Classification of a novel Serratia species, isolated from a wound swab in North Rhine-Westphalia: Proposal of Serratia sarumanii sp. nov.

Novel, white-pigmented, Gram-negative bacterial strains (K-M0706T, K-M0228, K-M0252, K-M0260) were isolated from clinical samples. With a similarity of up to 69.7 % to Serratia nevei S15T and up to 63.8 % to Serratia marcescens ATCC 13880T, as determined by digital DNA-DNA hybridization, the strains were assigned as novel species of the genus Serratia. The species can easily be differentiated from the red colored Serratia marcescens sensu stricto by its white phenotype. Discrimination between this strain and Serratia nevei is possible due to alpha-glucosidase activity and O/129-resistance, as shown for strain K-M0706T. The major fatty acids were determined as myristate, palmitate, cis-9,10-methylenehexadecanoate, linoleate, and (all cis-9,10)-methyleneoctadecanoate. These phenotypical and genomic data support the assignment of a novel species within the genus Serratia, named S. sarumanii due to its pathogenicity and white phenotype, with strain K-M0706T as the type strain.

Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines.

Genomic surveillance of the SARS-CoV-2 pandemic is crucial and mainly achieved by amplicon sequencing protocols. Overlapping tiled-amplicons are generated to establish contiguous SARS-CoV-2 genome sequences, which enable the precise resolution of infection chains and outbreaks. We investigated a SARS-CoV-2 outbreak in a local hospital and used nanopore sequencing with a modified ARTIC protocol employing 1200 bp long amplicons. We detected a long deletion of 168 nucleotides in the ORF8 gene in 76 samples from the hospital outbreak. This deletion is difficult to identify with the classical amplicon sequencing procedures since it removes two amplicon primer-binding sites. We analyzed public SARS-CoV-2 sequences and sequencing read data from ENA and identified the same deletion in over 100 genomes belonging to different lineages of SARS-CoV-2, pointing to a mutation hotspot or to positive selection. In almost all cases, the deletion was not represented in the virus genome sequence after consensus building. Additionally, further database searches point to other deletions in the ORF8 coding region that have never been reported by the standard data analysis pipelines. These findings and the fact that ORF8 is especially prone to deletions, make a clear case for the urgent necessity of public availability of the raw data for this and other large deletions that might change the physiology of the virus towards endemism.