Genomic surveillance of SARS-CoV-2 evolution by a centralised pipeline and weekly focused sequencing, Austria, January 2021 to March 2023.

BackgroundThe COVID-19 pandemic was largely driven by genetic mutations of SARS-CoV-2, leading in some instances to enhanced infectiousness of the virus or its capacity to evade the host immune system. To closely monitor SARS-CoV-2 evolution and resulting variants at genomic-level, an innovative pipeline termed SARSeq was developed in Austria.AimWe discuss technical aspects of the SARSeq pipeline, describe its performance and present noteworthy results it enabled during the pandemic in Austria.

Breakthrough Infections in SARS-CoV-2-Vaccinated Multiple Myeloma Patients Improve Cross-Protection against Omicron Variants.

Patients with multiple myeloma (MM) are a heterogenous, immunocompromised group with increased risk for COVID-19 morbidity and mortality but impaired responses to primary mRNA SARS-CoV-2 vaccination. The effects of booster vaccinations and breakthrough infections (BTIs) on antibody (Ab) levels and cross-protection to variants of concern (VOCs) are, however, not sufficiently evaluated. Therefore, we analysed humoral and cellular vaccine responses in MM patients stratified according to disease stage/treatment into group (1) monoclonal gammopathy of undetermined significance, (2) after stem cell transplant (SCT) without immunotherapy (IT), (3) after SCT with IT, and (4) progressed MM, and in healthy subjects (prospective cohort study).

WAVES (Web-based tool for Analysis and Visualization of Environmental Samples)-a web application for visualization of wastewater pathogen sequencing results.

Motivation: Environmental monitoring of pathogens provides an accurate and timely source of information for public health authorities and policymakers. In the last 2 years, wastewater sequencing proved to be an effective way of detection and quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants circulating in population. Wastewater sequencing produces substantial amounts of geographical and genomic data.

VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples.

Background: The genomes of SARS-CoV-2 are classified into variants, some of which are monitored as variants of concern (e.g. the Delta variant B.

Avirulent phenotype promotes adaptation to the intramacrophage environment.

, the causative agent of whooping cough, is an extracellular, strictly human pathogen. However, it has been shown that cells can escape phagocytic killing and survive in macrophages upon internalization. Our time-resolved RNA-seq data suggest that efficiently adapts to the intramacrophage environment and responds to host bactericidal activities.