Multiple mutations lead to 216 days of COVID-19 infection in HIV+ patient

Earlier studies conducted during the emergence of the pandemic suggested that the impact of SARS-COV-
2 is similar or perhaps slightly higher in patients already infected with HIV. A recent study by Prof. de Oliveira revises the earlier studies and suggests that patients infected with HIV could be infected with SARS-
COV2 for more than 7 months, compared to an average person who can shed the virus in 20 days. Such longevity of COVID infection in HIV patients can be attributed to their compromised immunity and the
continuous mutation of viruses in their body.

In September 2020, an HIV+ female patient was admitted to a hospital in South Africa for COVID-19 after
experiencing symptoms for 12 days. The patient was subjected to a cohort study on her existing HIV
infection and its immune response to the new SARS-COV2 infection. From day 0 (day of admission), she
was reviewed continuously for 216 days. The unnamed woman was asymptomatic at day 34 after being
kept continuously on non-high flow supplemental oxygen, but showed chest tightness along with low levels
of SpO2 (Oxygen saturation) after day 74. Subsequently, she underwent treatment for pneumonia and was
reviewed again on day 106 where she displayed severe fatigue. On day 190, antiretroviral therapy (which
was being used for the treatment of HIV) was switched to a fixed-dose combination of tenofovir,
lamivudine, and dolutegravir and on day 206, she achieved HIV viral load suppression.

The genome sequencing of the 6 samples collected over the period of 216 days reported several mutations,
which were associated with high-level resistance to antiretroviral drugs. Genomic and clinical data suggest
that virus evolution may have been driven by selective pressure from an impaired neutralizing antibody
response. The impairment of both cellular and humoral adaptive immunity from HIV was quite profound
enough to delay the clearance of SARS-CoV-2.

The SARS-COV2 PCR remained positive till 216 days with significant shifts in the virus population over the
time involving multiple mutations at key neutralizing antibody epitopes in the spike RBD and N terminal
domain (NTD). Unlike most other prolonged infection cases which were due to haematological malignancies or people receiving immunosuppressive therapies or other chronic medical condition, here
the virus evolution was not driven by the receipt of immune-based therapies.

Prof. de Oliveira suggests that more work is needed to understand immunogenicity, treatment
effectiveness in HIV patients, and to design optimal dosing strategies, particularly for those with advanced
HIV. He is currently the director of KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP) in
South Africa and has worked for over 20 years with viral outbreaks, including HIV, Hepatitis B and C,
Chikungunya, Dengue, SARS-CoV-2, Zika, and Yellow Fever Virus.

Most importantly, these studies highlight the need to include HIV-infected individuals in the strategies to
combat COVID-19 especially due to the extensive virus mutations in their bodies thereby generating new
variants and to be prioritized during the vaccine drive across the world.

Authors: Alex Dennis, Dr Rifat Kamarudheen(PhD from Dutch Institute for Fundamental Energy Research, Netherlands and at present Post Doctoral Researcher at EPFL (École Polytechnique fédérale de Lausanne) in Switzerland).

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