Effect of developmental changes in prolonged SARS-CoV-2 infection in an individual with advanced HIV immunosuppression.


In a recent study published in medRxiv*Server preprint Researchers evaluated the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on cell death and integration in immunocompromised hosts.

The study: SARS-CoV-2 develops progressive infection that leads to cell death and fusion in an immunosuppressed individual.  Image credit: Dotted Yeti/Shutterstock
Stady: SARS-CoV-2 develops progressive infection that leads to cell death and fusion in an immunosuppressed individual. Image credit: Dotted Yeti/Shutterstock

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In this study, the researchers estimated the induction of cell fusion and death during long-term SARS-CoV-2 infection.

To evaluate the immune response to SARS-CoV-2 infection, the team isolated live virus from a patient with advanced human immunodeficiency virus (HIV) disease who was included in the longitudinal collection.

Samples were taken from the study group as soon as possible after diagnosis, within the first month after diagnosis, and thereafter at three-month intervals. The team performed quantitative polymerase chain reaction (qPCR) using nasopharyngeal as well as pharyngeal swabs for six months after diagnosis, with virus isolation beginning on the sixth day after diagnosis (D6).

The team used the viruses isolated to express the human lung cell line H1299 that overexpresses the ACE2 receptor. Time-lapse microscopy was performed using carbon dioxide and temperature-controlled cells. A second assay was used to determine cell death occurring 24 hours after infection (HPI).

Infection was identified by staining for SARS-CoV-2 nucleocapsid protein, and the proportion of infected cells that died was measured by co-staining with a death detection dye. As cell-cell fusion depends on cell surface expression Spike proteinIn this study, the authors examined surface spike expression on infected cells 18 hpi generated by live virus on a confluent cell monolayer.


The team detected persistent SARS-CoV-2 infection in the participant with advanced HIV. D6 showed low-to-moderate immune evasion in plasma samples collected from critical subjects previously reported infection with either the SARS-CoV-2 wild-type strain or beta or delta variants. However, D190 showed broader immune escape than the ancestral strain F neutralizing antibodies induced by the delta variable.

A genetics study revealed a pattern consistent with the evolution of infection with a single ancestor virus. Viral isolates obtained on D6, D20, D34, D106 and D190 revealed changes in the spike as well as other viral genes compared to the ancestral strain. Notably, the neutralizing escape mutation E484K and several other variants were present at D6, while the neutralizing escape mutations K417T and F490S51 were present at D190.

Uninfected cells proliferated to confluence with few signs of cell death and cell fusion. On the other hand, cells infected with wild type SARS-CoV-2 showed cellular fusion in addition to cell death, and/or absence of cell division by 12 dpi. These changes appeared to be less significant in cells infected with Omicron BA.1 and early D6 isolates. However, compared to BA.1 and D6, the D190 isolate after six months showed higher combinatorial properties and cytotoxic/cytostatic properties.

Quantification of fusion across several separate experiments revealed that the frequency of fusion in uninfected cell cultures was low and did not improve over time. Infection with D614G virus increased the frequency of cell fusion, with about 40% of the nuclei of the 36-hp cell fusion. The number of fusions was steadily reduced with BA.1 infection, reaching less than half that of D614G infection.

By comparing the infection of BA.1 with the progenitor virus, the team found that while the proportion of infected cells was similar and somewhat higher in BA.1 than in the progenitor virus, the proportion of infected cells staining positively for the death-detection dye was significantly lower in BA.1. .

The team noted that surface ripples could be easily detected in the impermeable cells. On the other hand, the nucleocapsid protein was not found on the cell surface, despite its high amounts after permeabilization. Expression of the progenitor viral isolates was similar. BA.1 infection led to a significant decrease in cell surface, whereas BA.5 infection led to a slight increase in levels. D190 infections had a significantly lower surface elevation than the progenitor virus isolates, while D6 infections had a higher surface elevation.


Overall, the results of the study showed that the virus present in relatively early stages of infection led to cell fusion and death at levels comparable to SARS-CoV-2 Omicron BA.1 infection. However, virus that evolved within six months of infection showed fusion at intermediate levels between wild-type and BA.1 infection, while the induction of cell death was more similar to that of D614G infection. This indicates that, according to these criteria, the virus did not show any attenuation during its evolutionary course.

*Important note

medRxiv publishes preliminary scientific reports that have not been peer-reviewed and therefore should not be considered conclusive, directing clinical practice/health-related behaviour, or treated as hard information.


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