key: cord-0966555-zs44enls
authors: Walker, N. F.; Byrne, R. L.; Howard, A.; Nikolaou, E.; Farrar, M.; Glynn, S.; Cheliotis, K. S.; Cubas Atienzar, A. I.; Davies, K.; Reine, J.; Rashid-Gardner, Z.; German, E. L.; Solorzano, C.; Blandamer, T.; Hitchins, L.; Myerscough, C.; Grassner, B.; Biegner, E.; Collins, A. M.; Beadsworth, M.; Todd, S.; Hill, H.; Houlihan, C. F.; Nastouli, E.; Adams, E. R.; Mitsi, E.; Ferreira, D. M.
title: Detection of SARS-CoV-2 infection by saliva and nasopharyngeal sampling in frontline healthcare workers: an observational cohort study.
date: 2021-04-26
journal: nan
DOI: 10.1101/2021.04.23.21255964
sha: 93476fac69b25c956e87751b56935070444ce7cf
doc_id: 966555
cord_uid: zs44enls

Background The SARS-CoV-2 pandemic has caused an unprecedented strain on healthcare systems worldwide, including the UK National Health Service (NHS). During the first wave of SARS-CoV-2 transmission in UK, SARS-CoV-2 NHS diagnostic test availability was limited to self-isolating symptomatic staff. The burden of symptomatic and asymptomatic infection in healthcare workers (HCW) attending work was unknown. Methods We conducted an observational cohort study of SARS-CoV-2 infection in HCW working in an acute NHS Trust during the first wave of the COVID-19 pandemic, using serial self-collected saliva and nasopharyngeal (NP) samples. We also collected self-assessed symptom profiles and isolation behaviours. We retrospectively compared SARS-CoV-2 detection by RT-PCR from saliva (weekly) and NP swabs (twice weekly) from 85 individuals in this cohort and evaluated the association with symptoms. Findings Over a 12-week period from 30th March 2020, 40% (n=34/85, CI95% 31.3-51.8%) HCWs had evidence of SARS-CoV-2 infection by surveillance NP swab and/or saliva RT-qPCR. Agreement between paired saliva and NP swabs was poor (28.6%, CI95% 13.2-48.7%) with both methods detecting symptomatic and asymptomatic infections. Symptoms were reported by 47.1% (n=40) and self-isolation by 25.9% participants (n=22). Only 41.2% (n=14/34) participants with SARS-CoV-2 infection reported any symptoms within 14 days of the infection. Interpretation HCWs are a potential source of SARS-CoV-2 transmission in hospitals and symptom screening will identify the minority of infections in HCW. Saliva is an easily accessible fluid sample for screening for SARS-CoV-2 infection and in addition to NP swab, facilitated ascertainment of symptomatic and asymptomatic cases in this setting. Combined saliva and NP testing would improve detection of SARS-CoV-2 for surveillance. Better understanding of transmissibility from asymptomatic staff using transmission-based infection precautions, is required to inform policy.

We conducted an observational cohort study of SARS-CoV-2 infection in HCW working in an acute 49 NHS Trust during the first wave of the COVID-19 pandemic, using serial self-collected saliva and 50 nasopharyngeal (NP) samples. We also collected self-assessed symptom profiles and isolation 51 behaviours. We retrospectively compared SARS-CoV-2 detection by RT-PCR from saliva (weekly) 52 and NP swabs (twice weekly) from 85 individuals in this cohort and evaluated the association 53 with symptoms. 54 Findings 55 Over a 12-week period from 30 th March 2020, 40% (n=34/85, CI95% 31.3-51.8%) HCWs had 56 evidence of SARS-CoV-2 infection by surveillance NP swab and/or saliva RT-qPCR. Agreement 57 between paired saliva and NP swabs was poor (28.6%, CI95% 13.2-48.7%) with both methods 58 detecting symptomatic and asymptomatic infections. Symptoms were reported by 47.1% (n=40) 59 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. whilst attending work was also recognized as a major threat to infection prevention and control. 81 Transmission-based precautions (including PPE) were implemented widely, for the protection of 82 the staff and their patients. 83 The global SARS-CoV-2 pandemic response has been hindered by inadequate access to 84 diagnostics. Whilst reverse transcription polymerase chain reaction (RT-qPCR) assays for SARS- 85 CoV-2 on respiratory samples have proven the mainstay of clinical diagnosis, in the early stages 86 of the pandemic, testing capacity was extremely limited, and was initially reserved only for 87 hospitalised individuals meeting the COVID-19 case definition. The UK COVID-19 case definition 88 evolved during the outbreak, losing the initial geographic restrictions on 12 th March 2020 as 89 transmission became widespread (see Box 1). Loss of taste and smell was added as a symptom 90 to the case definition in May 2020. With coordinated national and global efforts, diagnostic 91 testing capacity has been scaled up, substantially. Currently, regular asymptomatic screening of 92 HCW is standard practice in the NHS utilizing both respiratory swabbing and saliva, however, 93 there has not been consensus on the optimal frequency or sample type.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) • a high temperature • a new, continuous cough • a loss of, or change to, your sense of smell or taste** Get a test and stay at home *initially for a minimum of 7 days as no community or occupational testing was available ** introduced into the case definition from 18 th May 2020 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted April 26, 2021. ; https://doi.org/10.1101/2021.04.23.21255964 doi: medRxiv preprint not conducted in real time and HCW followed national guidance for isolation based on symptoms. 104 We and others have previously demonstrated the utility of saliva as a reliable alternative to nasal were working in a patient facing role for at least five hours for at least one day during the study 121 period (12 weeks from enrolment). Participants were invited from areas caring for COVID-19 122 patients (Accident and Emergency (A/E), the acute medical unit, infectious diseases and 123 respiratory wards), and areas which aimed to be COVID-19 free (haematology, surgical wards).

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 26, 2021. ; https://doi.org/10.1101/2021.04.23.21255964 doi: medRxiv preprint ranging from 10 6 to 10 -6 plaque forming units per ml (pfu/ml) was used to spike 140µl of saliva 165 and swab samples. The limit of detection (LOD) was determined by the lowest concentration for 166 which all three RT-qPCR replicates amplified. For quantification of the gcn/ml, viral RNA of the 167 serial dilutions was extracted using QIAmp Viral RNA mini kit (Qiagen, Germany) and the gcn/ml 168 were calculated using the COVID-19 Genesig RT-qPCR kit (PrimerDesign, UK) with a ten-fold serial 169 dilution of quantified specific in vitro-transcribed RNA (Genesig, UK). At the time of the study, SARS-CoV-2 testing of staff who did not meet the UK COVID-19 case 176 definition (Box 1) was not routine, nor feasible due to lack of laboratory capacity and testing 177 reagents. Participants with symptoms that met the COVID-19 case definition were advised to self-178 isolate and seek COVID-19 diagnostic testing via the staff testing service when it became available 179 but also continued study procedures, except for self NP collection during periods of self-isolation. 180 Periods of self-isolation and standard-of-care test results were reported by participants to the 181 research team and recorded. Symptoms associated with each sample collected were scored on a 182 scale from 0 (no symptoms) to 6 (multiple symptoms consistent with the COVID-19 case 183 definition) for the purposes of analysis (see Box 2). Participants were assigned the highest code 184 for which they qualified.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 26, 2021. ; https://doi.org/10.1101/2021.04.23.21255964 doi: medRxiv preprint CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 26, 2021. ; https://doi.org/10.1101/2021.04.23.21255964 doi: medRxiv preprint Analytical sensitivity 285 The analytical sensitivity in spiked samples indicated the LOD for saliva was 10 -2 pfu/ml ( ≈ 2.0 x 286 10 1 gcn/ml) and for the NP swabs 10 0 pfu/ml ( ≈ 2.0 x 10 3 gcn/ml). However, amplification of one 287 or more replicates was recorded for saliva and NP swabs to concentrations 10 -6 (pfu/ml) and 10 -288 4 (pfu/ml), respectively. between the sensitivity of saliva and NP swabs (-3.4% (95% CI -9.9 to 2.1%) was found. 362 Interestingly, here we report from spiked saliva samples, that SARS-CoV-2 can be detected with 363 greater sensitivity in saliva compared to NP swabs by 100-fold As we continue to see SARS-CoV-364 2 cases reduce it will be important to quickly and accurately detect asymptomatic cases in the 365 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 26, 2021. ; https://doi.org/10.1101/2021.04.23.21255964 doi: medRxiv preprint community. It is important to note that in our paired analysis, 26% (n=9) SARS-CoV-2 infections 366 were missed by NP swabs and thereby saliva should still be considered an alternative to more 367 invasive, more costly swabbing (Bastos et al., 2021) . This study supports the use of saliva in 368 addition to NP sampling for optimal detection of infection. This dataset is unique in including both regular saliva analysis and NP swabbing into a HCW 371 surveillance study. As routine asymptomatic staff testing was not available during the study 372 period and laboratory capacity at the time did not permit contemporaneous analysis, the study 373 results were not available until after the study period and therefore did not influence participant 374 symptom reporting or self-isolation behavior. A minority of symptomatic participants with SARS- 375 CoV-2 infection met the COVID-19 case definition. A large proportion (58.8%) of SARS-CoV-2 376 infections detected in this HCW cohort were asymptomatic. This is considerably higher than 377 predicted from a recent systematic review and meta-analysis which found that the minority of Limitations of this study include some loss to follow up and withdrawal of participants with 403 resulting missing data. However, the overall retention in the study was good (over 80% at week 404 8) and return of samples was overall high. There was possible inconsistency of self-sampling 405 technique as participants were not supervised. Sample processing, which required one freeze-406 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted April 26, 2021. ; https://doi.org/10.1101/2021.04.23.21255964 doi: medRxiv preprint thaw cycle (NP swab) or two freeze-thaw cycles (saliva) prior to RNA extraction, possibly reduced 407 the overall yield of the PCR assay. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted April 26, 2021. ; https://doi.org/10.1101/2021.04.23.21255964 doi: medRxiv preprint

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We acknowledge and thank the participants of the SARS-CoV-2 Acquisition in Frontline Health Care