Variation around the dominant viral genome sequence contributes to viral load and outcome in patients with Ebola virus disease

Abstract

Background Viral load is a major contributor to outcome in patients with Ebola virus disease (EVD), with high values leading to a fatal outcome. Evidence from the 2013–2016 Ebola virus (EBOV) outbreak indicated that different genotypes of the virus can have different phenotypes in patients. Additionally, due to the error-prone nature of viral RNA synthesis in an individual patient, the EBOV genome exists around a dominant viral genome sequence. The minor variants within a patient may contribute to the overall phenotype in terms of viral protein function. To investigate the effects of these minor variants, blood samples from patients with acute EVD were deeply sequenced. Results We examine the minor variant frequency between patients with acute EVD who survived infection with those who died. Non-synonymous differences in viral proteins were identified that have implications for viral protein function. The greatest frequency of substitution was identified at three codon sites in the L gene—which encodes the viral RNA-dependent RNA polymerase (RdRp). Recapitulating this in an assay for virus replication, these substitutions result in aberrant viral RNA synthesis and correlate with patient outcome. Conclusions Together, these findings support the notion that in patients who survived EVD, in some cases, the genetic variability of the virus resulted in deleterious mutations that affected viral protein function, leading to reduced viral load. Such mutations may also lead to persistent strains of the virus and be associated with recrudescent infections.

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

“…Individual variations can be selected if they are advantageous or through founder effect or a mixture of both. In viruses with significant deletions in proteins, or the presence of stop codons, reported at a consensus sequence level, these may be balanced within the virus population with the presence of functional proteins at a minor variant level, similar to that observed in Ebola virus infection in humans [185].…”

“…Individual variations can be selected if they are advantageous or through founder effect or a mixture of both. In viruses with significant deletions in proteins, or the presence of stop codons, reported at a consensus sequence level, these may be balanced within the virus population with the presence of functional proteins at a minor variant level, similar to that observed in Ebola virus infection in humans [ 185 ]. Deep sequencing of clinical isolates can reveal important cooperative interactions between members of the virus population within a single host, and a better understanding of transmission bottlenecks will allow us to understand whether such interactions are perpetuated in transmission chains.…”

Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS

“…The minor variant population in infections has been shown to influence the kinetics of virus replication and be associated with patient outcome ( 36 ). Therefore, methodologies were developed that could be used to assess the minor variant frequency within a sample from a patient infected with MERS-CoV.…”

Sequence analysis of SARS-CoV-2 in nasopharyngeal samples from patients with COVID-19 illustrates population variation and diverse phenotypes, placing the in vitro growth properties of B.1.1.7 and B.1.351 lineage viruses in context

“…This potential disconnect is not restricted to SARS-CoV-2. The balance between consensus and minor variants and the presence of stop codons in virus populations within individual patients has been shown to influence the activity of the Ebola virus RNA dependent RNA polymerase and correlate with outcome in patients with Ebola virus disease (21). Within an individual person with SARS-CoV-2, these mixtures of functioning and presumably non-functioning viral proteins will potentially influence viral load.…”