Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission

Abstract

75Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between 76 countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 77 3-week period (April 2020), 1,032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK 78 teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-79 time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the 80 asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly 81 asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus 82 disease 2019 (COVID-19) >7 days prior to testing, most self-isolating, returning well. Clusters of HCW 83 infection were discovered on two independent wards. Viral genome sequencing showed that the majority of 84HCWs had the dominant lineage B•1. Our data demonstrates the utility of comprehensive screening of 85HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital 86 staff. 87 88

Rational use of SARS-CoV-2 polymerase chain reaction tests within institutions caring for the vulnerable

“…A transmission model parameterised to a typical hospital in the United Kingdom suggests that up to 20% of infections in patients and 89% of infections in healthcare workers may be a result of nosocomial transmission 7 . Consistent with that, SARS-CoV-2 infections in healthcare workers and staff have been observed to cluster on particular hospital wards 8 and a large proportion of hospital staff working in particularly exposed roles, such as housekeepers (34.5%) and those working in acute medicine (33.3%), show serological evidence of having been infected during the initial weeks of the pandemic 9 .…”

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

“…This analysis required over 150 hours to obtain enough samples from the joint posterior, while using the latest GPU accelerated implementations 21 on 15 parallel runs. With a combined chain length of over 2.2x10 9 states, and an average runtime of 0.9 hours per million states, the significant computational demands required make this approach impractical when speed is critical. On the other hand, we here use a maximum likelihood method implemented in the program TreeTime 16 to infer a time-scaled phylogenetic tree in a short amount of time (~3 hours for the data set analysed here).…”

“…Reverse transcription was carried out via SuperScript IV and cDNA was posteriorly amplified using Q5 R High-Fidelity DNA Polymerase (NEB) with the AR-TIC nCov-2019 primers and following the recommendations in the sequencing protocol of the ARTIC Network (https://artic.network/ncov-2019). Samples were multiplexed following the manufacturer's recommendations using the Oxford Nanopore Native Barcoding Expansion kits NBD104 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12) and NBD114 (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24), in conjunction with Ligation Sequencing Kit 109 (Oxford Nanopore). Sequencing was carried out on a MinION sequencer using R9.4.1 flow cells and MinKNOW 2.0 software.…”

“…Since the early days of the pandemic, there has been an important mobilisation of the scientific community to understand its epidemiology and help providing a real-time response. To this end, research teams around the world have massively sequenced and publicly released dozens of thousands of viral genome sequences to study the origin of the virus 5,6 , and to trace its spread at global, country or community-level scales [7][8][9] . In this context, a platform like Nexstrain 10 , already widely used and recognised by the academic community and beyond, has quickly become a reference to follow the travel history of SARS-CoV-2 lineages.…”

Overcoming Limitations in the Availability of Swabs Systems Used for SARS-CoV-2 Laboratory Diagnostics

“…In many regions hit by the COVID-19 pandemic, health authorities have put containment strategies in place 17 . Among these, broad RT-PCR testing of asymptomatic or symptomatic individuals, restrictions in transportation, tracing of social contacts, barrier precautions, isolation and quarantine measures are the most common ones [18][19][20][21] . While the detection of SARS-CoV-2 by RT-PCR is highly speci c for COVID -19, the sensitivity of the method is limited by several factors, including the employed swab sets [22][23][24] .…”