ABSTRACT
The ongoing SARS-CoV-2 pandemic, which emerged in December 2019, revolutionized genomic surveillance, leading to new means of tracking viral spread and monitoring genetic changes in their genomes over time. One of the key sequencing methods used during the pandemic is based on massively parallel short read sequencing based on Illumina technology. In this work, we present a highly scalable and easily deployable computational pipeline for the analysis of Illumina sequencing data, which is used in Slovak SARS-CoV-2 genomic surveillance efforts. We discuss several issues that arose during the pipeline design, and which could both provide useful insight into the analysis processes and serve as a guideline for optimized future outbreak surveillance projects. Copyright © 2021 for this paper by its authors.
ABSTRACT
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) led to a significant disease burden and disruptions in health systems. We describe the epidemiology and transmission characteristics of early coronavirus disease 2019 (COVID-19) cases in Bavaria, Germany. Cases were reverse transcription polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infections, reported from 20 January-19 March 2020. The incubation period was estimated using travel history and date of symptom onset. To estimate the serial interval, we identified pairs of index and secondary cases. By 19 March, 3546 cases were reported. A large proportion was exposed abroad (38%), causing further local transmission. Median incubation period of 256 cases with exposure abroad was 3.8 days (95%CI: 3.5-4.2). For 95% of infected individuals, symptom onset occurred within 10.3 days (95%CI: 9.1-11.8) after exposure. The median serial interval, using 53 pairs, was 3.5 days (95%CI: 3.0-4.2; mean: 3.9, s.d.: 2.2). Travellers returning to Germany had an important influence on the spread of SARS-CoV-2 infections in Bavaria in early 2020. Especially in times of low incidence, public health agencies should identify holiday destinations, and areas with ongoing local transmission, to monitor potential importation of SARS-CoV-2 infections. Travellers returning from areas with ongoing community transmission should be advised to quarantine to prevent re-introductions of COVID-19.