MERS-CoV Infection of Alpaca in a Region Where MERS-CoV is Endemic

of drug resistance. However, knowledge of strain genotype is no less clinically and epidemiologically relevant. A superspreading strain might be marked with other pathobiologically important features. In the case presented here (indeed emerging and MDR), the NGS-based in silico spoligotyping would confuse the MDR/extensively drug resistant SIT266 with "less dangerous" SIT264. To be precise, the revealed discrepancy is not inherent to the NGS technology itself. Although the general limitation of the use of short sequencing reads to infer repetitive genome regions is known, it did not pose a problem in our study. However, both bioinformatics tools predicted the spoligoprofile solely from the presence or absence of spacer sequences and did not take into account a "hiding" effect exerted by a putative IS6110 insertion on adjacent spacer under classical spoligotyping.