Potential recurrence of COVID-19 in a healthcare professional: SARS-CoV-2 genome sequencing confirms contagiousness after re-positivity.
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ABSTRACT:
SUBMITTER: Correia AM
PROVIDER: S-EPMC8450161 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundDespite increased testing efforts and the deployment of vaccines, COVID-19 cases and death toll continue to rise at record rates. Health systems routinely collect clinical and non-clinical information in electronic health records (EHR), yet little is known about how the minimal or intermediate spectra of EHR data can be leveraged to characterize patient SARS-CoV-2 pretest probability in support of interventional strategies.Methods and findingsWe modeled patient pretest probability for SARS-CoV-2 test positivity and determined which features were contributing to the prediction and relative to patients triaged in inpatient, outpatient, and telehealth/drive-up visit-types. Data from the University of Washington (UW) Medicine Health System, which excluded UW Medicine care providers, included patients predominately residing in the Seattle Puget Sound area, were used to develop a gradient-boosting decision tree (GBDT) model. Patients were included if they had at least one visit prior to initial SARS-CoV-2 RT-PCR testing between January 01, 2020 through August 7, 2020. Model performance assessments used area-under-the-receiver-operating-characteristic (AUROC) and area-under-the-precision-recall (AUPR) curves. Feature performance assessments used SHapley Additive exPlanations (SHAP) values. The generalized pretest probability model using all available features achieved high overall discriminative performance (AUROC, 0.82). Performance among inpatients (AUROC, 0.86) was higher than telehealth/drive-up testing (AUROC, 0.81) or outpatient testing (AUROC, 0.76). The two-week test positivity rate in patient ZIP code was the most informative feature towards test positivity across visit-types. Geographic and sociodemographic factors were more important predictors of SARS-CoV-2 positivity than individual clinical characteristics.ConclusionsRecent geographic and sociodemographic factors, routinely collected in EHR though not routinely considered in clinical care, are the strongest predictors of initial SARS-CoV-2 test result. These findings were consistent across visit types, informing our understanding of individual SARS-CoV-2 risk factors with implications for deployment of testing, outreach, and population-level prevention efforts.
| S-EPMC8516280 | biostudies-literature
Project description:We evaluated the clinical protection of BNT162b2 mRNA vaccine in healthcare workers (HCWs) and how COVID-19 manifestations and contagiousness change as the time since first dose increases. A matched (1:2 ratio) parallel cohort study was performed. During the first three months of vaccination campaign, HCWs of the entire health district ASL Città di Torino (Turin, Italy) were classified according to SARS-CoV-2-positivity in respect of the vaccination schedule: post-first-dose (fHCWs, <12 days), partially (PHCWs, ≥12 from first dose to ≤7 days after the second), and totally vaccinated (THCWs, ≥8 days after the second dose). Age-/sex-matched unvaccinated controls were randomly selected from all the SARS-CoV-2-positivity detected in the same district and period. Previous infections were excluded. Clinical and virologic data (ORF1ab gene cycle threshold values, Ct) were recorded. In total, 6800 HCWs received at least one dose, and 55 tested positive subsequently: 20 fHCWs, 25 PHCWs, 10 THCWs. Furthermore, 21.8% of breakthrough infections were in male, with a median age of 49 years (32-56), and 51.4% occurred while SARS-CoV-2 B.1.1.7 variant was predominant. The incident relative risk was 0.13 (0.12-0.15) for PHCWs and 0.06 (0.05-0.07) for THCWs. Compared to controls (n = 110), no difference was observed in fHCWs, while PHCWs and THCWs showed higher prevalence of asymptomatic infections, fewer signs/symptoms with a milder systemic involvement, and significantly higher Ct values (PHCWs 30.3 (24.1-35.5) vs. 22.3 (19.6-30.6), p = 0.023; THCWs 35.0 (31.3-35.9) vs. 22.5 (18.2-30.6), p = 0.024). Duration of symptoms was also shorter in THCWs (5 days (3-6) vs. 9 (7-14), p = 0.028). A linear increase of 3.81 points in Ct values was observed across the groups by vaccination status (p = 0.001) after adjusting for age, sex, comorbidities, and time between COVID-19 onset and swab collection. BNT162b2 decreased the risk of PCR-confirmed infections and severe disease, and was associated with a virologic picture of lesser epidemiologic concern as soon as 12 days after the first vaccine dose.
| S-EPMC8705309 | biostudies-literature
Project description:Repeated positivity and reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is a significant concern. Our study aimed to evaluate the clinical significance of repeatedly positive testing after coronavirus disease 2019 (COVID-19) recovery. We performed a systematic literature search following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. With available individual patient data reporting on repeatedly SARS-CoV-2 positive (RSP) patients, case reports, and case series were included in this analysis. We performed a descriptive analysis of baseline characteristics of repeatedly positive cases. We assessed the cases according to the length of their polymerase chain reaction (PCR) negative interval between the two episodes. Risk factors for the severity of second episodes were evaluated. Overall, we included 123 patients with repeated positivity from 56 publications, with a mean repeated positivity length of 47.8 ± 29.9 days. Younger patients were predominant in the delayed (>90 days) recurrent positive group. Furthermore, comparing patients with RSP intervals of below 60 and above 60 days, we found that a more severe disease course can be expected if the repeated positivity interval is shorter. Severe and critical disease courses might predict future repeatedly positive severe and critical COVID-19 episodes. In conclusion, our results show that the second episode of SARS-CoV-2 positivity is more severe if it happens within 60 days after the first positive PCR. On the other hand, the second episode's severity correlates with the first.
| S-EPMC8003803 | biostudies-literature
Project description:Enhanced community surveillance is a key pillar of the public health response to coronavirus disease 2019 (COVID-19). Asymptomatic carriage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a potentially significant source of transmission, yet remains relatively poorly understood. Disruption of dental services continues with significantly reduced capacity. Ongoing precautions include preappointment and/or at appointment COVID-19 symptom screening and use of enhanced personal protective equipment (PPE). This study aimed to investigate SARS-CoV-2 infection in dental patients to inform community surveillance and improve understanding of risks in the dental setting. Thirty-one dental care centers across Scotland invited asymptomatic-screened patients aged over 5 y to participate. Following verbal consent and completion of sociodemographic and symptom history questionnaire, trained dental teams took a combined oropharyngeal and nasal swab sample using standardized Viral Transport Medium-containing test kits. Samples were processed by the Lighthouse Lab and patients informed of their results by SMS/email with appropriate self-isolation guidance in the event of a positive test. All positive cases were successfully followed up by the national contact tracing program. Over a 13-wk period (from August 3, 2020, to October 31, 2020), 4,032 patients, largely representative of the population, were tested. Of these, 22 (0.5%; 95% CI, 0.5%-0.8%) tested positive for SARS-CoV-2. The positivity rate increased over the period, commensurate with uptick in community prevalence identified across all national testing monitoring data streams. To our knowledge, this is the first report of a COVID-19 testing survey in asymptomatic-screened patients presenting in a dental setting. The positivity rate in this patient group reflects the underlying prevalence in community at the time. These data are a salient reminder, particularly when community infection levels are rising, of the importance of appropriate ongoing infection prevention control and PPE vigilance, which is relevant as health care team fatigue increases as the pandemic continues. Dental settings are a valuable location for public health surveillance.
| S-EPMC8138329 | biostudies-literature
Project description: Not available
| S-BSST379 | biostudies-other
Project description:Whether a healthcare worker's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is community or hospital acquired affects prevention practices. We used virus sequencing to determine that infection of a healthcare worker who cared for 2 SARS-CoV-2-infected patients was probably community acquired. Appropriate personal protective equipment may have protected against hospital-acquired infection.
| S-EPMC7510721 | biostudies-literature
Project description:BackgroundHealthcare personnel (HCP) are at increased risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We posit that current infection control guidelines generally protect HCP from SARS-CoV-2 infection in a healthcare setting.MethodsIn this retrospective case series, we used viral genomics to investigate the likely source of SARS-CoV-2 infection in HCP at a major academic medical institution in the Upper Midwest of the United States between 25 March and 27 December 2020. We obtained limited epidemiological data through informal interviews and review of the electronic health record and combined this information with healthcare-associated viral sequences and viral sequences collected in the broader community to infer the most likely source of infection in HCP.ResultsWe investigated SARS-CoV-2 infection clusters involving 95 HCP and 137 possible patient contact sequences. The majority of HCP infections could not be linked to a patient or coworker (55 of 95 [57.9%]) and were genetically similar to viruses circulating concurrently in the community. We found that 10.5% of HCP infections (10 of 95) could be traced to a coworker. Strikingly, only 4.2% (4 of 95) could be traced to a patient source.ConclusionsInfections among HCP add further strain to the healthcare system and put patients, HCP, and communities at risk. We found no evidence for healthcare-associated transmission in the majority of HCP infections evaluated. Although we cannot rule out the possibility of cryptic healthcare-associated transmission, it appears that HCP most commonly become infected with SARS-CoV-2 via community exposure. This emphasizes the ongoing importance of mask wearing, physical distancing, robust testing programs, and rapid distribution of vaccines.
| S-EPMC8083259 | biostudies-literature
Project description:AimsTo explore the contagiousness and new SARS-CoV-2 mutations in pediatric COVID-19.MethodsThis cohort study enrolled all pediatric patients admitted to 8 hospitals in Zhejiang Province of China between 21 January and 29 February 2020, their family members and close-contact classmates. Epidemiological, demographic, clinical and laboratory data were collected. Bioinformatics was used to analyze the features of SARS-CoV-2. Individuals were divided into 3 groups by the first-generation case: Groups 1 (unclear), 2 (adult), and 3 (child). The secondary attack rate (SAR) and R0 were compared among the groups.ResultsThe infection rate among 211 individuals was 64% (135/211). The SAR in Groups 2 and 3 was 71% (73/103) and 3% (1/30), respectively; the median R0 in Groups 2 and 3 was 2 (range: 1-8) and 0 (range: 0-1), respectively. Compared with adult cases, the SAR and R0 of pediatric cases were significantly lower (p<0.05). We obtained SARS-CoV-2 sequences from the same infant's throat and fecal samples at a two-month interval and found that the new spike protein A958D mutation detected in the stool improved thermostability theoretically.ConclusionsChildren have lower ability to spread SARS-CoV-2. The new A958D mutation is a potential reason for its long residence in the intestine.
| S-EPMC8384730 | biostudies-literature
Project description:Olfactory dysfunction (OD) is a common manifestation of COVID-19 and may be useful for screening. Survey-based olfactory evaluation tends to underestimate the prevalence of OD, while psychophysical olfactory testing during a pandemic has the disadvantage of being time consuming, expensive, and requiring standardized laboratory settings. We aimed to develop a quick, simple, affordable, and reliable test to objectively assess the prevalence and diagnostic accuracy of OD in COVID-19. The olfactory function of 64 COVID-19 inpatients and 34 controls was evaluated using a questionnaire and a simple disposable odor identification test (SDOIT) developed for this study. Four SDOIT models were assessed: 10-SDOIT, 9-SDOIT, 8-SDOIT, and 4-SDOIT, with 10, 9, 8 and 4 samples, respectively. We found a high frequency of self-reported OD in COVID-19 patients, with 32.8% and 42.2% reporting current and recent OD, respectively. Different SDOIT models revealed smell impairment in 54.7-64.1% of COVID-19 patients. The combination of either 10-SDOIT results and self-reported OD, or 8-SDOIT results and self-reported OD, were the best predictors of COVID-19, both with an AUC value of 0.87 (0.85 and 0.86 for the age-matched subjects). OD is a common symptom of COVID-19. A combination of self-reported smell deterioration and OD psychophysically evaluated using SDOIT appears to be a good predictor of COVID-19.
| S-EPMC8507979 | biostudies-literature
Project description:Host-associated races of phytophagous insects provide a model for understanding how adaptation to a new environment can lead to reproductive isolation and speciation, ultimately enabling us to connect barriers to gene flow to adaptive causes of divergence. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on legume species and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. As host choice produces assortative mating, understanding the underlying mechanisms of choice will contribute directly to understanding of speciation. As host choice in the pea aphid is likely mediated by smell and taste, we use capture sequencing and SNP genotyping to test for the role of chemosensory genes in the divergence between eight host plant species across the continuum of differentiation and sampled at multiple locations across western Europe. We show high differentiation of chemosensory loci relative to control loci in a broad set of pea aphid races and localities, using a model-free approach based on principal component analysis. Olfactory and gustatory receptors form the majority of highly differentiated genes and include loci that were already identified as outliers in a previous study focusing on the three most closely related host races. Consistent indications that chemosensory genes may be good candidates for local adaptation and barriers to gene flow in the pea aphid open the way to further investigations aiming to understand their impact on gene flow and to determine their precise functions in response to host plant metabolites.
| S-EPMC6849616 | biostudies-literature