Screening for the alpha variant of SARS-CoV-2 (B.1.1.7) and the impact of this variant on circulating biomarkers in hospitalised patients

Control of SARS-CoV-2 transmission is complicated by the emergence of variants, especially those containing mutations in the spike protein. By enhancing infectivity and evading immunity, infection with these variants might result in more severe clinical outcomes as well as being more resistant to vaccines developed on the basis of the original prototypic virus variant. One such example is the alpha variant (B.1.1.7), which has been detected in more than 100 countries and rapidly become the dominant strain in the UK in late 2020 and early 2021. There is an urgent need to develop appropriate surveillance programmes to rapidly monitor the spread of variants and to better understand the role of variants in disease outcomes and immune evasion. The nucleotide sequencing method, the gold standard of variant detection, is unsuitable as a fast-response surveillance tool by frontline diagnostic services which require detection methods with short turnaround times. We developed a screening protocol based of sequential allele-specific qPCR for detection of the N501Y mutation and H69/V70 deletion present in the alpha/B.1.1.7 variant. We tested this protocol in previously confirmed positive samples from the Pathology Dept, University Hospital Coventry and Warwickshire during the second wave period in the UK (December 2020-March 2021). In these samples variant identity was confirmed by NGS sequencing via COG-UK. Our results identified increased incidence of variants containing both N501Y and {Delta}69/70 HV mutations, especially in patients admitted during January and early February 2021. This approach, which yields results within 3 hours, can be used as an initial rapid screening step with NGS as confirmatory follow-up. We also report that the increased prevalence of alpha/B.1.1.7 variant in admitted patients since mid-January 2021, a period that characterised peaked mortality rates, was associated with a sharp 2.5-fold rise in the mean circulating IL-6 level and to a lesser extent Troponin-T. More detailed biomarker analysis of a small cohort of patients (n=83), where variant status and clinical outcomes were available, demonstrated that deceased patients infected with the alpha/B.1.1.7 variant had significantly higher levels of inflammation and cell injury markers, especially IL-6 and LDH, compared to deceased patients infected with a non-alpha/B.1.1.7 variant, pointing towards a more severe inflammatory disease phenotype. In contrast, both groups survivors most biomarker exhibited levels below the group average, with distinct patterns of modified z-scores present.