Using Virus Sequencing to Determine Source of SARS-CoV-2 Transmission for Healthcare Worker.
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ABSTRACT:
SUBMITTER: Safdar N
PROVIDER: S-EPMC7510721 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Healthcare workers (HCWs) are at the frontlines of the COVID-19 pandemic and are at risk of exposure to SARS-CoV-2 infection from their interactions with patients and in the community. Limited availability of recommended personal protective equipment (PPE), in particular N95 respirators, has fueled concerns about whether HCWs are adequately protected from exposure while caring for patients. Understanding the source of SARS-CoV-2 infection in a HCW - the community or the healthcare system - is critical for understanding the effectiveness of hospital infection control and PPE practices. In Dane County, Wisconsin, community prevalence of SARS-CoV-2 is relatively low (cumulative prevalence of ~0.06% - positive cases / total population in Dane county as of April 17). Although SARS-CoV-2 infections in HCWs are often presumed to be acquired during the course of patient care, there are few reports unambiguously identifying the source of acquisition. The objective of this brief report was to determine the source of transmission of SARS-CoV-2 in a healthcare worker.
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Project description:This study describes a case of SARS-CoV-2 reinfection confirmed by whole-genome sequencing in a healthy physician who had been working in a COVID-19 hospital in Italy since the beginning of the pandemic. Nasopharyngeal swabs were obtained from the patient at each presentation as part of routine surveillance. Nucleic acid amplification testing was performed on the two samples to confirm SARS-CoV-2 infection, and serological tests were used to detect SARS-CoV-2 IgG antibodies. Comparative genome analysis with whole-genome sequencing was performed on nasopharyngeal swabs collected during the two episodes of COVID-19. The first COVID-19 episode was in March 2020, and the second was in January 2021. Both SARS-CoV-2 infections presented with mild symptoms, and seroconversion for SARS-CoV-2 IgG was documented. Genomic analysis showed that the viral genome from the first infection belonged to the lineage B.1.1.74, while that from the second infection to the lineage B.1.177. Epidemiological, clinical, serological, and genomic analyses confirmed that the second episode of SARS-CoV-2 infection in the healthcare worker met the qualifications for "best evidence" for reinfection. Further studies are urgently needed to assess the frequency of such a worrisome occurrence, particularly in the light of the recent diffusion of SARS-CoV-2 variants of concern.
| S-EPMC8150928 | biostudies-literature
Project description:BackgroundDuring the SARS-CoV-2 pandemic, healthcare workers (HCWs) are exposed to infection both at work and in their communities. Determining where HCWs might have been infected is challenging based on epidemiological data alone. At Akershus University Hospital, Norway, several clusters of possible intra-hospital SARS-CoV-2 transmission were identified based on routine contact tracing. To investigate these clusters further, we added whole genome sequencing (WGS) of SARS-CoV-2 virus to routine contact tracing among HCWs and between HCWs and patients. This study illustrates both the potential power and challenges with high-resolution genotyping in outbreak settings.AimThe aim was to determine whether clusters of suspected intra-hospital SARS-CoV-2 transmission could be resolved by combining WGS of SARS-CoV-2 with contact tracing data.MethodsEpidemiological data were collected during routine contact tracing of PCR-confirmed SARS-CoV-2 positive HCWs. Possible outbreaks were identified as wards with two or more infected HCWs defined as close contacts who tested positive for SARS-CoV-2 less than three weeks apart. Viral RNA from naso-/oropharyngeal samples underwent nanopore sequencing according to the manufacturer's instructions (Oxford Nanopore Technologies) in direct compliance to the Artic Network protocol (https://artic.network/ncov-2019).ResultsFive outbreaks were suspected from contact tracing. Viral consensus sequences from 24 HCWs, two patients and seven anonymous samples were analysed. Two outbreaks were confirmed, one refuted, two remained undetermined. One new potential outbreak was discovered.ConclusionCombined with epidemiological data, nanopore WGS was a useful tool for investigating intra-hospital SARS-CoV-2 transmission. WGS helped resolve questions about possible outbreaks and guide local infection prevention and control measures.
| S-EPMC7908852 | biostudies-literature
Project description:Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.
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Project description:Understanding the transmission mechanism of SARS-CoV-2 is a prerequisite to effective control measures. To investigate the potential modes of SARS-CoV-2 transmission, 21 COVID-19 patients from 12-47 days after symptom onset were recruited. We monitored the release of SARS-CoV-2 from the patients' exhaled breath and systematically investigated environmental contamination of air, public surfaces, personal necessities, and the drainage system. SARS-CoV-2 RNA was detected in 0 of 9 exhaled breath samples, 2 of 8 exhaled breath condensate samples, 1 of 12 bedside air samples, 4 of 132 samples from private surfaces, 0 of 70 samples from frequently touched public surfaces in isolation rooms, and 7 of 23 feces-related air/surface/water samples. The maximum viral RNA concentrations were 1857 copies/m3 in the air, 38 copies/cm2 in sampled surfaces and 3092 copies/mL in sewage/wastewater samples. Our results suggest that nosocomial transmission of SARS-CoV-2 can occur via multiple routes. However, the low detection frequency and limited quantity of viral RNA from the breath and environmental specimens may be related to the reduced viral load of the COVID-19 patients on later days after symptom onset. These findings suggest that the transmission dynamics of SARS-CoV-2 differ from those of SARS-CoV in healthcare settings.
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Project description:Hereby, we report a confirmed case of intrauterine SARS-CoV-2 transmission with rapid placental dysfunction and fetal distress.
| PRJEB40434 | ENA
Project description:Pork processing plants were apparent hotspots for SARS-CoV2 in the spring of 2020. As a result, the swine industry was confronted with a major occupational health, financial, and animal welfare crisis. The objective of this work was to describe the epidemiological situation within processing plants, develop mathematical models to simulate transmission in these plants, and test the effectiveness of routine PCR screening at minimizing SARS-CoV2 circulation. Cumulative incidence of clinical (PCR-confirmed) disease plateaued at ~2.5% to 25% across the three plants studied here. For larger outbreaks, antibody prevalence was approximately 30% to 40%. Secondly, we developed a mathematical model that accounts for asymptomatic, pre-symptomatic, and background "community" transmission. By calibrating this model to observed epidemiological data, we estimated the initial reproduction number (R) of the virus. Across plants, R generally ranged between 2 and 4 during the initial phase, but subsequently declined to ~1 after two to three weeks, most likely as a result of implementation/compliance with biosecurity measures in combination with population immunity. Using the calibrated model to simulate a range of possible scenarios, we show that the effectiveness of routine PCR-screening at minimizing disease spread was far more influenced by testing frequency than by delays in results, R, or background community transmission rates. Testing every three days generally averted about 25% to 40% of clinical cases across a range of assumptions, while testing every 14 days typically averted 7 to 13% of clinical cases. However, the absolute number of additional clinical cases expected and averted was influenced by whether there was residual immunity from a previous peak (i.e., routine testing is implemented after the workforce had experienced an initial outbreak). In contrast, when using PCR-screening to prevent outbreaks or in the early stages of an outbreak, even frequent testing may not prevent a large outbreak within the workforce. This research helps to identify protocols that minimize risk to occupational safety and health and support continuity of business for U.S. processing plants. While the model was calibrated to meat processing plants, the structure of the model and insights about testing are generalizable to other settings where large number of people work in close proximity.
| S-EPMC8412359 | biostudies-literature
Project description:BackgroundWe aimed to detect the risk factors for SARS-CoV-2 infection among healthcare workers (HCWs) in 2020 before the vaccination era.MethodsWe surveyed SARS-CoV-2 infection among the HCWs in a hospital through screening for antibody levels and the detection of viral RNA by RT-PCR between May 2020 and December 2020. Occupational and non-occupational potential predictors of disease were surveyed for the HCWs included in this study.ResultsAmong 1925 personnel in the hospital, 1732 were included to the study with a response rate of 90%. The overall infection rate of HCWs was 16.3% at the end of 2020, before vaccinations started. In the multivariate analysis, being janitorial staff (OR: 2.24, CI: 1.21-4.14, p = 0.011), being a medical secretary (OR: 4.17, CI: 2.12-8.18, p < 0.001), having at least one household member with a COVID-19 diagnosis (OR: 8.98, CI: 6.64-12.15, p < 0.001), and number of household members > 3 (OR: 1.67, CI: 1.26-2.22, p < 0.001) were found to be significantly associated with SARS-CoV-2 infection.ConclusionsMedical secretaries and janitorial staff were under increased risk of SARS-CoV-2 infection. The community-hospital gradient can explain the mode of transmission for infection among HCWs. In the setting of this study, community measures were less strict, whereas hospital infection control was adequate and provided necessary personal protective equipment. Increasing risk in larger households and households with diagnosed COVID-19 patient indicates the community-acquired transmission of the infection.
| S-EPMC8395820 | biostudies-literature