A new combination testing methodology to identify accurate and economical point-of-care testing strategies (preprint)

ABSTRACT Background Quick, cheap and accurate point-of-care testing is urgently needed to enable frequent, large-scale testing to contain COVID-19. Lateral flow tests for antigen and antibody detection are an obvious candidate for use in community-wide testing, because they are quick and cheap relative to lab-processed tests. However, their low accuracy has limited their adoption. We develop a new methodology to increase the diagnostic accuracy of a combination of cheap, quick and inaccurate index tests with correlated or discordant outcomes, and illustrate its performance on commercially available lateral flow immunoassays (LFIAs) for Sars-CoV-2 antibody detection. Methods and Findings We analyze laboratory test outcomes of 300 serum samples from health care workers detected with PCR-confirmed SARS-Cov-2 infection at least 21 days prior to sample collection, and 500 pre-pandemic serum samples, from a national seroprevalence survey, tested using eight LFIAs (Abbott, Biosure/Mologic, Orientgene-Menarini, Fortress, Biopanda I, Biopanda II, SureScreen and Wondfo) and Hybrid DABA as reference test. For each of 14 two-test combinations (e.g., Abbott, Fortress) and 16 three-test combinations (e.g., Abbott, Fortress, Biosure/Mologic) used on at least 100 positive and 100 negative samples, we classify an outcome sequence – e.g., (+,–) for (Abbott, Fortress) – as positive if its combination positive predictive value (CPPV) exceeds a given threshold, set between 0 and 1. Our main outcome measures are the sensitivity and specificity of different classification rules for classifying the outcomes of a combination test. We define testing possibility frontiers which represent sensitivity and false positive rates for different thresholds. The envelope of frontiers further enables test selection. The eight index tests individually meet neither the UK Medicines and Healthcare Products Regulatory Agency’s 98% sensitivity and 98% specificity criterion, nor the US Center for Disease Control’s 99.5% specificity criterion. Among these eight tests, the highest single-test LFIA specificity is 99.4% (with a sensitivity of 65.2%) and the highest single-test LFIA sensitivity is 93.4% (with a specificity of 97.4%). Using our methodology, a two-test combination meets the UK Medicines and Healthcare Products Regulatory Agency’s criterion, achieving sensitivity of 98.4% and specificity of 98.0%. While two-test combinations meeting the US Center for Disease Control’s 99.5% specificity criterion have sensitivity below 83.6%, a three-test combination delivers a specificity of 99.6% and a sensitivity of 95.8%. Conclusions Current CDC guidelines suggest combining tests, noting that “performance of orthogonal testing algorithms has not been systematically evaluated” and highlighting discordant outcomes. Our methodology combines available LFIAs to meet desired accuracy criteria, by identifying testing possibility frontiers which encompass benchmarks, enabling cost savings. Our methodology applies equally to antigen testing and can greatly expand testing capacity through combining less accurate tests, especially for use cases needing quick, accurate tests, e.g., entry to public spaces such as airports, nursing homes or hospitals.

Longevity of SARS-CoV-2 immune responses in haemodialysis patients and protection against reinfection (preprint)

Background Patients with end stage kidney disease (ESKD) receiving in-centre haemodialysis (ICHD) have had high rates of SARS-CoV-2 infection. Following infection, ICHD patients frequently develop serological evidence of infection, even with asymptomatic disease. The aim of this study is to investigate the durability and functionality of immune responses to SARS-CoV-2 infection in ICHD patients. Methods Three hundred and fifty-six ICHD patients were longitudinally screened for SARS-CoV-2 antibodies and underwent routine PCR-testing for symptomatic and asymptomatic infection. Patients were screened for nucleocapsid protein (anti-NP) and receptor binding domain (anti-RBD) antibodies. Patients who became seronegative at 6 months were investigated for SARS-CoV-2 specific T-cell responses. Results One hundred and twenty-nine (36.2%) patients had detectable antibody to anti-NP at Time 0, of which 127(98.4%) also had detectable anti-RBD. At 6 months, of 111 patients tested, 71(64.0%) and 97 (87.4%) remained anti-NP and anti-RBD seropositive respectively, p<0.001. For patients who retained antibody, both anti-NP and anti-RBD levels reduced significantly after 6 months. Ten patients who were anti-NP and anti-RBD seropositive at Time 0, had no detectable antibody at 6 months; of which 8 were found to have SARS-CoV-2 antigen specific T cell responses. Independent of antibody status at 6 months, patients with serological evidence of SARS-CoV-2 antibodies at Time 0, were at significantly lower risk of being diagnosed with infection Conclusions ICHD patients mount durable immune responses 6 months post SARS-CoV-2 infection, with <3% of patients showing no evidence of humoral or cellular immunity. These immune responses are associated with a reduced risk of subsequent reinfection.

Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England (preprint)

BackgroundUnderstanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. MethodsWe undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. FindingsWe demonstrated a seroprevalence of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic, and 16 (27%) were asymptomatic for core COVID-19 symptoms: fever, cough or anosmia. Specificity of anosmia for seropositivity was 95%, compared to 88% for fever cough and anosmia combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive. InterpretationSeroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response. FundingNIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC