In a recent study published on the bioRxiv * prepress server, U.S. researchers mapped the trajectory of the evolution within the host of coronavirus 2 (SARS-CoV-2) infection of acute acute respiratory syndrome.
Study: Evolutionary dynamics within the host and tissue compartmentation during acute SARS-CoV-2 infection. Image credit: ktsdesign / Shutterstock
Fund
Global large-scale genomic sequencing efforts and phylogenetic analyzes of clinical samples during the 2019 coronavirus disease pandemic (COVID-19) have captured the overall evolutionary dynamics of SARS-CoV-2. However, there is a lack of understanding of the evolutionary dynamics of SARS-CoV-2 within the host.
Although some studies have previously captured host SARS-CoV-2 dynamics, they have focused only on immunocompetent hosts. These studies showed low diversity within the host, with most samples containing 15 or fewer single-nucleotide (iSNV) intra-host variants. Taken together, data from these studies showed that the onset of selection-driven iSNV at a high frequency during acute infection is likely to be rare. In general, a high-resolution profile of the evolutionary dynamics of SARS-CoV-2 within the host is missing.
Furthermore, little is yet understood how pre-existing immunity, caused by vaccination or previous infection, influences the evolution of the SARS-CoV-2 host. More importantly, the potential for the emergence of variants escaping immunity in immunocompetent individuals with different vaccination states should be characterized.
About the study
In the present study, researchers recruited 32 students, faculty, and staff members from the University of Illinois at the United States (USA) for longitudinal sampling that allowed the detection of high-confidence SARS-CoV-2 variants for discover evolutionary dynamics ignored by less- frequent sampling strategies. Of these 32 study participants, 20 were naive individuals and 12 had pre-existing immunity acquired through vaccination or natural SARS-CoV-2 infection. From each individual, the team collected daily nasal swabs of middle cornet (MT) and saliva from naïve and immune individuals for repeated measurements of iSNV frequencies during the initial phase of infection. In this way, they generated high-resolution profiles of iSNV dynamics between tissue compartments and temporarily.
Study results
Evidence of strong positive selection was rare in the study cohort. However, the researchers observed some non-synonymous substitutions, including N: P67S, S: Q677H, and ORF1ab: P5402H from the lower detection limit to the high frequency. Substitution to S: Q677 arose independently in multiple SARS-CoV-2 substrates worldwide, supporting that mutations at this site may have an evolutionary advantage. The S: Q677H frequency was 56.5% when the participant in the associated study had an detectable viral load detectable in a nasal swab, indicating the potential for advanced transmission of this iSNV.
In addition, the authors observed competition between S: Q677H and S: P681H substitutions within the same individual, with S: Q677H emerging at a high frequency for a time in a day when the initially set frequency of S: P681H was decrease. However, the observed reversal to a single S: P681H genotype after day 7 showed that the selective advantage conferred by S: P681H was greater than that of S: Q677H. The widespread proliferation of S: P681H-containing SARS-CoV-2 lineages compared to S: Q677H further supports the aptitude advantage conferred by this mutation.
In addition, genome mapping revealed the accumulation of multiple hotspots of non-synonymous mutations that differ between naive and immune individuals. Observed enrichment of amino acid substitutions immediately upstream of the cleavage site of SARS-CoV-2 spike subunit 1 (S1) / S2 indicated that this region may be subject to stronger selection within of the host in humans. Therefore, in naive individuals, they identified hot spots at residues 402–457 in ORF1ab and 655–681 in S, directly adjacent to the S1 / S2 cleavage site. S1 / S2 cleavage site substitutions are characteristic features of the Omicron, Delta, and Alpha SARS-CoV-2 lineages. A recent study by Y. Liu et al. demonstrated that substitutions at the S1 / S2 cleavage site have been responsible for the increased relative fitness of the Delta variant compared to Alpha.
A high density of nucleocapsid (N) gene substitutions in immune study participants further validated previous data suggesting the importance of the N gene during human adaptation. Consequently, the researchers observed a hot spot of accumulation of mutations at N: 199-204.
Diversity of single-host nucleotide variants (iSNV) compared between samples and individuals. (A) Total iSNV count for each sample of each unvaccinated participant. Light gray boxes indicate the total iSNV count for all samples and horizontal black lines indicate the number of shared iSNVs for each participant. (B) iSNV counts for immune participants. (C) iSNV has individual samples with Ct <25 of naive participants depending on the number of days after enrollment (adjusted R-square = 0.05007, p = 0.02255). The line represents the linear regression. (D) iSNV has individual samples with Ct <25 of immune participants depending on the number of days after enrollment (adjusted R-square = 0.2857, p = 0.006359). The line represents the linear regression.
The researchers also observed several shared mutations within the untranslated regions of the SARS-CoV-2 genome, such as the three main untranslated regions (3 ‘UTR). The most common was a t29760c substitution in the 3 ‘UTR, shared between nine naive individuals. Future studies should investigate whether recurrent UTR mutations observed in the current study affect SARS-CoV-2 fitness within the host.
In addition, several study participants had extreme fluctuations in or near iSNVs. They fell sharply below the detection limit and returned to high frequencies days later. It was probably due to spatial structuring, as described for influenza virus by Amato et al. 2021. Spatial structuring promotes drift-driven fluctuations in iSNVs sampled due to bottleneck effects that may result from poor quality sampling of the viral population. This finding further emphasizes the advantages of longitudinal sampling.
Finally, the researchers observed a significant compartmentalization of tissues between the oral and nasal environments during SARS-CoV-2 infection in some study participants. This explains why sampling a single tissue site may not provide a complete picture of the diversity of SARS-CoV-2 within a host.
Conclusions
The study data provided a high-resolution profile of the evolutionary dynamics of SARS-CoV-2 within the host. The results of the study showed that the evolution of SARS-CoV-2 within the host in both naïve and immune individuals appeared to be driven primarily by stochastic forces during acute infections. In addition, the researchers identify mutational hotspots within the SARS-CoV-2 genome, according to selection pressure that promotes the emergence of iSNVs capable of advanced transmission.
In addition, they also detected significant compartmentalization of SARS-CoV-2 tissues between nasal swabs and saliva samples in many individuals. In addition, recurrent detection of successful and not-so-successful iSNVs on a global scale indicated areas of alliance and discrepancy between selective pressures within the host and between guests. These data shed light on the forces that shape the global patterns of the evolution of SARS-CoV-2.
* Important news
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered conclusive, guided by clinical practice / health-related behavior, or treated as established information.
Magazine reference:
- Evolutionary host dynamics and tissue compartmentation during acute SARS-CoV-2 infection, Mireille Farjo, Katia Koelle, Michael A. Martin, Laura L Gibson, Kimberly KO Walden, Gloria Rendon, Christopher J. Fields, Fadi Alnaji , Nicholas Gallagher, Chun Huai Luo, Heba H. Mostafa, Yukari C Manabe, Andrew Pekosz, Rebecca Lee Smith, David D McManus, Christopher B Brooke, bioRxiv prepress 2022, DOI: