Adaptation of advanced clinical virology assays from HIV-1 to SARS-CoV-2

Abstract

Purpose of review In response to the HIV–AIDS pandemic, great strides have been made in developing molecular methods that accurately quantify nucleic acid products of HIV-1 at different stages of viral replication and to assess HIV-1 sequence diversity and its effect on susceptibility to small molecule inhibitors and neutralizing antibodies. Here, we review how knowledge gained from these approaches, including viral RNA quantification and sequence analyses, have been rapidly applied to study SARS-CoV-2 and the COVID-19 pandemic. Recent findings Recent studies have shown detection of SARS-CoV-2 RNA in blood of infected individuals by reverse transcriptase PCR (RT-PCR); and, as in HIV-1 infection, there is growing evidence that the level of viral RNA in plasma may be related to COVID disease severity. Unlike HIV-1, SARS-CoV-2 sequences are highly conserved limiting SARS-CoV-2 sequencing applications to investigating interpatient genetic diversity for phylogenetic analysis. Sensitive sequencing technologies, originally developed for HIV-1, will be needed to investigate intrapatient SARS-CoV-2 genetic variation in response to antiviral therapeutics and vaccines. Summary Methods used for HIV-1 have been rapidly applied to SARS-CoV-2/COVID-19 to understand pathogenesis and prognosis. Further application of such methods should improve precision of therapy and outcome.

Minipool testing for SARS‐CoV‐2 RNA in United States blood donors

“…In contrast, other reports showed no blood‐based detection of viral RNA from symptomatic individuals 7 and limited to no viral RNA detection from asymptomatic or pre‐symptomatic blood donors including the absence of transfusion transmission following recipient tracing 8–16 . Age and PCR positivity in serum or plasma have been associated with mortality and progression to critical disease in hospitalized COVID‐19 patients 17–24 …”

“…[8][9][10][11][12][13][14][15][16] Age and PCR positivity in serum or plasma have been associated with mortality and progression to critical disease in hospitalized COVID-19 patients. [17][18][19][20][21][22][23][24] In March 2020, the U.S. REDS-IV-P program, which leverages access to the blood supply and blood donors, launched the REDS Epidemiology, Surveillance and Preparedness of the Novel SARS-CoV-2 (RESPONSE) study to investigate the theoretical blood safety risk, seroprevalence in blood donors, and SARS-CoV-2 pathogenesis through infected donor follow-up. In this manuscript, we report the findings from the first objective of the RESPONSE study: investigate the prevalence of SARS-CoV-2 RNAemia in blood donors in six U.S. areas with ongoing community transmission.…”

The Effect of Select SARS-CoV-2 N-Linked Glycan and Variant of Concern Spike Protein Mutations on C-Type Lectin-Receptor-Mediated Infection

“…Much like the seasonal flu, annual or even biannual booster shots are commonplace and necessary to combat the latest variants of the virus [ 7 , 8 ]. Even though the mutation rate of the polymerase for SARS-CoV-2 is an order of magnitude or so lower than for human immunodeficiency virus (HIV)-1, the ease of infection, relatively broad tropism and long course of infection allow for sufficient rates of mutations for the SARS-CoV-2 genome to escape immune detection and eventually establish breakthrough infection [ 9 , 10 , 11 ]. The evidence that COVID-19 will likely continue to mutate is perhaps best exemplified by how, globally, Delta strains were the dominant variant of SARS-CoV-2 for about 6 months between June and December of 2021, with nearly 100% of COVID-19 cases worldwide testing as the Delta variant for the latter 5 months of that period [ 6 ].…”