Background Whether SARS-CoV-2 positivity among symptomatic subjects reflects past or future disease may be difficult to ascertain. Methods We tested a cohort of 9449 employees at work at the Karolinska University Hospital, Stockholm, Sweden for SARS-CoV-2 RNA and antibodies, linked the testing results to sick leave records and determined associations with past or future sick leave using multinomial logistic regression. ClinicalTrials.gov NCT04411576. Results Subjects with high amounts of SARS-CoV-2 virus, as indicated by the Cycle threshold (Ct) value in the PCR, had the highest risk for sick leave in the two weeks after testing (OR 11.97 (CI 95% 6.29-22.80)) whereas subjects with low amounts of virus had the highest risk for sick leave in the past three weeks before testing (OR 6.31 (4.38-9.08)). Only 2.5% of employees were SARS-CoV-2 positive while 10.5% were positive by serology and 1.2% were positive in both tests. Serology-positive subjects were not at excess risk for future sick leave (OR 1.06 (95% CI, 0.71-1.57)). Conclusions High amounts of SARS-CoV-2 virus, as determined using PCR Ct values, associates with development of sickness in the next few weeks. The results support the concept that PCR Ct may be informative when testing for SARS-CoV-2 is performed.
De novo assembly of sequence reads from next generation sequencing platforms is a common strategy for detecting presence and sequencing of viruses in biospecimens. Amplification artifacts and presence of several related viruses in the same specimen can lead to assembly of erroneous, chimeric sequences. We now report that such chimeras can also occur between viral and non-viral biological sequences incorrectly joined together which may cause erroneous detection of viruses, highlighting the importance of performing a chimera checking step in bioinformatics pipelines. Using Illumina NextSeq and metagenomic sequencing, we analyzed 80 consecutive non-melanoma skin cancers (NMSCs) from 11 immunosuppressed patients together with 11 NMSCs from patients who had only developed 1 NMSC. We aligned high-quality reads against a Human Papillomavirus (HPV) database and found HPV sequences in 9/91 specimens. A previous bioinformatic analysis of the same crude sequencing data from some of these samples had found an additional 3 specimens to be HPV-positive after performing de novo assembly. The reason for the discrepancy was investigated and found to be mostly caused by chimeric sequences containing both viral and non-viral sequences. Non-viral sequences were present in these 3 samples. To avoid erroneous detection of HPV when performing sequencing, we thus developed a novel script to identify HPV chimeric sequences.
CoV-2 infections amongst personnel providing home care services for older persons in Stockholm, Sweden (Brief Report).
Objectives Most COVID-19 related infections and deaths may occur in healthcare outside hospitals. Here we explored SARS-CoV-2 infections among healthcare workers (HCWs) in this setting. Design All healthcare providers in Stockholm, Sweden were asked to recruit HCWs at work for a study of past or present SARS-CoV-2 infections among HCWs. Study participants This study reports the results from 839 HCWs, mostly employees of primary care centers, sampled in June 2020. Results SARS-CoV-2 seropositivity was found among 12% (100/839) of HCWs, ranging from 0% to 29% between care units. Seropositivity decreased by age and was highest among HCWs <40 years of age. Within this age group there was 19% (23/120) seropositivity among women and 11% (15/138) among men (p<0.02). Current infection, as measured using PCR, was found in only 1% and the typical testing pattern of pre-symptomatic potential “superspreaders” found in only 2/839 subjects. Conclusions Previous SARS-CoV-2 infections were common among younger HCWs in this setting. Pre-symptomatic infection was uncommon, in line with the strong variability in SARS-CoV-2 exposure between units. Prioritizing infection prevention and control including sufficient and adequate personal protective equipment, and vaccination for all HCWs are important to prevent nosocomial infections and infections as occupational injuries during an ongoing pandemic.
BackgroundPre-symptomatic subjects are spreaders of SARS-CoV-2 infection, and strategies that could identify these subjects, particularly in hospital settings, are needed.MethodsWe tested a cohort of 9449 employees at work at the Karolinska University Hospital, Stockholm, Sweden for SARS-CoV-2 RNA and antibodies, linked the screening results to sick leave records and examined the association between screening results and past or future sick leave using multinomial logistic regression.ResultsWe found that healthcare workers with high amounts of SARS-CoV-2 virus, as indicated by the Cycle threshold (Ct) value in the PCR, had the highest risk for sick leave in the two weeks after testing (OR 11·97 (CI 95% 6·29-22·80)) whereas subjects with low amounts of virus had the highest risk for sick leave in the past three weeks before testing (OR 6·31 (4·38-9·08)). Only 2·5% of employees were SARS-CoV-2 positive while 10·5% were positive by serology and 1·2% were positive in both tests. Serology-positive subjects were not at excess risk for future sick leave (OR 1·06 (95% CI, 0·71-1·57)), but virus-positive subjects had a 7·23 fold (95% CI, 4·52-11·57)) increased risk for sick leave within two weeks post testing.ConclusionsScreening of asymptomatic healthcare workers for high amounts of SARS-CoV-2 virus using Ct values will identify pre-symptomatic subjects who will develop disease in the next few weeks. Identification of potentially contagious, pre-symptomatic subjects is likely critical for protecting patients and healthcare workers.Main pointHealthy healthcare workers with low amounts of SARS-CoV-2 nucleic acids will previously have had the disease. Presence of a high amount of SARS-CoV-2 nucleic acids predicts future symptomatic disease.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.