Municipal and neighbourhood level wastewater surveillance and subtyping of an influenza virus outbreak.

Recurrent influenza epidemics and pandemic potential are significant risks to global health. Public health authorities use clinical surveillance to locate and monitor influenza and influenza-like cases and outbreaks to mitigate hospitalizations and deaths. Currently, global integration of clinical surveillance is the only reliable method for reporting influenza types and subtypes to warn of emergent pandemic strains. The utility of wastewater surveillance (WWS) during the COVID-19 pandemic as a less resource intensive replacement or complement for clinical surveillance has been predicated on analyzing viral fragments in wastewater. We show here that influenza virus targets are stable in wastewater and partitions favorably to the solids fraction. By quantifying, typing, and subtyping the virus in municipal wastewater and primary sludge during a community outbreak, we forecasted a citywide flu outbreak with a 17-day lead time and provided population-level viral subtyping in near real-time to show the feasibility of influenza virus WWS at the municipal and neighbourhood levels in near real time using minimal resources and infrastructure.

Wastewater to clinical case (WC) ratio of COVID-19 identifies insufficient clinical testing, onset of new variants of concern and population immunity in urban communities.

Clinical testing has been the cornerstone of public health monitoring and infection control efforts in communities throughout the COVID-19 pandemic. With the anticipated reduction of clinical testing as the disease moves into an endemic state, SARS-CoV-2 wastewater surveillance (WWS) will have greater value as an important diagnostic tool. An in-depth analysis and understanding of the metrics derived from WWS is required to interpret and utilize WWS-acquired data effectively (McClary-Gutierrez et al., 2021; O'Keeffe, 2021). In this study, the SARS-CoV-2 wastewater signal to clinical cases (WC) ratio was investigated across seven cities in Canada over periods ranging from 8 to 21 months. This work demonstrates that significant increases in the WC ratio occurred when clinical testing eligibility was modified to appointment-only testing, identifying a period of insufficient clinical testing (resulting in a reduction to testing access and a reduction in the number of daily tests) in these communities, despite increases in the wastewater signal. Furthermore, the WC ratio decreased significantly in 6 of the 7 studied locations, serving as a potential signal of the emergence of the Alpha variant of concern (VOC) in a relatively non-immunized community (40-60 % allelic proportion), while a more muted decrease in the WC ratio signaled the emergence of the Delta VOC in a relatively well-immunized community (40-60 % allelic proportion). Finally, a significant decrease in the WC ratio signaled the emergence of the Omicron VOC, likely because of the variant's greater effectiveness at evading immunity, leading to a significant number of new reported clinical cases, even when community immunity was high. The WC ratio, used as an additional monitoring metric, could complement clinical case counts and wastewater signals as individual metrics in its potential ability to identify important epidemiological occurrences, adding value to WWS as a diagnostic technology during the COVID-19 pandemic and likely for future pandemics.

Mortality due to COVID-19 in Spain and its association with environmental factors and determinants of health.

Background: The objective of this study was to identify which air pollutants, atmospheric variables and health determinants could influence COVID-19 mortality in Spain. This study used information from 41 of the 52 provinces in Spain (from Feb. 1, to May 31, 2021). Generalized Linear Models (GLM) with Poisson link were carried out for the provinces, using the Rate of Mortality due to COVID-19 (CM) per 1,000,000 inhabitants as dependent variables, and average daily concentrations of PM10 and NO2 as independent variables. Meteorological variables included maximum daily temperature (Tmax) and average daily absolute humidity (HA). The GLM model controlled for trend, seasonalities and the autoregressive character of the series. Days with lags were established. The relative risk (RR) was calculated by increases of 10 g/m3 in PM10 and NO2 and by 1 â„ƒ in the case of Tmax and 1 g/m3 in the case of HA. Later, a linear regression was carried out that included the social determinants of health. Results: Statistically significant associations were found between PM10, NO2 and the CM. These associations had a positive value. In the case of temperature and humidity, the associations had a negative value. PM10 being the variable that showed greater association, with the CM followed of NO2 in the majority of provinces. Anyone of the health determinants considered, could explain the differential geographic behavior. Conclusions: The role of PM10 is worth highlighting, as the chemical air pollutant for which there was a greater number of provinces in which it was associated with CM. The role of the meteorological variables-temperature and HA-was much less compared to that of the air pollutants. None of the social determinants we proposed could explain the heterogeneous geographical distribution identified in this study. Supplementary Information: The online version contains supplementary material available at 10.1186/s12302-022-00617-z.

Short-term influence of environmental factors and social variables COVID-19 disease in Spain during first wave (Feb-May 2020).

This study aims to identify the combined role of environmental pollutants and atmospheric variables at short term on the rate of incidence (TIC) and on the hospital admission rate (TIHC) due to COVID-19 disease in Spain. This study used information from 41 of the 52 provinces of Spain (from Feb. 1, 2021 to May 31, 2021). Using TIC and TIHC as dependent variables, and average daily concentrations of PM10 and NO2 as independent variables. Meteorological variables included maximum daily temperature (Tmax) and average daily absolute humidity (HA). Generalized linear models (GLM) with Poisson link were carried out for each provinces The GLM model controlled for trend, seasonalities, and the autoregressive character of the series. Days with lags were established. The relative risk (RR) was calculated by increases of 10 µg/m3 in PM10 and NO2 and by 1 °C in the case of Tmax and 1 g/m3 in the case of HA. Later, a linear regression was carried out that included the social determinants of health. Statistically significant associations were found between PM10, NO2, and the rate of COVID-19 incidence. NO2 was the variable that showed greater association, both for TIC as well as for TIHC in the majority of provinces. Temperature and HA do not seem to have played an important role. The geographic distribution of RR in the studied provinces was very much heterogeneous. Some of the health determinants considered, including income per capita, presence of airports, average number of diesel cars per inhabitant, average number of nursing personnel, and homes under 30 m2 could explain the differential geographic behavior. As findings indicates, environmental factors only could modulate the incidence and severity of COVID-19. Moreover, the social determinants and public health measures could explain some patterns of geographically distribution founded.

Near real-time determination of B.1.1.7 in proportion to total SARS-CoV-2 viral load in wastewater using an allele-specific primer extension PCR strategy.

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed millions of lives to date. Antigenic drift has resulted in viral variants with putatively greater transmissibility, virulence, or both. Early and near real-time detection of these variants of concern (VOC) and the ability to accurately follow their incidence and prevalence in communities is wanting. Wastewater-based epidemiology (WBE), which uses nucleic acid amplification tests to detect viral fragments, is a reliable proxy of COVID-19 incidence and prevalence, and thus offers the potential to monitor VOC viral load in a given population. Here, we describe and validate a primer extension PCR strategy targeting a signature mutation in the N gene of SARS-CoV-2. This allows quantification of B.1.1.7 versus non-B.1.1.7 allele frequency in wastewater without the need to employ quantitative RT-PCR standard curves. We show that the wastewater B.1.1.7 profile correlates with its clinical counterpart and benefits from a near real-time and facile data collection and reporting pipeline. This assay can be quickly implemented within a current SARS-CoV-2 WBE framework with minimal cost; allowing early and contemporaneous estimates of B.1.1.7 community transmission prior to, or in lieu of, clinical screening and identification. Our study demonstrates that this strategy can provide public health units with an additional and much needed tool to rapidly triangulate VOC incidence/prevalence with high sensitivity and lineage specificity.

Short-term associations of air pollution and meteorological variables on the incidence and severity of COVID-19 in Madrid (Spain): a time series study.

BACKGROUND: There are studies that analyze the role of meteorological variables on the incidence and severity of COVID-19, and others that explore the role played by air pollutants, but currently there are very few studies that analyze the impact of both effects together. This is the aim of the current study. We analyzed data corresponding to the period from February 1 to May 31, 2020 for the City of Madrid. As meteorological variables, maximum daily temperature (Tmax) in ºC and mean daily absolute humidity (AH) in g/m3 were used corresponding to the mean values recorded by all Spanish Meteorological Agency (AEMET) observatories in the Madrid region. Atmospheric pollutant data for PM10 and NO2 in µg/m3 for the Madrid region were provided by the Spanish Environmental Ministry (MITECO). Daily incidence, daily hospital admissions per 100.000 inhabitants, daily ICU admissions and daily death rates per million inhabitants were used as dependent variables. These data were provided by the ISCIII Spanish National Epidemiology Center. Generalized linear models with Poisson link were performed between the dependent and independent variables, controlling for seasonality, trend and the autoregressive nature of the series. RESULTS: The results of the single-variable models showed a negative association between Tmax and all of the dependent variables considered, except in the case of deaths, in which lower temperatures were associated with higher rates. AH also showed the same behavior with the COVID-19 variables analyzed and with the lags, similar to those obtained with Tmax. In terms of atmospheric pollutants PM10 and NO2, both showed a positive association with the dependent variables. Only PM10 was associated with the death rate. Associations were established between lags 12 and 21 for PM10 and between 0 and 28 for NO2, indicating a short-term association of NO2 with the disease. In the two-variable models, the role of NO2 was predominant compared to PM10. CONCLUSIONS: The results of this study indicate that the environmental variables analyzed are related to the incidence and severity of COVID-19 in the Community of Madrid. In general, low temperatures and low humidity in the atmosphere affect the spread of the virus. Air pollution, especially NO2, is associated with a higher incidence and severity of the disease. The impact that these environmental factors are small (in terms of relative risk) and by themselves cannot explain the behavior of the incidence and severity of COVID-19.

Impact of environmental factors and Sahara dust intrusions on incidence and severity of COVID-19 disease in Spain. Effect in the first and second pandemic waves.

Scientific evidence suggests that Saharan dust intrusions in Southern Europe contribute to the worsening of multiple pathologies and increase the concentrations of particulate matter (PM) and other pollutants. However, few studies have examined whether Saharan dust intrusions influence the incidence and severity of COVID-19 cases. To address this question, in this study we carried out generalized linear models with Poisson link between incidence rates and daily hospital admissions and average daily concentrations of PM10, NO2, and O3 in nine Spanish regions for the period from February 1, 2020 to December 31, 2020. The models were adjusted by maximum daily temperature and average daily absolute humidity. Furthermore, we controlled for trend, seasonality, and the autoregressive nature of the series. The variable relating to Saharan dust intrusions was introduced using a dichotomous variable, NAF, averaged across daily lags in ranges of 0-7 days, 8-14 days, 14-21 days, and 22-28 days. The results obtained in this study suggest that chemical air pollutants, and especially NO2, are related to the incidence and severity of COVID-19 in Spain. Furthermore, Saharan dust intrusions have an additional effect beyond what is attributable to the variation in air pollution; they are related, in different lags, to both the incidence and hospital admissions rates for COVID-19. These results serve to support public health measures that minimize population exposure on days with particulate matter advection from the Sahara.

Does exposure to noise pollution influence the incidence and severity of COVID-19?

Research that analyzes the effect of different environmental factors on the impact of COVID-19 focus primarily on meteorological variables such as humidity and temperature or on air pollution variables. However, noise pollution is also a relevant environmental factor that contributes to the worsening of chronic cardiovascular diseases and even diabetes. This study analyzes the role of short-term noise pollution levels on the incidence and severity of cases of COVID-19 in Madrid from February 1 to May 31, 2020. The following variables were used in the study: daily noise levels averaged over 14 days; daily incidence rates, average cumulative incidence over 14 days; hospital admissions, Intensive Care Unit (ICU) admissions and mortality due to COVID-19. We controlled for the effect of the pollutants PM10 and NO2 as well as for variables related to seasonality and autoregressive nature. GLM models with Poisson regressions were carried out using significant variable selection (p < 0.05) to calculate attributable RR. The results of the modeling using a single variable show that the levels of noise (leq24 h) were related to the incidence rate, the rate of hospital admissions, the ICU admissions and the rate of average cumulative incidence over 14 days. These associations presented lags, and the first association was with incidence (lag 7 and lag 10), then with hospital admissions (lag 17) and finally ICU admissions (lag 22). There was no association with deaths due to COVID-19. In the results of the models that included PM10, NO2, Leq24 h and the control variables simultaneously, we observed that only Leq24 h went on to become a part of the models using COVID-19 variables, including the 14-day average cumulative incidence. These results show that noise pollution is an important environmental variable that is relevant in relation to the incidence and severity of COVID-19 in the Province of Madrid.