The ability of single genes vs full genomes to resolve time and space in outbreak analysis

Abstract

BackgroundInexpensive pathogen genome sequencing has had a transformative effect on the field of phylodynamics, where ever increasing volumes of data have promised real-time insight into outbreaks of infectious disease. As well as the sheer volume of pathogen isolates being sequenced, the sequencing of whole pathogen genomes, rather than select loci, has allowed phylogenetic analyses to be carried out at finer time scales, often approaching serial intervals for infections caused by rapidly evolving RNA viruses. Despite its utility, whole genome sequencing of pathogens has not been adopted universally and targeted sequencing of loci is common in some pathogen-specific fields.ResultsIn this study we highlighted the utility of sequencing whole genomes of pathogens by re-analysing a well-characterised collection of Ebola virus sequences in the form of complete viral genomes (≈19 kb long) or the rapidly evolving glycoprotein (GP, ≈2 kb long) gene. We have quantified changes in phylogenetic, temporal, and spatial inference resolution as a result of this reduction in data and compared these to theoretical expectations.ConclusionsWe propose a simple intuitive metric for quantifying temporal resolution, i.e. the time scale over which sequence data might be informative of various processes as a quick back-of-the-envelope calculation of statistical power available to molecular clock analyses.

An epidemiological surveillance of hand foot and mouth disease in paediatric patients and in community: A Singapore retrospective cohort study, 2013–2018

“…There are temporal resolution limits inherent within viral genomes as the loss of information associated with such short sequences leads to decreased phylogenetic and molecular clock signals ( S1 Text ). Coupled with the highly uneven and inadequate sampling of CV-A6 viruses worldwide, it is currently not possible to infer transmission, migration and origins of these viruses [ 32 ]. Our effort to determine the temporal event of CV-A6 genetic shifts in the past with global CV-A6 strains were rather futile as most of the CV-A6 sequences in GeneBank were just partial VP1 sequences yielding a highly diffuse temporal signal ( Fig 4C ).…”

Genotypic diversity and dynamic nomenclature ofParechovirus A

“…23,29,72 Whole genome sequences could offer valuable additional genetic information to better resolve the phylogenetic relationships of PeV. 73 However, PeVs have high rates of recombination. With GARD we found 2098 potential breakpoints in the whole genome alignment, and this implies that even with whole genome data unravelling the evolutionary history of PeV-A is likely to be difficult.…”

Epidemiologic Linkage of COVID-19 Outbreaks at Two University-affiliated Hospitals in the Seoul Metropolitan Area in March 2020

“… 10 11 Korea Centers for Disease Control and Prevention (KCDC) reviewed seven major COVID-19 nosocomial outbreaks in South Korea affecting 39 to 196 patients, 5 but no molecular epidemiological investigations were reported. Whole genome sequencing (WGS) is a powerful tool for epidemiological analysis of newly emerging viral disease outbreaks 12 13 and currently is an established technique to classify the clades and lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to investigate the evolution and epidemiology of the virus. 14 15 At the clade level, it is possible to match dominant clones to certain regions.…”