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There is a high level of cryptic diversity; of the 17 "species" for which multiple isolates are examined here only eight are monophyletic [ 17].
In the case where multiple isolates are linked to the same outbreak (e.g. outbreak 129 547 in Table 1), some pairs are established with isolates at rank ≤2.
Our data also suggests that, if multiple isolates are obtained from a suspected source population, there will likely be added value in generating WGS data on many or all of them rather than sequencing a representative isolate.
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All STs with multiple isolates were composed of isolates with the same serotype.
Multiple isolates were subcultured from one or both of the two different selective agar plates for each sample.
Furthermore, although decreasing viral fitness coincided with decreasing plasma VL for 4 of 6 subjects from whom multiple isolates were obtained, overall, viral fitness did not correlate with plasma VL for the 14 PULSE subjects investigated (Borderline statistical significance p = 0.051; Figure 5).
Multiple isolates were collected from 17 women.
Multiple isolates were associated with a significant increase in mortality.
If multiple isolates were available from a patient, only the one first isolated was analyzed.
One sequence type was found for 6 of 9 patients for whom multiple isolates were typed.
With the exception of RV135, sequences represented by multiple isolates were geographically localised.
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