Rapid Increase in SARS-CoV-2 P.1 Lineage Leading to Codominance with B.1.1.7 Lineage, British Columbia, Canada, January-April 2021.
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ABSTRACT:
SUBMITTER: Hogan CA
PROVIDER: S-EPMC8544957 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:On January 5 2021, Ecuadorian COVID-19 genomic surveillance program detected a suspicious case of the B.1.1.7 lineage (alpha variant) of SARS-CoV-2 in Los Rios province, later confirmed by genome sequencing. The patient travelled from the UK by the end of December 2020. By contact tracing, several new cases were detected confirming B.1.1.7 transmission and spreading in Ecuador.
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Project description:Within 5 weeks in 2021, B.1.1.7 became the dominant severe acute respiratory syndrome coronavirus 2 lineage at an outpatient testing site in Berlin, Germany. Compared with outpatients with wild-type virus infection, patients with B.1.1.7 had similar cycle threshold values, more frequent sore throat and travel history, and less frequent anosmia/ageusia.
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Project description:BackgroundMotivated by concerns of inadequate vaccination coverage and the potential for outbreaks of vaccine-preventable diseases, Canadian provinces have been discussing, implementing and tightening policies requiring documentation of vaccination for school enrolment. We sought to understand the acceptability of 14 potential vaccination policy levers among parents and other adults in British Columbia.MethodsA representative online panel of 1308 adults in BC was surveyed in April 2017. Respondents were representative of the BC population by sex, age, geographic residence and percentage of household with children younger than 19 years. We used Poisson regression to estimate predictors of policy endorsement.ResultsMost respondents (> 80%) held positive attitudes toward vaccination. Policies such as mandatory documentation of vaccination at school entry were supported by more than 75% of all respondents. Punitive policies, such as denial of child tax benefits for nonvaccination, were supported by less than 40% of respondents. In multivariable regression, respondents with positive attitudes toward vaccination were significantly more likely to strongly support all potential policies. Additionally, female respondents and respondents with postsecondary education were significantly more likely to strongly support policies involving additional requirements for parents.InterpretationMost adults in BC held favourable attitudes toward vaccination, and strong support existed for policies designed to support vaccination. This study provides evidence that most adults in BC are supportive of vaccination and, when presented with a wide range of options, would likely be supportive of information and requirement policy options designed to increase vaccination uptake.
| S-EPMC6498448 | biostudies-literature
Project description:To assess SARS-CoV-2 variants spread, we analysed 36,590 variant-specific reverse-transcription-PCR tests performed on samples from 12 April-7 May 2021 in France. In this period, contrarily to January-March 2021, variants of concern (VOC) β (B.1.351 lineage) and/or γ (P.1 lineage) had a significant transmission advantage over VOC α (B.1.1.7 lineage) in Île-de-France (15.8%; 95% confidence interval (CI): 15.5-16.2) and Hauts-de-France (17.3%; 95% CI: 15.9-18.7) regions. This is consistent with VOC β's immune evasion abilities and high proportions of prior-SARS-CoV-2-infected persons in these regions.
| S-EPMC8193991 | biostudies-literature
Project description:SARS-CoV-2 variants with multiple amino acid mutations in the spike protein are emerging in different parts of the world, raising concerns regarding their possible impact on human immune response and vaccine efficacy against the virus. Recently, a variant named lineage B.1.1.7 was detected and shown to be rapidly spreading across the UK since November 2020. As surveillance for these SARS-CoV-2 variants of concern (VOCs) becomes critical, we have investigated the use of environmental surveillance (ES) for the rapid detection and quantification of B.1.1.7 viruses in sewage as a way of monitoring its expansion that is independent on the investigation of identified clinical cases. Next-generation sequencing analysis of amplicons synthesized from sewage concentrates revealed the presence of B.1.1.7 mutations in viral sequences, first identified in a sample collected in London on 10 November 2020 and shown to rapidly increase in frequency to >95% in January 2021, in agreement with clinical data over the same period. We show that ES can provide an early warning of VOCs becoming prevalent in the population and that, as well as B.1.1.7, our method can detect VOCs B.1.351 and P.1, first identified in South Africa and Brazil, respectively, and other viruses carrying critical spike mutation E484K, known to have an effect on virus antigenicity. Although we did not detect such mutation in viral RNAs from sewage, we did detect mutations at amino acids 478, 490, and 494, located close to amino acid 484 in the spike protein structure and known to also have an effect on antigenicity. IMPORTANCE The recent appearance and growth of new SARS-CoV-2 variants represent a major challenge for the control of the COVID-19 pandemic. These variants of concern contain mutations affecting antigenicity, which raises concerns on their possible impact on human immune response to the virus and vaccine efficacy against them. Here, we show how environmental surveillance for SARS-CoV-2 can be used to help us understand virus transmission patterns and provide an early warning of variants becoming prevalent in the population. We describe the detection and quantification of variant B.1.1.7, first identified in southeast England in sewage samples from London (UK) before widespread transmission of this variant was obvious from clinical cases. Variant B.1.1.7 was first detected in a sample from early November 2020, with the frequency of B.1.1.7 mutations detected in sewage rapidly increasing to >95% in January 2021, in agreement with increasing SARS-CoV-2 infections associated with B.1.1.7 viruses.
| S-EPMC8269227 | biostudies-literature
Project description:IntroductionMitigation behaviors are key to preventing SARS-CoV-2 transmission. We identified the behaviors associated with secondary transmission from confirmed SARS-CoV-2 primary cases to household contacts and described the characteristics associated with reporting these behaviors.MethodsHouseholds with confirmed SARS-CoV-2 infections were recruited in California and Colorado from January to April 2021. Self-reported behaviors and demographics were collected through interviews. We investigated behaviors associated with transmission and individual and household characteristics associated with behaviors using univariable and multivariable logistic regression with generalized estimating equations to account for household clustering.ResultsAmong household contacts of primary cases, 43.3% (133 of 307) became infected with SARS-CoV-2. When an adjusted analysis was conducted, household contacts who slept in the same bedroom with the primary case (AOR=2.19; 95% CI=1.25, 3.84) and ate food prepared by the primary case (AOR=1.98; 95% CI=1.02, 3.87) had increased odds of SARS-CoV-2 infection. Household contacts in homes ≤2,000 square feet had increased odds of sleeping in the same bedroom as the primary case compared with those in homes >2,000 square feet (AOR=3.97; 95% CI=1.73, 9.10). Parents, siblings, and other relationships (extended family, friends, or roommates) of the primary case had decreased odds of eating food prepared by the primary case compared with partners.ConclusionsSleeping in the same bedroom as the primary case and eating food prepared by the primary case were associated with secondary transmission. Household dimension and relationship to the primary case were associated with these behaviors. Our findings encourage innovative means to promote adherence to mitigation measures that reduce household transmission.
| S-EPMC9069230 | biostudies-literature
Project description:Legionella spp. present in some human-made water systems can cause Legionnaires' disease in susceptible individuals. Although legionellae have been isolated from the natural environment, variations in the organism's abundance over time and its relationship to aquatic microbiota are poorly understood. Here, we investigated the presence and diversity of legionellae through 16S rRNA gene amplicon and metagenomic sequencing of DNA from isolates collected from seven sites in three watersheds with varied land uses over a period of 1 year. Legionella spp. were found in all watersheds and sampling sites, comprising up to 2.1% of the bacterial community composition. The relative abundance of Legionella tended to be higher in pristine sites than in sites affected by agricultural activity. The relative abundance levels of Amoebozoa, some of which are natural hosts of legionellae, were similarly higher in pristine sites. Compared to other bacterial genera detected, Legionella had both the highest richness and highest alpha diversity. Our findings indicate that a highly diverse population of legionellae may be found in a variety of natural aquatic sources. Further characterization of these diverse natural populations of Legionella will help inform prevention and control efforts aimed at reducing the risk of Legionella colonization of built environments, which could ultimately decrease the risk of human disease. IMPORTANCE Many species of Legionella can cause Legionnaires' disease, a significant cause of bacterial pneumonia. Legionella in human-made water systems such as cooling towers and building plumbing systems are the primary sources of Legionnaires' disease outbreaks. In this temporal study of natural aquatic environments, Legionella relative abundance was shown to vary in watersheds associated with different land uses. Analysis of the Legionella sequences detected at these sites revealed highly diverse populations that included potentially novel Legionella species. These findings have important implications for understanding the ecology of Legionella and control measures for this pathogen that are aimed at reducing human disease.
| S-EPMC5541159 | biostudies-literature
Project description:Oil and gas well leakage is of public concern primarily due to the perceived risks of aquifer contamination and greenhouse gas (GHG) emissions. This study examined well leakage data from the British Columbia Oil and Gas Commission (BC OGC) to identify leakage pathways and initially quantify incident rates of leakage and GHG emissions from leaking wells. Three types of leakage are distinguished: "surface casing vent flow" (SCVF), "outside the surface casing leakage" (OSCL), and "cap leakage" (CL). In British Columbia (BC), the majority of reported incidents involve SCVF of gases, which does not pose a risk of aquifer contamination but does contribute to GHG emissions. Reported liquid leakage of brines and hydrocarbons is rarer. OSCL and CL of gas are more serious problems due to the risk of long-term leakage from abandoned wells; some were reported to be leaking gas several decades after they were permanently abandoned. According to the requirements of provincial regulation, 21,525 have been tested for leakage. In total, 2,329 wells in BC have had reported leakage during the lifetime of the well. This represents 10.8% of all wells in the assumed test population. However, it seems likely that wells drilled and/or abandoned before 2010 have unreported leakage. In BC, the total GHG emission from gas SCVF is estimated to reach about 75,000 t/y based on the existing inventory calculation; however, this number is likely higher due to underreporting.
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Project description:Following the spread of the SARS-CoV-2 B.1.1.7 variant, social distancing was strengthened in France in January 2021. Using a two-strain mathematical model calibrated on genomic surveillance, we estimated that curfew measures allowed hospitalisations to plateau by decreasing transmission of the historical strains while B.1.1.7 continued to grow. School holidays appear to have further slowed down progression in February. Without progressively strengthened social distancing, a rapid surge of hospitalisations is expected, despite the foreseen increase in vaccination rhythm.
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Project description:OBJECTIVE: This study examined the rates and distribution of serious work-related injuries by demographic, work and injury characteristics in British Columbia, Canada from 2002-2008, using population-based data. METHODS: Claims for workers with a serious injury were extracted from workers' compensation data. Serious injuries were defined by long duration, high cost, serious medical diagnosis, or fatality. Workforce estimates were used to calculate stratum-specific rates. Rate-ratios (RR) and 95% CIs were calculated using negative binomial regression for the comparison of rates, adjusting for gender, age and occupation. RESULTS: Women had a lower overall serious injury rate compared to men (RR: 0.93, 95% CI: 0.87-0.99). The 35-44 age group had the highest overall rate compared to the youngest age group. The rate for severe strains/sprains was similarly high for men and women in the 35-44 age group, although there was a differential pattern by gender for other injury types: the rate of fracture was similar across age groups for men, but increased with age for women (RR: 2.7, 95% CI: 2.2-3.3); and the rate of severe falls increased with age for men and women, with a larger three-fold increase for older women (men: RR: 1.8, 95% CI: 1.7-2.1; women: RR: 3.2, 95% CI: 2.7-3.7). CONCLUSIONS: The risk of serious injuries is higher among specific age groups with different patterns emerging for men and women. Variations persisted within similar injury types and occupation groups in our adjusted models. These results provide evidence for the burden of serious injuries and a basis for future analytic research. Given projected demographic shifts and increasing workforce participation of older workers, intervention programs should be carefully implemented with consideration to demographic groups at risk for serious injuries in the workplace.
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