They are what you eat: Shaping of viral populations through nutrition and consequences for virulence

Honce, Rebekah; Schultz‐Cherry, Stacey

doi:10.1371/journal.ppat.1008711

Cited by 8 publications

(11 citation statements)

References 48 publications

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“…If we are to re-evaluate our assumptions in modeling the evolutionary history of SARS-CoV-2, we must also consider single nucleotide variants (SNVs) and their impact on presumed rates of evolution. SNVs are acquired in RNA viruses, including coronaviruses, at a rate 103–107-times greater per nucleotide copied than DNA viruses [ 10 , 11 ]. During replication SNVs are purged or retained resulting in the formation of quasi-species with greater fitness than that of the parent or ‘master’ sequence [ 11 ].…”

mentioning

confidence: 99%

“…SNVs are acquired in RNA viruses, including coronaviruses, at a rate 103–107-times greater per nucleotide copied than DNA viruses [ 10 , 11 ]. During replication SNVs are purged or retained resulting in the formation of quasi-species with greater fitness than that of the parent or ‘master’ sequence [ 11 ]. This increase in fitness is accounted for by the acquisition of mutations across SNVs, which result in selection, competition and genetic drift acting upon the entire viral ‘swarm’ [ 11 ].…”

mentioning

confidence: 99%

“…During replication SNVs are purged or retained resulting in the formation of quasi-species with greater fitness than that of the parent or ‘master’ sequence [ 11 ]. This increase in fitness is accounted for by the acquisition of mutations across SNVs, which result in selection, competition and genetic drift acting upon the entire viral ‘swarm’ [ 11 ]. Frequently present in recombinant coronaviruses, such as SARS-CoV-2 and RaTG13, quasi-species allow for either the evolution of the ‘master’ consensus sequence or the entirety of its mutant spectrum [ 10 , 11 , 15 ].…”

mentioning

confidence: 99%

“…This increase in fitness is accounted for by the acquisition of mutations across SNVs, which result in selection, competition and genetic drift acting upon the entire viral ‘swarm’ [ 11 ]. Frequently present in recombinant coronaviruses, such as SARS-CoV-2 and RaTG13, quasi-species allow for either the evolution of the ‘master’ consensus sequence or the entirety of its mutant spectrum [ 10 , 11 , 15 ]. The optional duality of these simultaneous processes and corresponding outcomes allows for either stasis or rapid evolution in the observed consensus sequence (10 - 4 substitutions per site per year versus 10 - 1 –10 - 2 substitutions per site per year) [ 10 , 11 ].…”

mentioning

confidence: 99%

“…Frequently present in recombinant coronaviruses, such as SARS-CoV-2 and RaTG13, quasi-species allow for either the evolution of the ‘master’ consensus sequence or the entirety of its mutant spectrum [ 10 , 11 , 15 ]. The optional duality of these simultaneous processes and corresponding outcomes allows for either stasis or rapid evolution in the observed consensus sequence (10 - 4 substitutions per site per year versus 10 - 1 –10 - 2 substitutions per site per year) [ 10 , 11 ]. It follows, therefore, that the calculation of the nonsynonymous to synonymous (dN/dS) substitution rate ratio of RNA in the phylogenetic analysis should account for these factors, where appropriate [ 15 ].…”

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confidence: 99%

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What is the Intermediate Host Species of SARS-CoV-2?

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Stebbing

2021

Future Virol.

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What is the Intermediate Host Species of SARS-CoV-2?

Friend

Stebbing

2021

Future Virol.

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A general approach to identify low-frequency variants within influenza samples collected during routine surveillance

et al. 2022

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Influenza viruses exhibit considerable diversity between hosts. Additionally, different quasispecies can be found within the same host. High-throughput sequencing technologies can be used to sequence a patient-derived virus population at sufficient depths to identify low-frequency variants (LFV) present in a quasispecies, but many challenges remain for reliable LFV detection because of experimental errors introduced during sample preparation and sequencing. High genomic copy numbers and extensive sequencing depths are required to differentiate false positive from real LFV, especially at low allelic frequencies (AFs). This study proposes a general approach for identifying LFV in patient-derived samples obtained during routine surveillance. Firstly, validated thresholds were determined for LFV detection, whilst balancing both the cost and feasibility of reliable LFV detection in clinical samples. Using a genetically well-defined population of influenza A viruses, thresholds of at least 104 genomes per microlitre and AF of ≥5 % were established as detection limits. Secondly, a subset of 59 retained influenza A (H3N2) samples from the 2016–2017 Belgian influenza season was composed. Thirdly, as a proof of concept for the added value of LFV for routine influenza monitoring, potential associations between patient data and whole genome sequencing data were investigated. A significant association was found between a high prevalence of LFV and disease severity. This study provides a general methodology for influenza LFV detection, which can also be adopted by other national influenza reference centres and for other viruses such as SARS-CoV-2. Additionally, this study suggests that the current relevance of LFV for routine influenza surveillance programmes might be undervalued.

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SARS-CoV-2 Point Mutation and Deletion Spectra, and Their Association with Different Disease Outcome

Martínez-González

Soria

Vázquez-Sirvent

et al. 2022

Preprint

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Mutant spectra of RNA viruses are important to understand viral pathogenesis, and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultra-deep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of thirty nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19.

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They are what you eat: Shaping of viral populations through nutrition and consequences for virulence

Cited by 8 publications

References 48 publications

What is the Intermediate Host Species of SARS-CoV-2?

What is the Intermediate Host Species of SARS-CoV-2?

A general approach to identify low-frequency variants within influenza samples collected during routine surveillance

SARS-CoV-2 Point Mutation and Deletion Spectra, and Their Association with Different Disease Outcome

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