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.
| S-EPMC7276045 | biostudies-literature
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.
| S-EPMC8009659 | biostudies-literature
Project description:So far, only a few reports about reinfections with SARS-CoV-2 have been published, and they often lack detailed immunological and virological data. We report about a SARS-CoV-2 reinfection with a genetically distinct SARS-CoV-2 variant in an immunocompetent female healthcare worker that has led to a mild disease course. No obvious viral escape mutations were observed in the second virus variant. The infectious virus was shed from the patient during the second infection episode despite the presence of neutralizing antibodies in her blood. Our data indicate that a moderate immune response after the first infection, but not a viral escape, did allow for reinfection and live virus shedding.
| S-EPMC8070424 | biostudies-literature
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.
| S-EPMC7446651 | biostudies-literature
Project description: Not available
| S-EPMC8559300 | biostudies-literature
Project description:BackgroundWe report an outbreak investigation to map intra-hospital transmission among health care workers (HCW) using epidemiological and whole-genome sequencing data.MethodsFourteen clinical wards (COVID-19 and non-COVID-19) with high infection rates of SARS-CoV-2 among HCW were selected and demographical, epidemiological and sequencing data were collected of all HCW testing positive by RT-PCR. Clustered cases were identified based on first disease onsets and differences in single nucleotide polymorphisms (SNP's) and were analysed for additional characteristics.ResultsData was collected for 123 HCW. Out of 123 HCW, 65 (53%) worked at eight non-COVID-19 wards, 56 (46%) at four COVID-19 wards, one (<1%) worked on several wards and for one (<1%) it was unknown. One major cluster (n = 34) and three minor clusters (n = 2,3,4; total n = 9) comprising of 43 HCW (35%) were found after comparing our study population (n = 123) with the circulating regional sequences (n = 819). In clustered cases work was most often the suspected source of infection and continuing work while having symptoms occurred in all clusters, ranging from 1-6 days.ConclusionOur findings strongly indicate transmission of SARS-CoV-2 among HCW. Whole-genome sequencing is useful for identification of clusters and can give direction to targeted infection prevention measures.
| S-EPMC10065229 | biostudies-literature
Project description:As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1-3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
| S-EPMC9433318 | biostudies-literature
Project description:Hereby, we report a confirmed case of intrauterine SARS-CoV-2 transmission with rapid placental dysfunction and fetal distress.
| PRJEB40434 | ENA