SARS-CoV-2 Genome Sequencing Methods Differ in Their Abilities To Detect Variants from Low-Viral-Load Samples.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic surveillance has been vital in understanding the spread of coronavirus disease 2019 (COVID-19), the emergence of viral escape mutants, and variants of concern. However, low viral loads in clinical specimens affect variant calling for phylogenetic analyses and detection of low-frequency variants, important in uncovering infection transmission chains. We systematically evaluated three widely adopted SARS-CoV-2 whole-genome sequencing methods for their sensitivity, specificity, and ability to reliably detect low-frequency variants. Our analyses reveal that the ARTIC v3 protocol consistently displays high sensitivity for generating complete genomes at low viral loads compared with the probe-based Illumina Respiratory Viral Oligo panel and a pooled long-amplicon method. We show substantial variability in the number and location of low-frequency variants detected using the three methods, highlighting the importance of selecting appropriate methods to obtain high-quality sequence data from low-viral-load samples for public health and genomic surveillance purposes.

A network-based laboratory data processing system for use with the Coulter STKS haematology analyser.

A highly automated laboratory data processing environment for use with Coulter STKS haematology analysers is described. This in-house system is based on a network of personal computers running Novell Network software and communicating with an IBM mainframe. The system captures the leucocyte scatterplot graphic and numeric parameters from the blood analysers, integrating this with patient demographic and request data held on the host computer. This composite picture is then reviewed on the network by laboratory personnel before generating printed reports. The system has provided greater data integrity, reduced paper flow and improved efficiency in the laboratory's operations and lays the foundations for dealing effectively with the next generation of advanced haematology analysers.