HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens

Abstract

Humanity is currently facing the challenge of two devastating pandemics caused by two very different RNA viruses: HIV-1, which has been with us for decades, and SARS-CoV-2, which has swept the world in the course of a single year. The same evolutionary strategies that drive HIV-1 evolution are at play in SARS-CoV-2. Single nucleotide mutations, multi-base insertions and deletions, recombination, and variation in surface glycans all generate the variability that, guided by natural selection, enables both HIV-1's extraordinary diversity and SARS-CoV-2's slower pace of mutation accumulation. Even though SARS-CoV-2 diversity is more limited, recently emergent SARS-CoV-2 variants carry Spike mutations that have important phenotypic consequences in terms of both antibody resistance and enhanced infectivity. We review and compare how these mutational patterns manifest in these two distinct viruses to provide the variability that fuels their evolution by natural selection.

Emergence and phenotypic characterization of C.1.2, a globally detected lineage that rapidly accumulated mutations of concern

“…Like several other VOCs, C.1.2 has accumulated a number of substitutions beyond what would be expected from the background SARS-CoV-2 evolutionary rate. Thissuggests the likelihood that these mutations arose during a period of accelerated evolution in a single individual with prolonged viral infection through virus-host co-evolution[19][20][21] . Deletions within the NTD (like Y144del, seen in C.1.2 and other VOCs) have been evident in cases of prolonged infection, further supporting this hypothesis[22][23][24] .C.1.2 contains many mutations that have been identified in all four VOCs (Alpha, Beta, Delta and Gamma) and three VOIs (Kappa, Eta and Lambda) as well as additional mutations within the NTD (C136F), RBD (Y449H), and adjacent to the furin cleavage site (N679K).…”

Update on and Future Directions for Use of Anti–SARS-CoV-2 Antibodies: National Institutes of Health Summit on Treatment and Prevention of COVID-19

“…The Summit included an update on emerging SARS-CoV-2 variants based on data from the Global Initiative on Sharing All Influenza Data as of 9 June 2021 ( 42 ). All emerging variants of interest have mutations in the N -terminal domain or the receptor-binding domain; many also carry mutations at the furin cleavage site ( 43 ). Many of these mutations have been shown to confer partial resistance to convalescent sera and neutralizing antibodies, indicative of immune pressure as a selective force ( 43 ).…”

“…All emerging variants of interest have mutations in the N -terminal domain or the receptor-binding domain; many also carry mutations at the furin cleavage site ( 43 ). Many of these mutations have been shown to confer partial resistance to convalescent sera and neutralizing antibodies, indicative of immune pressure as a selective force ( 43 ). Publicly available databases that are searchable and up to date contain information on SARS-CoV-2 therapeutics and resistance, including virus variants and spike mutations versus mAbs ( 26 , 44 ).…”

Evolutionary dynamics of indels in SARS-CoV-2 spike glycoprotein

“…A key reason for indels being less common is that they are more deleterious due to frame-shifting compared to SNPs (Choi et al, 2012;Lin et al, 2017;Mills et al, 2006). As SARS-CoV-2 has been shown to accumulate indels (Fischer et al, 2021), we are only beginning to explore them and appreciate their myriad roles. For example, Chrisman et al (2021) have looked at indels in the SARS-CoV-2 genome and mapped it to regions of discontinuous transcription breakpoints.…”

“…SARS-CoV-2 belongs to the general class of enveloped viruses (which include influenza and human immunodeficiency viruses among others) that show great plasticity and immune evasiveness due to a protective lipid bilayer and embedded glycoproteins that are heavily Nglycosylated and used as a "glycan shield" (Casalino et al, 2020;Cui et al, 2009;Watanabe et al, 2019). Several genomic features such as point mutations, insertions and deletions (indels), and recombinations impart high diversity within enveloped viruses and profoundly increase their adaptability (Fischer et al, 2021). In fact, the envelop glycoproteins of these viruses are particularly variable and found to evolve quickly under selection pressure.…”