Group Vaccination Five Days before a COVID-19 Outbreak in a Long-Term Care Facility.

Rapid vaccination may be of benefit in long-term care facilities (LTCF) that are affected by an ongoing COVID-19 outbreak. However, there are concerns regarding the safety and effectiveness of such an approach, particularly regarding the vaccination of pre-symptomatic patients. Here, we report the effectiveness of vaccination in a German LTCF hit by an outbreak that was detected 5 days after the first vaccine doses were administered. In detail, 66.7% of the unvaccinated patients experienced an unfavorable course; this proportion was much lower (33.3%) among the vaccinated patients. Even though this study is limited by a small number of patients, the observation and the comparison with related published data shows that vaccination (i) is safe and (ii) may still be of benefit when given shortly before an infection or even in pre-symptomatic LTCF-patients.

poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.

In response to the SARS-CoV-2 pandemic, a highly increased sequencing effort has been established worldwide to track and trace ongoing viral evolution. Technologies, such as nanopore sequencing via the ARTIC protocol are used to reliably generate genomes from raw sequencing data as a crucial base for molecular surveillance. However, for many labs that perform SARS-CoV-2 sequencing, bioinformatics is still a major bottleneck, especially if hundreds of samples need to be processed in a recurring fashion. Pipelines developed for short-read data cannot be applied to nanopore data. Therefore, specific long-read tools and parameter settings need to be orchestrated to enable accurate genotyping and robust reference-based genome reconstruction of SARS-CoV-2 genomes from nanopore data. Here we present poreCov, a highly parallel workflow written in Nextflow, using containers to wrap all the tools necessary for a routine SARS-CoV-2 sequencing lab into one program. The ease of installation, combined with concise summary reports that clearly highlight all relevant information, enables rapid and reliable analysis of hundreds of SARS-CoV-2 raw sequence data sets or genomes. poreCov is freely available on GitHub under the GNUv3 license: github.com/replikation/poreCov.