![]() For example, genomic analysis can shed light on the emergence of variants to reconstruct transmission chains in an epidemic 5, 6, 7, 8, 9. ![]() While classical epidemiological techniques such as contact tracing remain integral to the epidemic control toolkit, they can be supported and strengthened by modern technological approaches 4. The control and/or elimination of infectious diseases depend on identifying and interrupting transmission chains, particularly during acute epidemics 1, 2, 3. ![]() Our approach further highlights the critical role bottlenecks play in reserving the within-host diversity during transmission. In this work we show that, beyond the presence and absence of within-host variants, differences arising in the relative abundance of iSNVs (allelic frequency) can infer transmission pairs more precisely. We observe that within-host single nucleotide variants (iSNVs) are maintained over multiple transmission steps and present a model for inferring the likelihood that a given pair of sequenced samples are linked by transmission. In this work, we assess the utility of deep-sequenced genomic surveillance (where genomic regions are sequenced hundreds to thousands of times) using a mouse transmission model involving controlled spread of the pathogenic bacterium Citrobacter rodentium from infected to naïve female animals. However, the role of such variation in transmission is understudied due to a lack of experimental and clinical datasets that capture pathogen diversity in both donor and recipient hosts. One way to identify transmission pairs – two hosts in which infection was transmitted from one to the other – is using the variation of the pathogen within each single host (within-host variation). Identifying and interrupting transmission chains is important for controlling infectious diseases.
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