Systematic Genomic Surveillance of SARS-CoV-2 Virus on Illumina Sequencing Platforms in the Slovak Republic-One Year Experience

Tracking the prevalence and emergence of SARS-CoV-2 variants of concern using a regional genomic surveillance program

SARS-CoV-2 molecular testing coupled with whole-genome sequencing is instrumental for real-time genomic surveillance. Genomic surveillance is critical for monitoring the spread of variants of concern (VOCs) as well as discovery of novel variants. Since the beginning of the pandemic, millions of SARS-CoV-2 genomes have been deposited into public sequence databases. This is the result of efforts of both national and regional diagnostic laboratories. In this study, we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the United States. We demonstrate that consistent daily sampling is sufficient to track the regional prevalence and emergence of VOCs and recapitulate national trends. Similar sampling efforts should be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories.

IMPORTANCE

In our manuscript, we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the United States. We demonstrate that consistent daily sampling is sufficient to track the regional prevalence and emergence of variants of concern (VOCs). Similar sampling efforts should be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories. While the SARS-CoV-2 pandemic has evolved into a more endemic form, we still believe that additional real-world information about sampling, procedures, and data interpretation is valuable for ongoing as well as future genomic surveillance efforts. Our study should be of substantial interest to clinical virologists.

Validation of the VirCapSeq-VERT system for differential diagnosis, detection, and surveillance of viral infections

IMPORTANCE

Broad range assay for accurate and sensitive diagnostics.

Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020-2022

ABSTRACTGlobal and even national genome surveillance approaches do not provide the resolution necessary for rapid and accurate direct response by local public health authorities. Hence, a regional network of microbiological laboratories in collaboration with the health departments of all districts of the German federal state of Mecklenburg-Western Pomerania (M-V) was formed to investigate the regional molecular epidemiology of circulating SARS-CoV-2 lineages between 11/2020 and 03/2022. More than 4750 samples from all M-V counties were sequenced using Illumina and Nanopore technologies. Overall, 3493 (73.5%) sequences fulfilled quality criteria for time-resolved and/or spatially-resolved maximum likelihood phylogenic analyses and k-mean/ median clustering (KMC). We identified 116 different Pangolin virus lineages that can be assigned to 16 Nextstrain clades. The ten most frequently detected virus lineages belonged to B.1.1.7, AY.122, AY.43, BA.1, B.1.617.2, BA.1.1, AY.9.2, AY.4, P.1 and AY.126. Time-resolved phylogenetic analyses showed the occurrence of virus clades as determined worldwide, but with a substantial delay of one to two months. Further spatio-temporal phylogenetic analyses revealed a regional outbreak of a Gamma variant limited to western M-V counties. Finally, KMC elucidated a successive introduction of the various virus lineages into M-V, possibly triggered by vacation periods with increased (inter-) national travel activities. The COVID-19 pandemic in M-V was shaped by a combination of several SARS-CoV-2 introductions, lockdown measures, restrictive quarantine of patients and the lineage specific replication rate. Complementing global and national surveillance, regional surveillance adds value by providing a higher level of surveillance resolution tailored to local health authorities.

Tracking the prevalence and emergence of SARS CoV2 variants of concern using a regional genomic surveillance program

SARS-CoV-2 molecular testing coupled with whole genome sequencing is instrumental for real-time genomic surveillance. Genomic surveillance is critical for monitoring the spread of variants of concern (VOC) as well as novel variant discovery. Since the beginning of the pandemic millions of SARS-CoV-2 genomes have been deposited into public sequence databases. This is the result of efforts of both national and regional diagnostic laboratories. Here we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the USA. We demonstrate that consistent daily sampling is sufficient to track the regional prevalence and emergence of VOC. Similar sampling efforts should be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories.

Vitamin D Deficiency Prevalence in Hospitalized Patients with COVID-19 Significantly Decreased during the Pandemic in Slovakia from 2020 to 2022 Which Was Associated with Decreasing Mortality

The coronavirus disease 2019 (COVID-19) pandemic has led to changes in lifestyle, which could influence vitamin D status on a population level. The purpose of our study was to compare 25-hydroxyvitamin D (25[OH]D) levels in patients hospitalized because of severe COVID-19 during two waves of the pandemic (2020/21 vs. 2021/22). A total of 101 patients from the 2021/22 wave were compared with 101 sex- and age-matched subjects from the 2020/21 wave. Patients from both groups were hospitalized during the winter season from 1 December to 28 February. Men and women were analyzed together and separately. The mean 25(OH)D concentration increased from 17.8 ± 9.7 ng/mL to 25.2 ± 12.6 ng/mL between waves. The prevalence of vitamin D deficiency (<20 ng/mL) decreased from 82% to 54%. The prevalence of adequate serum 25(OH)D concentration (>30 ng/mL) increased from 10% to 34% (p < 0.0001). The proportion of patients with a history of vitamin D supplementation increased from 18% to 44% (p < 0.0001). Low serum 25(OH)D concentration was independently associated with mortality after adjusting for age and sex for the whole cohort of patients (p < 0.0001). The prevalence of inadequate vitamin D status in hospitalized patients with COVID-19 in Slovakia decreased significantly, probably due to a higher rate of vitamin D supplementation during the COVID-19 pandemic.