Fig. 3 Whole-genome analysis a) ARTIC workflow b)-c) sequence variation as the virus evolves
The availability of the first genome sequences means that molecular analyses can be designed. In the early stages of an outbreak, it may be that genome sequences of the pathogen which have been obtained from different patients do not vary appreciably, but over time, as the pathogen is transmitted more widely from person to person, more genomic polymorphism is likely to emerge. Whole-genome sequencing of strains from large numbers of patients, obtained, for instance, using the protocol from the ARTIC group (Fig. 3a), can be used to monitor the rate of the pathogen’s evolution (Fig. 3b) and can provide insight into patterns of its transmission. Whole-genome sequences can also be used to develop accurate, rapid and high-throughput analyses for wide-scale testing and screening (Fig. 3c; 148,476 sequences analysed Nov. 2020).
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