is possible that in other patients with HIV, the infection also lingers in the body for a long time, leading to the emergence of potentially more deadly strains of SARS-CoV-2. In this case, HIV carriers who do not take ART can become “a factory of new strains for the whole world,” fears the study's lead author, geneticist Tulio de Oliveira.

“This shows that the virus can gain benefits until we can slow it down, and we need to slow its spread around the world,” says immunologist Bruce Walker.

It is estimated that about 8 million people in the world are living with HIV without knowing about the infection. And 1.7 million people have problems with treatment and ART does not help them enough. Thus, almost 10 million people can become carriers of COVID-19 for many months and thus give the virus the opportunity to mutate freely.

However, without the necessary data on HIV carriers infected with COVID-19, it is too early to draw conclusions about the extent of the risks. Earlier, the attention of scientists was attracted by an elderly woman with leukemia, in whose body SARS-CoV-2 lasted 105 days. She had no symptoms of COVID-19-doctors discovered the disease when the woman was in the hospital with severe anemia. Doctors regularly took samples from the woman's upper respiratory tract, but even on the 70th day, they detected the virus in concentrations sufficient to make the patient contagious. He completely disappeared only on the 105th day.

“We expected that this could happen, but we have not seen reports of it,” the researchers note.

The infection probably persisted for so long because of the patient's weakened immune system, they say. Her body couldn't produce enough antibodies to get rid of the virus. Doctors injected the woman with plasma with antibodies, but this did not have any effect.

In addition, during the disease, the virus mutated. However, the mutations did not affect the ability of the virus to persist in the body. This turned out to be one of the longest known periods during which a patient with SARS-CoV-2 was infected without experiencing symptoms. However, doctors observed a similar pattern in influenza and the Middle East respiratory syndrome. They believe that in the future there will be more reports of SARS-CoV-2 detection in the body over time.

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