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Human cytomegalovirus (HCMV) is the most common congenital infection. Several HCMV vaccines are in development, but none have yet been approved. An understanding of the kinetics of CMV replication and transmission may inform the rational design of vaccines to prevent this infection. The salivary glands (SG) are an important site of sustained CMV replication following primary infection and during viral reactivation from latency. As such, the strength of the immune response in the SG likely influences viral dissemination within and between hosts. To study the relationship between the immune response and viral replication in the SG, and viral dissemination from the SG to other tissues, mice were infected with low doses of murine CMV (MCMV). Following intra-SG inoculation, we characterized the viral and immunological dynamics in the SG, blood, and spleen, and identified organ-specific immune correlates of protection. Using these data, we constructed compartmental mathematical models of MCMV infection. Model fitting to data and analysis indicate the importance of cellular immune responses in different organs and point to a threshold of infection within the SG necessary for the establishment and spread of infection.
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Muromegalovirus , Glándulas Salivales , Animales , Glándulas Salivales/virología , Glándulas Salivales/inmunología , Ratones , Muromegalovirus/inmunología , Muromegalovirus/fisiología , Replicación Viral/fisiología , Cinética , Infecciones por Herpesviridae/inmunología , Infecciones por Herpesviridae/virología , Infecciones por Citomegalovirus/inmunología , Infecciones por Citomegalovirus/virología , Infecciones por Citomegalovirus/transmisión , Biología ComputacionalRESUMEN
BACKGROUND: British Columbia (BC) Canada has a large take-home naloxone (THN) program, implemented as part of the provincial response to the ongoing toxic unregulated drug supply emergency. Ascertaining the rate of use of THN kits is vital to understanding the full impact of the program. However, this is a challenging problem due to under-reporting of kit distribution. This study aims to estimate the total number of THN kits used based on the number of THN kits shipped, the number of THN kits reported as distributed, and the number of THN kits reported as used. METHODS: We used BC THN shipment and distribution records (February 2015 to August 2023) to inform a simple Bayesian model of naloxone kit distribution and use. A logistic regression term by health region and distribution site type was incorporated to account for variable under-reporting, and a convolution term was incorporated to account for kit distribution. RESULTS: We find the number of THN kits reported as used, and the number of total THN kits distributed, are largely under-reported. An estimated 1,500 (95 % CrI: 1,430 - 1,590) THN kits per 10,000 BC population were used, of which 288 per 10,000 had been reported as used. Of all the THN kits shipped, the model estimated that 43 % (95 % CrI: 41-45 %) of kits were used. We also found variation in both distribution and use by distribution site type, with kits distributed from overdose prevention sites having the highest rate of use (56 %; 95 % CrI: 53-59 %). CONCLUSION: Across all sites, kit use is approximately five times higher than has been reported. Our framework can also be applied to other localities where THN programs operate, in order to better estimate the true reach and impact of take home naloxone distribution.
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Teorema de Bayes , Sobredosis de Droga , Naloxona , Antagonistas de Narcóticos , Humanos , Naloxona/administración & dosificación , Colombia Británica , Antagonistas de Narcóticos/administración & dosificación , Sobredosis de Droga/epidemiologíaRESUMEN
BACKGROUND AND OBJECTIVES: Pediatric COVID-19 cases are often mild or asymptomatic, which has complicated estimations of disease burden using existing testing practices. We aimed to determine the age-specific population seropositivity and risk factors of SARS-CoV-2 seropositivity among children and young adults during the pandemic in British Columbia (BC). METHODS: We conducted two cross-sectional serosurveys: phase 1 enrolled children and adults < 25 years between November 2020-May 2021 and phase 2 enrolled children < 10 years between June 2021-May 2022 in BC. Participants completed electronic surveys and self-collected finger-prick dried blood spot (DBS) samples. Samples were tested for immunoglobulin G antibodies against ancestral spike protein (S). Descriptive statistics from survey data were reported and two multivariable analyses were conducted to evaluate factors associated with seropositivity. RESULTS: A total of 2864 participants were enrolled, of which 95/2167 (4.4%) participants were S-seropositive in phase 1 across all ages, and 61/697 (8.8%) unvaccinated children aged under ten years were S-seropositive in phase 2. Overall, South Asian participants had a higher seropositivity than other ethnicities (13.5% vs. 5.2%). Of 156 seropositive participants in both phases, 120 had no prior positive SARS-CoV-2 test. Young infants and young adults had the highest reported seropositivity rates (7.0% and 7.2% respectively vs. 3.0-5.6% across other age groups). CONCLUSIONS: SARS-CoV-2 seropositivity among unvaccinated children and young adults was low in May 2022, and South Asians were disproportionately infected. This work demonstrates the need for improved diagnostics and reporting strategies that account for age-specific differences in pandemic dynamics and acceptability of testing mechanisms.
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COVID-19 , Personas no Vacunadas , Niño , Humanos , Lactante , Adulto Joven , Anticuerpos Antivirales , Pueblo Asiatico , COVID-19/epidemiología , Estudios Transversales , Inmunoglobulina G , Estudios Seroepidemiológicos , Colombia Británica/epidemiologíaRESUMEN
OBJECTIVE: To determine the SARS-CoV-2 seroprevalence among school workers within the Greater Vancouver area, British Columbia, Canada, after the first Omicron wave. DESIGN: Cross-sectional study by online questionnaire, with blood serology testing. SETTING: Three main school districts (Vancouver, Richmond and Delta) in the Vancouver metropolitan area. PARTICIPANTS: Active school staff enrolled from January to April 2022, with serology testing between 27 January and 8 April 2022. Seroprevalence estimates were compared with data obtained from Canadian blood donors weighted over the same sampling period, age, sex and postal code distribution. PRIMARY AND SECONDARY OUTCOMES: SARS-CoV-2 nucleocapsid antibody testing results adjusted for test sensitivity and specificity, and regional variation across school districts using Bayesian models. RESULTS: Of 1850 school staff enrolled, 65.8% (1214/1845) reported close contact with a COVID-19 case outside the household. Of those close contacts, 51.5% (625/1214) were a student and 54.9% (666/1214) were a coworker. Cumulative incidence of COVID-19 positive testing by self-reported nucleic acid or rapid antigen testing since the beginning of the pandemic was 15.8% (291/1845). In a representative sample of 1620 school staff who completed serology testing (87.6%), the adjusted seroprevalence was 26.5% (95% CrI 23.9% to 29.3%), compared with 32.4% (95% CrI 30.6% to 34.5%) among 7164 blood donors. CONCLUSION: Despite frequent COVID-19 exposures reported, SARS-CoV-2 seroprevalence among school staff in this setting remained no greater than the community reference group. Results are consistent with the premise that many infections were acquired outside the school setting, even with Omicron.
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COVID-19 , SARS-CoV-2 , Humanos , Colombia Británica , Estudios Transversales , Teorema de Bayes , Estudios Seroepidemiológicos , Anticuerpos AntiviralesRESUMEN
We prospectively studied SARS-CoV-2 transmission at schools in an era of variants of concern, offering all close contacts serial viral asymptomatic testing up to 14 days. From the 69 primary cases detected in schools, 392 close contacts were identified and offered asymptomatic testing. A total of 229 (58%) were close school contacts, and of these, 3 tested positive (1.3%), 2 of which were detected through asymptomatic testing. This is in contrast to the 117 household contacts, where 43 (37%) went on to become secondary cases. Routine asymptomatic testing of close contacts should be examined in the context of local testing rates, preventive measures, programmatic costs, and health impacts of asymptomatic transmission. IMPORTANCE There is concern that schools may be a setting where asymptomatic infections might result in significant "silent" transmission of SARS-CoV-2, particularly after the emergence of more transmissible variants of concern. After the programmatic implementation of a strategy of asymptomatic testing of close COVID-19 contacts as part of contact tracing in the school setting, the majority of the secondary cases were still found to have occurred in home or social contacts. However, for the 6.2% of secondary cases that occurred in close school contacts, the majority were detected through asymptomatic testing. The potential added yield of this approach needs to be considered within the overall setting, including consideration of the local epidemiology, ongoing goals of case and contact management, additional costs, logistical challenges for families, and possible health impacts of asymptomatic transmission.
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COVID-19 , SARS-CoV-2 , Colombia Británica/epidemiología , COVID-19/epidemiología , Prueba de COVID-19 , Trazado de Contacto , HumanosRESUMEN
A vaccine to prevent congenital cytomegalovirus infection (cCMV) is a public health priority. cCMV results from maternal primary or non-primary CMV infection (reinfection, or reactivation of chronic infection) during pregnancy. Young children are a major source of transmission to pregnant women because they shed CMV at high viral loads for prolonged periods. CMV vaccines evaluated in clinical trials so far have demonstrated only approximately 50% efficacy against maternal primary infection. None of these have been approved, as higher levels of vaccine efficacy are assumed to be required to substantially reduce cCMV prevalence. Here, we designed a mathematical model to capture the relationship between viral shedding by young children and maternal CMV infections during pregnancy. Using this model, we were able to quantify the impact of CMV post-infection immunity on protecting against reinfection and viral shedding. There was a 36% reduction in the risk of infection to a seropositive person with post-infection immunity (reinfection) versus a seronegative person without this immunity (primary infection), given the same exposure. Viral shedding following reinfection was only 34% the quantity of that following primary infection. Our model also predicted that a vaccine that confers the equivalent of post-infection immunity, when given to young children, would markedly reduce both CMV transmission to pregnant women and the prevalence of cCMV. Thus, we predict that existing vaccine candidates that have been shown to be only modestly protective may in fact be highly effective at preventing cCMV by interrupting child-to-mother transmission.
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Enfermedades Transmisibles , Infecciones por Citomegalovirus , Vacunas contra Citomegalovirus , Enfermedades Fetales , Complicaciones Infecciosas del Embarazo , Preescolar , Enfermedades Transmisibles/tratamiento farmacológico , Citomegalovirus , Femenino , Humanos , Transmisión Vertical de Enfermedad Infecciosa/prevención & control , Embarazo , Complicaciones Infecciosas del Embarazo/epidemiología , Reinfección , Vacunación/métodosRESUMEN
Following the emergence of COVID-19 at the end of 2019, several mathematical models have been developed to study the transmission dynamics of this disease. Many of these models assume homogeneous mixing in the underlying population. However, contact rates and mixing patterns can vary dramatically among individuals depending on their age and activity level. Variation in contact rates among age groups and over time can significantly impact how well a model captures observed trends. To properly model the age-dependent dynamics of COVID-19 and understand the impacts of interventions, it is essential to consider heterogeneity arising from contact rates and mixing patterns. We developed an age-structured model that incorporates time-varying contact rates and population mixing computed from the ongoing BC Mix COVID-19 survey to study transmission dynamics of COVID-19 in British Columbia (BC), Canada. Using a Bayesian inference framework, we fit four versions of our model to weekly reported cases of COVID-19 in BC, with each version allowing different assumptions of contact rates. We show that in addition to incorporating age-specific contact rates and mixing patterns, time-dependent (weekly) contact rates are needed to adequately capture the observed transmission dynamics of COVID-19. Our approach provides a framework for explicitly including empirical contact rates in a transmission model, which removes the need to otherwise model the impact of many non-pharmaceutical interventions. Further, this approach allows projection of future cases based on clear assumptions of age-specific contact rates, as opposed to less tractable assumptions regarding transmission rates.
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COVID-19 , Teorema de Bayes , Colombia Británica/epidemiología , COVID-19/epidemiología , Humanos , Modelos TeóricosRESUMEN
OBJECTIVES: Few studies reported COVID-19 cases in schools during the 2020/21 academic year in a setting of uninterrupted in-person schooling. The main objective was to determine the SARS-CoV-2 seroprevalence among school staff in Vancouver public schools. DESIGN: Cumulative incident COVID-19 cases among all students and school staff based on public health data, with an embedded cross-sectional serosurvey among a school staff sample that was compared to period, age, sex and geographical location-weighted data from blood donors. SETTING: Vancouver School District (British Columbia, Canada) from kindergarten to grade 12. PARTICIPANTS: Active school staff enrolled from 3 February to 23 April 2021 with serology testing from 10 February to 15 May 2021. MAIN OUTCOME MEASURES: SARS-CoV-2 seroprevalence among school staff, based on spike (S)-based (unvaccinated staff) or N-based serology testing (vaccinated staff). RESULTS: Public health data showed the cumulative incidence of COVID-19 among students attending in-person was 9.8 per 1000 students (n=47 280), and 13 per 1000 among school staff (n=7071). In a representative sample of 1689 school staff, 78.2% had classroom responsibilities, and spent a median of 17.6 hours in class per week (IQR: 5.0-25 hours). Although 21.5% (363/1686) of surveyed staff self-reported close contact with a COVID-19 case outside of their household (16.5% contacts were school-based), 5 cases likely acquired the infection at school based on viral testing. Sensitivity/Specificity-adjusted seroprevalence in 1556/1689 staff (92.1%) was 2.3% (95% CI: 1.6% to 3.2%), comparable to a sex, age, date and residency area-weighted seroprevalence of 2.6% (95% CI: 2.2% to 3.1%) among 5417 blood donors. CONCLUSION: Seroprevalence among staff was comparable to a reference group of blood donors from the same community. These data show that in-person schooling could be safely maintained during the 2020/21 school year with mitigation measures, in a large school district in Vancouver, Canada.
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COVID-19 , SARS-CoV-2 , Colombia Británica/epidemiología , COVID-19/epidemiología , Estudios Transversales , Humanos , Estudios SeroepidemiológicosRESUMEN
Estimates of the basic reproduction number (R 0) for COVID-19 are particularly variable in the context of transmission within locations such as long-term healthcare (LTHC) facilities. We sought to characterize the heterogeneity of R 0 across known outbreaks within these facilities. We used a unique comprehensive dataset of all outbreaks that occurred within LTHC facilities in British Columbia, Canada as of 21 September 2020. We estimated R 0 in 18 LTHC outbreaks with a novel Bayesian hierarchical dynamic model of susceptible, exposed, infected and recovered individuals, incorporating heterogeneity of R 0 between facilities. We further compared these estimates to those obtained with standard methods that use the exponential growth rate and maximum likelihood. The total size of outbreaks varied dramatically, with range of attack rates 2%-86%. The Bayesian analysis provided an overall estimate of R 0 = 2.51 (90% credible interval 0.47-9.0), with individual facility estimates ranging between 0.56 and 9.17. Uncertainty in these estimates was more constrained than standard methods, particularly for smaller outbreaks informed by the population-level model. We further estimated that intervention led to 61% (52%-69%) of all potential cases being averted within the LTHC facilities, or 75% (68%-79%) when using a model with multi-level intervention effect. Understanding of transmission risks and impact of intervention are essential in planning during the ongoing global pandemic, particularly in high-risk environments such as LTHC facilities.
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BACKGROUND: The US overdose crisis is driven by fentanyl, heroin, and prescription opioids. One evidence-based policy response has been to broaden naloxone distribution, but how much naloxone a community would need to reduce the incidence of fatal overdose is unclear. We aimed to estimate state-level US naloxone need in 2017 across three main naloxone access points (community-based programmes, provider prescription, and pharmacy-initiated distribution) and by dominant opioid epidemic type (fentanyl, heroin, and prescription opioid). METHODS: In this modelling study, we developed, parameterised, and applied a mechanistic model of risk of opioid overdose and used it to estimate the expected reduction in opioid overdose mortality after deployment of a given number of two-dose naloxone kits. We performed a literature review and used a modified-Delphi panel to inform parameter definitions. We refined an established model of the population at risk of overdose by incorporating changes in the toxicity of the illicit drug supply and in the naloxone access point, then calibrated the model to 2017 using data obtained from proprietary data sources, state health departments, and national surveys for 12 US states that were representative of each epidemic type. We used counterfactual modelling to project the effect of increased naloxone distribution on the estimated number of opioid overdose deaths averted with naloxone and the number of naloxone kits needed to be available for at least 80% of witnessed opioid overdoses, by US state and access point. FINDINGS: Need for naloxone differed by epidemic type, with fentanyl epidemics having the consistently highest probability of naloxone use during witnessed overdose events (range 58-76% across the three modelled states in this category) and prescription opioid-dominated epidemics having the lowest (range 0-20%). Overall, in 2017, community-based and pharmacy-initiated naloxone access points had higher probability of naloxone use in witnessed overdose and higher numbers of deaths averted per 100 000 people in state-specific results with these two access points than with provider-prescribed access only. To achieve a target of naloxone use in 80% of witnessed overdoses, need varied from no additional kits (estimated as sufficient) to 1270 kits needed per 100 000 population across the 12 modelled states annually. In 2017, only Arizona had sufficient kits to meet this target. INTERPRETATION: Opioid epidemic type and how naloxone is accessed have large effects on the number of naloxone kits that need to be distributed, the probability of naloxone use, and the number of deaths due to overdose averted. The extent of naloxone distribution, especially through community-based programmes and pharmacy-initiated access points, warrants substantial expansion in nearly every US state. FUNDING: National Institute of Health, National Institute on Drug Abuse.
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Sobredosis de Droga , Sobredosis de Opiáceos , Analgésicos Opioides/uso terapéutico , Sobredosis de Droga/tratamiento farmacológico , Sobredosis de Droga/epidemiología , Fentanilo , Heroína/uso terapéutico , Humanos , Naloxona/uso terapéutico , Antagonistas de Narcóticos/uso terapéutico , Epidemia de Opioides , Prescripciones , Estados Unidos/epidemiologíaRESUMEN
Epstein-Barr virus (EBV) is transmitted by saliva and is a major cause of cancer, particularly in people living with HIV/AIDS. Here, we describe the frequency and quantity of EBV detection in the saliva of Ugandan adults with and without HIV-1 infection and use these data to develop a novel mathematical model of EBV infection in the tonsils. Eligible cohort participants were not taking antiviral medications, and those with HIV-1 infection had a CD4 count >200 cells/mm3. Over a 4-week period, participants provided daily oral swabs that we analysed for the presence and quantity of EBV. Compared with HIV-1 uninfected participants, HIV-1 coinfected participants had an increased risk of EBV detection in their saliva (IRR = 1.27, 95% CI = 1.10-1.47) and higher viral loads in positive samples. We used these data to develop a stochastic, mechanistic mathematical model that describes the dynamics of EBV, infected cells, and immune response within the tonsillar epithelium to analyse potential factors that may cause EBV infection to be more severe in HIV-1 coinfected participants. The model, fit using Approximate Bayesian Computation, showed high fidelity to daily oral shedding data and matched key summary statistics. When evaluating how model parameters differed among participants with and without HIV-1 coinfection, results suggest HIV-1 coinfected individuals have higher rates of B cell reactivation, which can seed new infection in the tonsils and lower rates of an EBV-specific immune response. Subsequently, both these traits may explain higher and more frequent EBV detection in the saliva of HIV-1 coinfected individuals.
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Coinfección/virología , Infecciones por Virus de Epstein-Barr/complicaciones , Infecciones por Virus de Epstein-Barr/virología , Infecciones por VIH/complicaciones , VIH-1 , Tonsila Palatina/virología , Adolescente , Adulto , Linfocitos B/inmunología , Estudios de Cohortes , Coinfección/inmunología , Biología Computacional , Infecciones por Virus de Epstein-Barr/inmunología , Femenino , Infecciones por VIH/inmunología , Herpesvirus Humano 4/inmunología , Herpesvirus Humano 4/aislamiento & purificación , Herpesvirus Humano 4/fisiología , Humanos , Inmunidad Celular , Masculino , Persona de Mediana Edad , Modelos Biológicos , Tonsila Palatina/inmunología , Saliva/virología , Procesos Estocásticos , Uganda , Carga Viral , Esparcimiento de Virus , Adulto JovenRESUMEN
Following successful non-pharmaceutical interventions (NPI) aiming to control COVID-19, many jurisdictions reopened their economies and borders. As little immunity had developed in most populations, re-establishing higher contact carried substantial risks, and therefore many locations began to see resurgence in COVID-19 cases. We present a Bayesian method to estimate the leeway to reopen, or alternatively the strength of change required to re-establish COVID-19 control, in a range of jurisdictions experiencing different COVID-19 epidemics. We estimated the timing and strength of initial control measures such as widespread distancing and compared the leeway jurisdictions had to reopen immediately after NPI measures to later estimates of leeway. Finally, we quantified risks associated with reopening and the likely burden of new cases due to introductions from other jurisdictions. We found widely varying leeway to reopen. After initial NPI measures took effect, some jurisdictions had substantial leeway (e.g., Japan, New Zealand, Germany) with > 0.99 probability that contact rates were below 80% of the threshold for epidemic growth. Others had little leeway (e.g., the United Kingdom, Washington State) and some had none (e.g., Sweden, California). For most such regions, increases in contact rate of 1.5-2 fold would have had high (> 0.7) probability of exceeding past peak sizes. Most jurisdictions experienced June-August trajectories consistent with our projections of contact rate increases of 1-2-fold. Under such relaxation scenarios for some regions, we projected up to â¼100 additional cases if just one case were imported per week over six weeks, even between jurisdictions with comparable COVID-19 risk. We provide an R package covidseir to enable jurisdictions to estimate leeway and forecast cases under different future contact patterns. Estimates of leeway can establish a quantitative basis for decisions about reopening. We recommend a cautious approach to reopening economies and borders, coupled with strong monitoring for changes in transmission.
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COVID-19/prevención & control , Teorema de Bayes , COVID-19/epidemiología , COVID-19/transmisión , Control de Enfermedades Transmisibles , Predicción , Humanos , Riesgo , SARS-CoV-2RESUMEN
IMPORTANCE: An effective vaccine against SARS-CoV-2 will reduce morbidity and mortality and allow substantial relaxation of physical distancing policies. However, the ability of a vaccine to prevent infection or disease depends critically on protecting older individuals, who are at highest risk of severe disease. OBJECTIVE: We quantitatively estimated the relative benefits of COVID-19 vaccines, in terms of preventing infection and death, with a particular focus on effectiveness in elderly people. DESIGN: We applied compartmental mathematical modelling to determine the relative effects of vaccines that block infection and onward transmission, and those that prevent severe disease. We assumed that vaccines showing high efficacy in adults would be deployed, and examined the effects of lower vaccine efficacy among the elderly population. SETTING AND PARTICIPANTS: Our mathematical model was calibrated to simulate the course of an epidemic among the entire population of British Columbia, Canada. Within our model, the population was structured by age and levels of contact. MAIN OUTCOME(S) AND MEASURE(S): We assessed the effectiveness of possible vaccines in terms of the predicted number of infections within the entire population, and deaths among people aged 65 years and over. RESULTS: In order to reduce the overall rate of infections in the population, high rates of deployment to all age groups will be critical. However, to substantially reduce mortality among people aged 65 years and over, a vaccine must directly protect a high proportion of people in that group. CONCLUSIONS AND RELEVANCE: Effective vaccines deployed to a large fraction of the population are projected to substantially reduce infection in an otherwise susceptible population. However, even if transmission were blocked highly effectively by vaccination of children and younger adults, overall mortality would not be substantially reduced unless the vaccine is also directly protective in elderly people. We strongly recommend: (i) the inclusion of people aged 65 years and over in future trials of COVID-19 vaccine candidates; (ii) careful monitoring of vaccine efficacy in older age groups following vaccination.
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Factores de Edad , Vacunas contra la COVID-19/inmunología , COVID-19/prevención & control , Anciano , Colombia Británica , Humanos , PandemiasRESUMEN
The province of British Columbia is currently experiencing the highest rate of apparent opioid-related deaths within Canada. This dramatic increase in overdose deaths has been primarily driven by the increase of fentanyl and fentanyl-analogues within the unregulated, highly unpredictable and toxic street drug supply. A public health emergency was declared in B.C. in April 2016. After the emergency was declared, overdose-related death rates continued to rise, reaching unprecedented levels. In the context of enhanced collaboration between government organizations and researchers, a series of mathematical studies improved the ability of government and service providers to understand the impact of scaled-up strategies, including harm reduction and treatment services. In this commentary we describe how government agencies collaborated with researchers and other experts to use modelling results, and describe lessons learned for enhancing these collaborations. Mathematical modelling provides a viable and timely approach to the generation of intelligence, combining disparate data to assess the on-going impact of a comprehensive package of interventions during a public health emergency, and enhancing accountability for investments.
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Sobredosis de Droga , Sobredosis de Opiáceos , Trastornos Relacionados con Opioides , Analgésicos Opioides/uso terapéutico , Colombia Británica , Sobredosis de Droga/tratamiento farmacológico , Fentanilo , Política de Salud , Humanos , Naloxona/uso terapéuticoRESUMEN
Extensive non-pharmaceutical and physical distancing measures are currently the primary interventions against coronavirus disease 2019 (COVID-19) worldwide. It is therefore urgent to estimate the impact such measures are having. We introduce a Bayesian epidemiological model in which a proportion of individuals are willing and able to participate in distancing, with the timing of distancing measures informed by survey data on attitudes to distancing and COVID-19. We fit our model to reported COVID-19 cases in British Columbia (BC), Canada, and five other jurisdictions, using an observation model that accounts for both underestimation and the delay between symptom onset and reporting. We estimated the impact that physical distancing (social distancing) has had on the contact rate and examined the projected impact of relaxing distancing measures. We found that, as of April 11 2020, distancing had a strong impact in BC, consistent with declines in reported cases and in hospitalization and intensive care unit numbers; individuals practising physical distancing experienced approximately 0.22 (0.11-0.34 90% CI [credible interval]) of their normal contact rate. The threshold above which prevalence was expected to grow was 0.55. We define the "contact ratio" to be the ratio of the estimated contact rate to the threshold rate at which cases are expected to grow; we estimated this contact ratio to be 0.40 (0.19-0.60) in BC. We developed an R package 'covidseir' to make our model available, and used it to quantify the impact of distancing in five additional jurisdictions. As of May 7, 2020, we estimated that New Zealand was well below its threshold value (contact ratio of 0.22 [0.11-0.34]), New York (0.60 [0.43-0.74]), Washington (0.84 [0.79-0.90]) and Florida (0.86 [0.76-0.96]) were progressively closer to theirs yet still below, but California (1.15 [1.07-1.23]) was above its threshold overall, with cases still rising. Accordingly, we found that BC, New Zealand, and New York may have had more room to relax distancing measures than the other jurisdictions, though this would need to be done cautiously and with total case volumes in mind. Our projections indicate that intermittent distancing measures-if sufficiently strong and robustly followed-could control COVID-19 transmission. This approach provides a useful tool for jurisdictions to monitor and assess current levels of distancing relative to their threshold, which will continue to be essential through subsequent waves of this pandemic.
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COVID-19/prevención & control , Modelos Biológicos , Distanciamiento Físico , Teorema de Bayes , Colombia Británica/epidemiología , COVID-19/epidemiología , COVID-19/transmisión , HumanosRESUMEN
U.S. Immigration and Customs Enforcement (ICE) facilities house thousands of undocumented immigrants in environments discordant with the public health recommendations to reduce the transmission of 2019 novel coronavirus (COVID-19). Using ICE detainee population data obtained from the ICE Enforcement and Removal Operations (ERO) website as of March 2, 2020, we implemented a simple stochastic susceptible-exposed-infected-recovered model to estimate the rate of COVID-19 transmission within 111 ICE detention facilities and then examined impacts on regional hospital intensive care unit (ICU) capacity. Models considered three scenarios of transmission (optimistic, moderate, pessimistic) over 30-, 60-, and 90-day time horizons across a range of facility sizes. We found that 72% of individuals are expected to be infected by day 90 under the optimistic scenario (R0 = 2.5), while nearly 100% of individuals are expected to be infected by day 90 under a more pessimistic (R0 = 7) scenario. Although asynchronous outbreaks are more likely, day 90 estimates provide an approximation of total positive cases after all ICE facility outbreaks. We determined that, in the most optimistic scenario, coronavirus outbreaks among a minimum of 65 ICE facilities (59%) would overwhelm ICU beds within a 10-mile radius and outbreaks among a minimum of 8 ICE facilities (7%) would overwhelm local ICU beds within a 50-mile radius over a 90-day period, provided every ICU bed was made available for sick detainees. As policymakers seek to rapidly implement interventions that ensure the continued availability of life-saving medical resources across the USA, they may be overlooking the pressing need to slow the spread of COVID-19 infection in ICE's detention facilities. Preventing the rapid spread necessitates intervention measures such as granting ICE detainees widespread release from an unsafe environment by returning them to the community.
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Betacoronavirus , Infecciones por Coronavirus , Emigración e Inmigración , Pandemias , Neumonía Viral , Adulto , COVID-19 , Infecciones por Coronavirus/epidemiología , Cultura , Femenino , Humanos , Masculino , Neumonía Viral/epidemiología , Prisiones/estadística & datos numéricos , SARS-CoV-2RESUMEN
Single particle tracking (SPT), where individual molecules are fluorescently labelled and followed over time, is an important tool that allows the spatiotemporal dynamics of subcellular biological systems to be studied at very fine temporal and spatial resolution. Mathematical models of particle motion are typically based on Brownian diffusion, reflecting the noisy environment that biomolecules inhabit. In order to study changes in particle behaviour within individual tracks, Hidden Markov models (HMM) featuring multiple diffusive states have been used as a descriptive tool for SPT data. However, such models are typically specified with an a priori defined number of particle states and it has not been clear how such assumptions have affected their outcomes. Here, we propose a method for simultaneously inferring the number of diffusive states alongside the dynamic parameters governing particle motion. Our method is an infinite HMM (iHMM) with the general framework of Bayesian nonparametric models. We directly extend previous applications of these concepts in molecular biophysics to the SPT framework and propose and test an additional constraint with the goal of accelerating convergence and reducing computational time. We test our iHMM using simulated data and apply it to a previously analyzed large SPT dataset for B cell receptor motion on the plasma membrane of B cells of the immune system.
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Teorema de Bayes , Membrana Celular/metabolismo , Movimiento , Receptores de Antígenos de Linfocitos B/metabolismo , Estadísticas no Paramétricas , DifusiónRESUMEN
Pre-exposure prophylaxis (PrEP) has the potential to greatly reduce transmission of HIV. However, significant questions remain around how behavioural factors may influence its impact within target populations. We used a 2014 sexual behaviour survey to modify and recalibrate a mathematical model of HIV infection dynamics within the population of gay, bisexual and other men who have sex with men (GBMSM) in the Greater Vancouver area of British Columbia, Canada. We performed a clustering analysis on the survey data to divide the population into categories associated with their reported risk of HIV exposure as well as their reported testing habits and attitudes towards PrEP. We found a positive association between reported risk and testing behaviour and level of awareness/interest in PrEP. Using the cluster groups to structure the population, we then estimated the impact of PrEP on HIV transmission in our study population. We found that the association between behaviour and interest in PrEP substantially boosted the population-level effectiveness of PrEP. Within our model, if PrEP adoption was unrelated to risk and testing, an additional 206 (95% credible interval 5-261), new infections representing 15% of total infections are predicted to occur among GBMSM over ten years, compared to where PrEP is adopted by individuals according to their level of interest. Our results underscore the importance of incorporating behavioural data into models when predicting the impact of future public health interventions.
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Infecciones por VIH/prevención & control , Conocimientos, Actitudes y Práctica en Salud , Profilaxis Pre-Exposición/estadística & datos numéricos , Asunción de Riesgos , Conducta Sexual/estadística & datos numéricos , Adulto , Colombia Británica , Análisis por Conglomerados , Infecciones por VIH/epidemiología , Hábitos , Homosexualidad Masculina , Humanos , Masculino , Persona de Mediana Edad , Modelos Teóricos , Salud Pública , Medición de Riesgo , Minorías Sexuales y de Género , Encuestas y CuestionariosRESUMEN
When B cells encounter antigens on the surface of an antigen-presenting cell (APC), B cell receptors (BCRs) are gathered into microclusters that recruit signaling enzymes. These microclusters then move centripetally and coalesce into the central supramolecular activation cluster of an immune synapse. The mechanisms controlling BCR organization during immune synapse formation, and how this impacts BCR signaling, are not fully understood. We show that this coalescence of BCR microclusters depends on the actin-related protein 2/3 (Arp2/3) complex, which nucleates branched actin networks. Moreover, in murine B cells, this dynamic spatial reorganization of BCR microclusters amplifies proximal BCR signaling reactions and enhances the ability of membrane-associated antigens to induce transcriptional responses and proliferation. Our finding that Arp2/3 complex activity is important for B cell responses to spatially restricted membrane-bound antigens, but not for soluble antigens, highlights a critical role for Arp2/3 complex-dependent actin remodeling in B cell responses to APC-bound antigens.
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Proteína 3 Relacionada con la Actina/metabolismo , Proteínas Similares a la Angiopoyetina/metabolismo , Linfocitos B/inmunología , Sinapsis Inmunológicas/metabolismo , Activación de Linfocitos , Receptores de Antígenos de Linfocitos B/metabolismo , Transducción de Señal , Actinas/metabolismo , Proteína 2 Similar a la Angiopoyetina , Animales , Ratones Endogámicos C57BLRESUMEN
BACKGROUND AND AIMS: The province of British Columbia (BC) Canada has experienced a rapid increase in illicit drug overdoses and deaths during the last 4 years, with a provincial emergency declared in April 2016. These deaths have been driven primarily by the introduction of synthetic opioids into the illicit opioid supply. This study aimed to measure the combined impact of large-scale opioid overdose interventions implemented in BC between April 2016 and December 2017 on the number of deaths averted. DESIGN: We expanded on the mathematical modelling methodology of our previous study to construct a Bayesian hierarchical latent Markov process model to estimate monthly overdose and overdose-death risk, along with the impact of interventions. SETTING AND CASES: Overdose events and overdose-related deaths in BC from January 2012 to December 2017. INTERVENTIONS: The interventions considered were take-home naloxone kits, overdose prevention/supervised consumption sites and opioid agonist therapy MEASUREMENTS: Counterfactual simulations were performed with the fitted model to estimate the number of death events averted for each intervention and in combination. FINDINGS: Between April 2016 and December 2017, BC observed 2177 overdose deaths (77% fentanyl-detected). During the same period, an estimated 3030 (2900-3240) death events were averted by all interventions combined. In isolation, 1580 (1480-1740) were averted by take-home naloxone, 230 (160-350) by overdose prevention services and 590 (510-720) were averted by opioid agonist therapy. CONCLUSIONS: A combined intervention approach has been effective in averting overdose deaths during British Columbia's opioid overdose crisis in the period since declaration of a public health emergency (April 2016-December 2017). However, the absolute numbers of overdose deaths have not changed.