Genome Sequences of Rare Human Enterovirus Genotypes Recovered from Clinical Respiratory Samples in Bern, Switzerland

ABSTRACT We report on genomic sequences of human enteroviruses (EVs) that were identified in respiratory samples in Bern, Switzerland, in 2018 and 2019. Besides providing sequences for coxsackievirus A2, echovirus 11, and echovirus 30, we determined the sequences of rare EV-D68 and EV-C105 genotypes circulating in Switzerland.

T he viral genus Enterovirus belongs to the family Picornaviridae, which is associated with several human diseases (1). Some genotypes are predominantly isolated from respiratory samples (2,3), e.g., the recently discovered species C genotypes enterovirus-C104 (EV-C104), EV-C105, and EV-C117 (4) or the well-known genotype EV-D68, which was linked to outbreaks of severe respiratory illness in children in summer 2014 in North America and cases of acute flaccid paralysis (5,6). Various outbreaks of EV-D68 have since been reported worldwide (7)(8)(9).
Sequence analysis showed that the Bern EV-D68 case clustered with subclade B3 sequences isolated from the United States (Fig. 1A), one of the most commonly reported EV-68 clades circulating worldwide in 2018 (16,17). Analysis of all EV-C105 sequences The closest sequence was that associated with the highest score via the NCBI BLASTn algorithm.

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(VP1) in GenBank showed that the two identified Bern EV-C105 isolates may correspond to different circulating strains (Fig. 1B). Only a few genome sequences of this globally circulating genotype (4, 18-20) are available to date (Fig. 1B).
Here, we report the first near-complete sequence of the EV-D68 genotype in Bern, Switzerland. Outbreaks of EV-D68 were reported widely in Europe in 2018 (16,21,22). Together with six published sequences reported in 2018 in Basel, Switzerland (17), our study sheds light on the recent circulation of EV-D68 in Switzerland, a country with few data on this genotype to date. Furthermore, we present the first two sequences of the rarely reported EV-C105 genotype in Switzerland. Data availability. The consensus genome sequences and associated raw data were deposited in the European Nucleotide Archive (ENA) under BioProject accession number PRJEB51320; the corresponding accession numbers for samples are provided in Table 1.

ACKNOWLEDGMENTS
The project was financed by the Institute for Infectious Diseases, University of Bern, Switzerland.