Following on from a recent analysis of enterovirus D68 (EV-D68) samples from outbreaks in Sweden in 2014 and 2016 (preprint here), we have been able to obtain near full-length genome (NFLG) sequences from three EV-D68 samples from Stockholm from September/October this year. We believe that these are the first available full-length sequences for this season.
The samples can be seen on Nextstrain:
https://nextstrain.org/enterovirus/d68
The samples are shown in the context of the previously analyzed sequences below (circled in red):
As can be seen, the sequences fall in the B3 clade, consistent with unpublished reports based on VP1 sequences from elsewhere in Europe for samples this season. Interestingly, these samples do not root among the most recent 2016 outbreak samples, but deeper in the B3 subclade. In addition, two sequences are genetically closely related, but one is distinct, suggesting the presence of two B3 lineages in Stockholm.
The samples were obtained from patients with respiratory symptoms. No cases of acute flaccid myelitis have been reported in Sweden this season.
Consensus sequences for these three samples can be found here:
Dates are in the sequence names, in the format "YYMMDD"
Authors
Robert Dyrdak - Karolinska Institute, Stockholm, Sweden
Monika Mastafa - Karolinska Institute, Stockholm, Sweden
Emma Hodcroft - Biozentrum, University of Basel, Basel, Switzerland
Richard Neher - Biozentrum, University of Basel, Basel, Switzerland
Jan Albert - Karolinska Institute, Stockholm, Sweden