Data Descriptor : Long-term chloride concentrations in North American and European freshwater lakes

Anthropogenic sources of chloride in a lake catchment, including road salt, fertilizer, and wastewater, can elevate the chloride concentration in freshwater lakes above background levels. Rising chloride concentrations can impact lake ecology and ecosystem services such as fisheries and the use of lakes as drinking water sources. To analyze the spatial extent and magnitude of increasing chloride concentrations in freshwater lakes, we amassed a database of 529 lakes in Europe and North America that had greater than or equal to ten years of chloride data. For each lake, we calculated climate statistics of mean annual total precipitation and mean monthly air temperatures from gridded global datasets. We also quantified land cover metrics, including road density and impervious surface, in buffer zones of 100 to 1,500m surrounding the perimeter of each lake. This database represents the largest global collection of lake chloride data. We hope that long-term water quality measurements in areas outside Europe and North America can be added to the database as they become available in the future.Peer reviewe

Aligning staff schedules, testing, and isolation reduces the risk of COVID-19 outbreaks in carceral and other congregate settings: A simulation study

COVID-19 outbreaks in congregate settings remain a serious threat to the health of disproportionately affected populations such as people experiencing incarceration or homelessness, the elderly, and essential workers. An individual-based model accounting for individual infectiousness over time, staff work schedules, and testing and isolation schedules was developed to simulate community transmission of SARS-CoV-2 to staff in a congregate facility and subsequent transmission within the facility that could cause an outbreak. Systematic testing strategies in which staff are tested on the first day of their workweek were found to prevent up to 16% more infections than testing strategies unrelated to staff schedules. Testing staff at the beginning of their workweek, implementing timely isolation following testing, limiting test turnaround time, and increasing test frequency in high transmission scenarios can supplement additional mitigation measures to aid outbreak prevention in congregate settings

Distributions and parameter values used in analytic framework and model simulations.

The latent period is defined as the time between exposure and onset of infectiousness, the incubation period as the time between exposure and both symptoms and peak infectiousness (even in the absence of symptoms), and the infectious period as the total time a case is infectious.</p

Number of expected infections generated in a facility from model simulations comparing random and systematic testing strategies across transmission scenarios, test frequencies, and delays isolating infectious individuals who have tested positive.

Systematic testing strategies (■, ➕) prevent more infections than random strategies (●, ▲) across all transmission scenarios (indicated by community prevalence across the x axis and by reproduction number across the panels) and test frequencies (indicated by different colored symbols with blue corresponding to the highest test frequency of 4 tests per week and red the lowest test frequency of biweekly testing). More infections are expected in transmission scenarios with higher within-facility and higher community prevalence. Preventing delays between testing and isolation of positives (squares compared to crosses and triangles compared to circles) and increasing test frequency (red = lowest frequency, blue = highest frequency) also reduces the number of infections. The horizontal gray line serves as a reference to assess the testing frequency needed to maintain (corresponding to one infection every ten days) across different transmission scenarios. Error bars represent the interquartile range of derived from 100 simulations per scenario run for 180 days among 700 staff.</p

Analytic framework exploring effects of variable infectiousness through time, testing frequencies, and delays on SARS-CoV-2 transmission.

A) Example infectiousness profile for , tlatent = 4, tincubation = 5, tinfectious = 9, with line indicating infectiousness (rt) through time and shaded area demonstrating infectiousness slice removed if tiso = 7, leading to . B) as a function of tiso with same parameters as in A and point indicating scenario depicted in A. C) Boxplots showing distributions of as a function of testing frequency, f, and delay in obtaining test results, d, incorporating uncertainty in tlatent, tincubation, and tinfectious by drawing n = 100 parameter sets for each, with baseline . Boxplots indicate median, interquartile range, and full range of values of . D) Probability isolation occurs as a function of testing frequency, f, delay in obtaining test results, d, and days from exposure to isolation τ, i.e. tiso≤τ, demonstrating that delays in obtaining test results substantially reduce the probability of prompt isolation, particularly among most frequent testing scenarios.</p

Outdoor Residential Water Use Restrictions during Recent Drought Suppressed Disease Vector Abundance in Southern California

The California state government put restrictions on outdoor residential water use, including landscape irrigation, during the 2012-2016 drought. The public health implications of these actions are largely unknown, particularly with respect to mosquito-borne disease transmission. While residential irrigation facilitates persistence of mosquitoes by increasing the availability of standing water, few studies have investigated its effects on vector abundance. In two study sub-regions in the Los Angeles Basin, we examined the effect of outdoor residential water use restrictions on the abundance of the most important regional West Nile virus vector, Culex quinquefasciatus. Using spatiotemporal random forest models fit to Cx. abundance during drought and non-drought years, we generated counterfactual estimates of Cx. abundance under a hypothetical drought scenario without water use restrictions. We estimate that Cx. abundance would have been 44% and 39% larger in West Los Angeles and Orange counties, respectively, if outdoor water usage had remained unchanged. Our results suggest that drought, without mandatory water use restrictions, may counterintuitively increase the availability of larval habitats for vectors in naturally dry, highly irrigated settings and such mandatory water use restrictions may constrain Cx. abundance, which could reduce the risk of mosquito-borne disease while helping urban utilities maintain adequate water supplies

Thermal thresholds heighten sensitivity of West Nile virus transmission to changing temperatures in coastal California

Temperature is widely known to influence the spatio-temporal dynamics of vector-borne disease transmission, particularly as temperatures vary across critical thermal thresholds. When temperature conditions exhibit such 'transcritical variation', abrupt spatial or temporal discontinuities may result, generating sharp geographical or seasonal boundaries in transmission. Here, we develop a spatio-temporal machine learning algorithm to examine the implications of transcritical variation for West Nile virus (WNV) transmission in the Los Angeles metropolitan area (LA). Analysing a large vector and WNV surveillance dataset spanning 2006-2016, we found that mean temperatures in the previous month strongly predicted the probability of WNV presence in pools of Culex quinquefasciatus mosquitoes, forming distinctive inhibitory (10.0-21.0°C) and favourable (22.7-30.2°C) mean temperature ranges that bound a narrow 1.7°C transitional zone (21-22.7°C). Temperatures during the most intense months of WNV transmission (August/September) were more strongly associated with infection probability in Cx. quinquefasciatus pools in coastal LA, where temperature variation more frequently traversed the narrow transitional temperature range compared to warmer inland locations. This contributed to a pronounced expansion in the geographical distribution of human cases near the coast during warmer-than-average periods. Our findings suggest that transcritical variation may influence the sensitivity of transmission to climate warming, and that especially vulnerable locations may occur where present climatic fluctuations traverse critical temperature thresholds

Early evidence of inactivated enterovirus 71 vaccine impact against hand, foot, and mouth disease in a major center of ongoing transmission in China, 2011-2018: a longitudinal surveillance study

BackgroundEnterovirus 71 (EV71) is a major causative agent of hand, foot, and mouth disease (HFMD), associated with severe manifestations of the disease. Pediatric immunization with inactivated EV71 vaccine was initiated in 2016 in the Asia-Pacific region, including China. We analyzed a time series of HFMD cases attributable to EV71, coxsackievirus A16 (CA16), and other enteroviruses in Chengdu, a major transmission center in China, to assess early impacts of immunization.MethodsReported HFMD cases were obtained from China's notifiable disease surveillance system. We compared observed postvaccination incidence rates during 2017-2018 with counterfactual predictions made from a negative binomial regression and a random forest model fitted to prevaccine years (2011-2015). We fit a change point model to the full time series to evaluate whether the trend of EV71 HFMD changed following vaccination.ResultsBetween 2011 and 2018, 279 352 HFMD cases were reported in the study region. The average incidence rate of EV71 HFMD in 2017-2018 was 60% (95% prediction interval [PI], 41%-72%) lower than predicted in the absence of immunization, corresponding to an estimated 6911 (95% PI, 3246-11 542) EV71 cases averted over 2 years. There were 52% (95% PI, 42%-60%) fewer severe HFMD cases than predicted. However, the incidence rate of non-CA16 and non-EV71 HFMD was elevated in 2018. We identified a significant decline in the trend of EV71 HFMD 4 months into the postvaccine period.ConclusionsWe provide the first real-world evidence that programmatic vaccination against EV71 is effective against childhood HFMD and present an approach to detect early vaccine impact or intended consequences from surveillance data

Prenatal and early-life exposure to the Great Chinese Famine increased the risk of tuberculosis in adulthood across two generations.

Global food security is a major driver of population health, and food system collapse may have complex and long-lasting effects on health outcomes. We examined the effect of prenatal exposure to the Great Chinese Famine (1958-1962)-the largest famine in human history-on pulmonary tuberculosis (PTB) across consecutive generations in a major center of ongoing transmission in China. We analyzed &gt;1 million PTB cases diagnosed between 2005 and 2018 in Sichuan Province using age-period-cohort analysis and mixed-effects metaregression to estimate the effect of the famine on PTB risk in the directly affected birth cohort (F1) and their likely offspring (F2). The analysis was repeated on certain sexually transmitted and blood-borne infections (STBBI) to explore potential mechanisms of the intergenerational effects. A substantial burden of active PTB in the exposed F1 cohort and their offspring was attributable to the Great Chinese Famine, with more than 12,000 famine-attributable active PTB cases (&gt;1.23% of all cases reported between 2005 and 2018). An interquartile range increase in famine intensity resulted in a 6.53% (95% confidence interval [CI]: 1.19-12.14%) increase in the ratio of observed to expected incidence rate (incidence rate ratio, IRR) in the absence of famine in F1, and an 8.32% (95% CI: 0.59-16.6%) increase in F2 IRR. Increased risk of STBBI was also observed in F2. Prenatal and early-life exposure to malnutrition may increase the risk of active PTB in the exposed generation and their offspring, with the intergenerational effect potentially due to both within-household transmission and increases in host susceptibility