Transmission dynamics and associated mortality of nosocomial COVID-19 throughout 2021: a retrospective study at a large teaching hospital in London.

BACKGROUND: The impact of nosocomial SARS-CoV-2 infections has changed significantly since 2020. However, there is a lack of up-to-date evidence of the epidemiology of these infections which is essential in order to appropriately guide infection control policy. AIMS: To identify the secondary attack rate of SARS-CoV-2 infection and associated mortality across different variants of concern. METHODS: A single-centre retrospective study of all nosocomial SARS-CoV-2 exposure events was conducted between 31st December 2020 and 31st December 2021. A secondary attack rate was calculated for nosocomial acquisition of SARS-CoV-2 infection and time to positivity. Positive contacts were assessed for all-cause 30-day mortality. RESULTS: A total of 346 sequential index exposure events were examined, and 1378 susceptible contacts identified. Two hundred susceptible contacts developed SARS-CoV-2 infection (secondary attack rate of 15.5%). The majority of index cases (59%) did not result in any secondary SARS-CoV-2 infection. Where close contacts developed SARS-CoV-2 infection, 80% were detected within the first five days since last contact with the index case. The overall associated mortality among positive contacts across 2021 was 9%, with an estimated reduction of 68% when comparing periods of high Omicron versus Alpha transmission. CONCLUSION: Our findings describe that most SARS-CoV-2 infections are detected within five days of contact with an index case; we have also demonstrated a considerably lower mortality rate with the Omicron variant in comparison to previous variants. These findings have important implications for informing and supporting infection control protocols to allow movement through the hospital, and ensure patients access care safely.

Evaluating the performance characteristics of five lateral flow assays for the detection of the SARS-CoV-2 nucleocapsid antigen.

In response to the COVID-19 pandemic, lateral flow assays (LFAs) for the detection of SARS-CoV-2 antigen have been proposed as a complementary option to the more costly and time consuming reverse-transcriptase polymerase chain reaction (RT-PCR). We assessed five commercially available SARS-CoV-2 antigen detecting LFAs (ASSUT EUROPE (Rome, Italy), Besthree (Taizhou, China), Encode (Zhuhai, China), Fortress (Antrim UK), and Hughes Medical (Buckinghamshire, UK), using samples collected from hospitalised individuals with COVID-19 and compared these results against established RT-PCR assays with the aim of estimating test performance characteristics. We performed a diagnostic accuracy study of the five LFAs on 110 inpatients with confirmed COVID-19 and 75 COVID-19 negative control participants. Assay evaluation was performed using a modified version of each manufacturer's protocol allowing for parallel testing of a single sample on multiple assays. Additional variables were studied including infection acquisition, oxygenation requirements at time of swabbing, and patient outcomes. The 110 patients were 48% (53) female, with mean age 67 years (range 26-100 years), and 77% (85) cases were community onset SARS-CoV-2. Across the five assays, sensitivity ranged from 64 (95% CI 53-73) to 76% (95% CI 65-85); Fortress performed best with sensitivity of 76% (95% CI 65-85). Specificity was high across all assays with 4/5 LFAs achieving 100%. LFA sensitivity was not dependant on RT-PCR cycle thresholds. SARS-CoV-2 antigen detecting LFAs may complement RT-PCR testing to facilitate early diagnosis and provide community testing strategies for identification of patients with COVID-19, however we find suboptimal test performance characteristics across a range of commercially available manufacturers, below WHO and MHRA pre-set sensitivity performance thresholds. With such variation in sensitivity between LFAs and PCR testing and between assay brands, we advise caution in the deployment of LFAs outside of environments with clinical oversight.

Point-of-care SARS-CoV-2 serological assays for enhanced case finding in a UK inpatient population.

Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic. Case identification is currently made by real-time polymerase chain reaction (PCR) during the acute phase and largely restricted to healthcare laboratories. Serological assays are emerging but independent validation is urgently required to assess their utility. We evaluated five different point-of-care (POC) SARS-CoV-2 antibody test kits against PCR, finding concordance across the assays (n = 15). We subsequently tested 200 patients using the OrientGene COVID-19 IgG/IgM Rapid Test Cassette and find a sensitivity of 74% in the early infection period (day 5-9 post symptom onset), with 100% sensitivity not seen until day 13, demonstrating inferiority to PCR testing in the infectious period. Negative rate was 96%, but in validating the serological tests uncovered potential false-negatives from PCR testing late-presenting cases. A positive predictive value (PPV) of 37% in the general population precludes any use for general screening. Where a case definition is applied however, the PPV is substantially improved (95.4%), supporting use of serology testing in carefully targeted, high-risk populations. Larger studies in specific patient cohorts, including those with mild infection are urgently required to inform on the applicability of POC serological assays to help control the spread of SARS-CoV-2 and improve case finding of patients that may experience late complications.