Correction: SARS-CoV-2 transmission routes from genetic data: A Danish case study.
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ABSTRACT:
SUBMITTER: PLOS ONE Staff
PROVIDER: S-EPMC8691616 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe first cases of COVID-19 caused by the SARS-CoV-2 virus were reported in China in December 2019. The disease has since spread globally. Many countries have instated measures to slow the spread of the virus. Information about the spread of the virus in a country can inform the gradual reopening of a country and help to avoid a second wave of infections. Our study focuses on Denmark, which is opening up when this study is performed (end-May 2020) after a lockdown in mid-March.MethodsWe perform a phylogenetic analysis of 742 publicly available Danish SARS-CoV-2 genome sequences and put them into context using sequences from other countries.ResultsOur findings are consistent with several introductions of the virus to Denmark from independent sources. We identify several chains of mutations that occurred in Denmark. In at least one case we find evidence that the virus spread from Denmark to other countries. A number of the mutations found in Denmark are non-synonymous, and in general there is a considerable variety of strains. The proportions of the most common haplotypes remain stable after lockdown.ConclusionEmploying phylogenetic methods on Danish genome sequences of SARS-CoV-2, we exemplify how genetic data can be used to trace the introduction of a virus to a country. This provides alternative means for verifying existing assumptions. For example, our analysis supports the hypothesis that the virus was brought to Denmark by skiers returning from Ischgl. On the other hand, we identify transmission routes which suggest that Denmark was part of a network of countries among which the virus was being transmitted. This challenges the common narrative that Denmark only got infected from abroad. Our analysis concerning the ratio of haplotypes does not indicate that the major haplotypes appearing in Denmark have a different degree of virality.
| S-EPMC7595399 | biostudies-literature
Project description: Not available
| S-EPMC10758742 | biostudies-literature
Project description:The unexpected pandemic with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has challenged the healthcare sector as regards preventing and controlling the virus from spreading between patients and hospital personnel. The massive spread of the pandemic has led state authorities to introduce restrictions on society and public behavior unprecedented in modern times. First, we describe the Danish effort regarding standard precautions, personal protective equipment, and disinfection in the healthcare setting with Denmark as an example. As regards, the number of coronavirus disease 2019 (COVID-19)-related hospital submissions, deaths, and infected healthcare workers in Denmark is not the hardest hit country compared with others. This cannot be explained by the hardness of the restrictions alone. Several aspects concerning the person-to-person spread of SARS-CoV-2 are not fully understood and require more experimental studies. The dogma is that virus transmission happens through either respiratory droplets or contact routes. However, it is likely not the whole truth, as we describe scenarios where droplets and/or direct contact cannot alone explain how all patients were infected. Aspects of the physiology of airborne transmission are considered, as several parameters are in play beyond particle size and respiratory rate. These are ozone concentration, ambient temperature, and humidity. In a hospital environment, these factors are not necessarily all controllable, making infection prevention and control a challenge.
| S-EPMC8239927 | biostudies-literature
Project description:BackgroundWe aimed to investigate the overall secondary attack rates (SAR) of COVID-19 in student residences and to identify risk factors for higher transmission.MethodsWe retrospectively analysed the SAR in living units of student residences which were screened in Leuven (Belgium) following the detection of a COVID-19 case. Students were followed up in the framework of a routine testing and tracing follow-up system. We considered residence outbreaks followed up between October 30th 2020 and May 25th 2021. We used generalized estimating equations (GEE) to evaluate the impact of delay to follow-up, shared kitchen or sanitary facilities, the presence of a known external infection source and the recent occurrence of a social gathering. We used a generalized linear mixed model (GLMM) for validation.ResultsWe included 165 student residences, representing 200 residence units (N screened residents = 2324). Secondary transmission occurred in 68 units which corresponded to 176 secondary cases. The overall observed SAR was 8.2%. In the GEE model, shared sanitary facilities (p = 0.04) and the recent occurrence of a social gathering (p = 0.003) were associated with a significant increase in SAR in a living unit, which was estimated at 3% (95%CI 1.5-5.2) in the absence of any risk factor and 13% (95%CI 11.4-15.8) in the presence of both. The GLMM confirmed these findings.ConclusionsShared sanitary facilities and the occurrence of social gatherings increase the risk of COVID-19 transmission and should be considered when screening and implementing preventive measures.
| S-EPMC9491668 | biostudies-literature
Project description:Data from the Danish SARS-CoV-2 wastewater surveillance
| PRJEB65603 | ENA
Project description:Identifying the exact transmission route(s) of infectious diseases in indoor environments is a crucial step in developing effective intervention strategies. In this study, we proposed a comparative analysis approach and built a model to simulate outbreaks of 3 different in-flight infections in a similar cabin environment, that is, influenza A H1N1, severe acute respiratory syndrome (SARS) coronavirus (CoV), and norovirus. The simulation results seemed to suggest that the close contact route was probably the most significant route (contributes 70%, 95% confidence interval [CI]: 67%-72%) in the in-flight transmission of influenza A H1N1 transmission; as a result, passengers within 2 rows of the index case had a significantly higher infection risk than others in the outbreak (relative risk [RR]: 13.4, 95% CI: 1.5-121.2, P = .019). For SARS CoV, the airborne, close contact, and fomite routes contributed 21% (95% CI: 19%-23%), 29% (95% CI: 27%-31%), and 50% (95% CI: 48%-53%), respectively. For norovirus, the simulation results suggested that the fomite route played the dominant role (contributes 85%, 95% CI: 83%-87%) in most cases; as a result, passengers in aisle seats had a significantly higher infection risk than others (RR: 9.5, 95% CI: 1.2-77.4, P = .022). This work highlighted a method for using observed outbreak data to analyze the roles of different infection transmission routes.
| S-EPMC7165818 | 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
Project description:BackgroundThe pathogenesis of COVID-19 emerges as complex, with multiple factors leading to injury of different organs. Some of the studies on aspects of SARS-CoV-2 cell entry and innate immunity have produced seemingly contradictory claims. In this situation, a comprehensive comparative analysis of a large number of related datasets from several studies could bring more clarity, which is imperative for therapy development.MethodsWe therefore performed a comprehensive comparative study, analyzing RNA-Seq data of infections with SARS-CoV-2, SARS-CoV and MERS-CoV, including data from different types of cells as well as COVID-19 patients. Using these data, we investigated viral entry routes and innate immune responses.Results and conclusionFirst, our analyses support the existence of cell entry mechanisms for SARS and SARS-CoV-2 other than the ACE2 route with evidence of inefficient infection of cells without expression of ACE2; expression of TMPRSS2/TPMRSS4 is unnecessary for efficient SARS-CoV-2 infection with evidence of efficient infection of A549 cells transduced with a vector expressing human ACE2. Second, we find that innate immune responses in terms of interferons and interferon simulated genes are strong in relevant cells, for example Calu3 cells, but vary markedly with cell type, virus dose, and virus type.
| S-EPMC8195239 | biostudies-literature
Project description:BackgroundEarly reports of COVID-19 in pregnancy described management by caesarean, strict isolation of the neonate and formula feeding. Is this practice justified?ObjectiveTo estimate the risk of the neonate becoming infected with SARS-CoV-2 by mode of delivery, type of infant feeding and mother-infant interaction.Search strategyTwo biomedical databases were searched between September 2019 and June 2020.Selection criteriaCase reports or case series of pregnant women with confirmed COVID-19, where neonatal outcomes were reported.Data collection and analysisData were extracted on mode of delivery, infant infection status, infant feeding and mother-infant interaction. For reported infant infection, a critical analysis was performed to evaluate the likelihood of vertical transmission.Main resultsForty nine studies included information on mode of delivery and infant infection status for 655 women and 666 neonates. In all, 28/666 (4%) tested positive postnatally. Of babies born vaginally, 8/292 (2.7%) tested positivecompared with 20/374 (5.3%) born by Caesarean. Information on feeding and baby separation were often missing, but of reported breastfed babies 7/148 (4.7%) tested positive compared with 3/56 (5.3%) for reported formula fed ones. Of babies reported as nursed with their mother 4/107 (3.7%) tested positive, compared with 6/46 (13%) for those who were reported as isolated.ConclusionsNeonatal COVID-19 infection is uncommon, rarely symptomatic, and the rate of infection is no greater when the baby is born vaginally, breastfed or remains with the mother.Tweetable abstractRisk of neonatal infection with COVID-19 by delivery route, infant feeding and mother-baby interaction.
| S-EPMC7323034 | biostudies-literature
Project description:Structural genetic variants like copy number variants (CNVs) comprise a large part of human genetic variation and may be inherited as well as somatically acquired. Recent studies have reported the presence of somatically acquired structural variants in the human genome and it has been suggested that they may accumulate in elderly individuals. To further explore the presence and the age-related acquisition of somatic structural variants in the human genome, we investigated CNVs acquired over a period of 10 years in 86 elderly Danish twins as well as CNV discordances between co-twins of 18 monozygotic twin pairs. Furthermore, the presence of mosaic structural variants was explored.
2016-06-23 | GSE76390 | GEO