Abstract
During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online “immuno-analytics” resource that combines epitope, sequence, protein and SARS-CoV-2 mutation analysis. SARS-CoV-2 spike and nucleocapsid proteins are both vaccine and serological diagnostic targets. Using the tool, the nucleocapsid protein appears to be a sub-optimal target for use in serological platforms. Spike D614G (and nsp12 L314P) mutations were most frequent (> 86%), whilst spike A222V/L18F have recently increased. Also, Orf3a proteins may be a suitable target for serology. The tool can accessed from: http://genomics.lshtm.ac.uk/immuno (online); https://github.com/dan-ward-bio/COVID-immunoanalytics (source code).
Highlights
COVID-19, the disease caused by the Severe acute respiratory syndrome (SARS)-CoV-2 virus, was first characterised in the city of Wuhan, Hubei, and has spread to 190 countries
Utility and discussion To demonstrate the functionality of the immunoanalytics tool, we present an analysis of the SARS-CoV-2 spike, nucleocapsid and orf3a proteins, which are vaccine and serological targets
Comparing the predictive metascores of the nucleocapsid protein variant sites, we observed an increase of 26% over the global median, indicating that nucleocapsid protein non-synonymous mutations may impact epitope variability more than those found in orf3a
Summary
COVID-19, the disease caused by the SARS-CoV-2 virus, was first characterised in the city of Wuhan, Hubei, and has spread to 190 countries. The majority of infections are either asymptomatic or result in mild flulike symptoms, with severe cases of viral pneumonia affecting between 1.0% (≥ 20 years) and 18.4% (≥ 80 years) of diagnosed patients [3]. The demand for serological diagnostics is high, because these tests are capable of detecting SARSCoV-2 antibodies, which are biomarkers indicative of current infection that remains present after viral clearance [6]. These tools are essential to address crucial sero-epidemiological questions, like understanding viral (2021) 13:4 prevalence across a population, the percentage of asymptomatic patients and longevity of antibody responses post infection
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