SARS-CoV-2 is a coronavirus causing a globalized outbreak called COVID-19. SARS-CoV-2 transmission is associated with inhalation of contaminated respiratory droplets and could causes severe ...complications. Until today several “waves” of infections have been observed despite implementation of strict health policies. Decisions for such sanitary measures are based on population health monitoring. Unfortunately, for COVID-19, a significant proportion of individuals are asymptomatic but play a role in the virus transmission.
To overcome these limitations, several strategies were developed including genome quantification in wastewater that could allow monitoring of the health status of population, since shedding of SARS-CoV-2 in patient stool is frequent. Wastewater-based epidemiology (WBE) was established and several countries implemented this approach to allow COVID-19 outbreak monitoring. In France, the OBEPINE project performed a quantitative analysis of SARS-CoV-2 in raw wastewater samples collected from major wastewater treatment plants (WWTP) since March 2020.
In the greater Paris area 1101 samples (507 for five WWTP and 594 for sewer) were collected. This 16 months monitoring allows us to observe the outbreak dynamics. Comparison of WBE indicators with health data lead to several important observation; the good level of correlation with incidence rates, the average 3 days lead time, and the sensitivity (WBE change when incidence is > to 7/100000 inhabitants). We also compared the local monitoring (city level) with the regional monitoring, to help cluster identification.
Moreover, variants of concern (VOC) emerged due to the selection pressure. We developed a specific RT-qPCR method targeting the deletion H69-V70 in the spike protein, using this deletion as a proxy of the B.1.1.7 presence in the wastewater. With this data we demonstrate the predominant role played by this strain in the third wave.
All these results allow a better description and understanding of the pandemic and highlight the role of such WBE indicators.
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•Genome quantification of pathogens in wastewater allow monitoring of the health status of population.•Bi weekly sampling allows description of WBE indicators lag with incidence and sensibility at the regional or local level.•RT qPCR tools, targeting specific mutations allow dynamic monitoring of VOC in wastewater and population.•Variant monitoring in Wastewater demonstrates the important role played by some strains in the third wave.
Abstract
Background
Viral respiratory tract infections (VRTIs) are among the most common diseases, but the risks of superinfection for different virus species have never been compared.
Methods
...Multicenter retrospective study conducted among adults who tested positive for VRTIs with reverse-transcription polymerase chain reaction. We compared characteristics between influenza (A or B) and paramyxoviruses (respiratory syncytial virus, parainfluenza virus types 1 and 3, and human metapneumovirus) and identified predictors of superinfection and hospitalization.s
Results
Five hundred ninety patients had VRTI, including 347 (59%) influenza and 243 paramyxovirus infections with comparable rates of superinfections (53% vs 60%). In multivariate analyses, the predictors of superinfections were age >75 years (adjusted odds ratio, 2.37 95% confidence interval, 1.65–3.40), chronic respiratory disease (1.79 1.20–2.67), and biological abnormalities, including neutrophil count >7000/µL (1.98 1.34–2.91), eosinophil count <50/µL (2.53 1.61–3.98, and procalcitonin level >0.25ng/mL (2.8 1.65–4.73). The predictors of hospitalization were age >75 years old (adjusted odds ratio, 3.49 95% confidence interval, 2.17–5.63), paramyxovirus infection (2.28 1.39–3.75), long-term use of inhaled corticosteroids (2.49 1.13–5.49), and biological abnormalities, including neutrophil count >7000/µL (2.38 1.37–4.12) and procalcitonin level >0.25ng/mL (2.49 1.23–5.02). Kaplan-Meier survival curves showed that influenza-infected patients had a higher mortality rate than those with paramyxovirus infections (8.9% vs 4.5%, respectively; P = .02).
Conclusions
Our study revealed a high rate of superinfection (56%), not related to viral species. However influenza virus was associated with a poorer prognosis than paramyxoviruses, pleading for a broader and large-scale vaccination of individual at risk of VRTIs.
In our in-hospital setting study, viral respiratory tract infections are at high risk of superinfection (56%), regardless of virus species, and require improving vaccination coverage among patients at risk.
Infection with SARS-CoV-2 variant Omicron is considered to be less severe than infection with variant Delta, with rarer occurrence of severe disease requiring intensive care. Little information is ...available on comorbid factors, clinical conditions and specific viral mutational patterns associated with the severity of variant Omicron infection. In this multicenter prospective cohort study, patients consecutively admitted for severe COVID-19 in 20 intensive care units in France between December 7th 2021 and May 1st 2022 were included. Among 259 patients, we show that the clinical phenotype of patients infected with variant Omicron (n = 148) is different from that in those infected with variant Delta (n = 111). We observe no significant relationship between Delta and Omicron variant lineages/sublineages and 28-day mortality (adjusted odds ratio 95% confidence interval = 0.68 0.35-1.32; p = 0.253). Among Omicron-infected patients, 43.2% are immunocompromised, most of whom have received two doses of vaccine or more (85.9%) but display a poor humoral response to vaccination. The mortality rate of immunocompromised patients infected with variant Omicron is significantly higher than that of non-immunocompromised patients (46.9% vs 26.2%; p = 0.009). In patients infected with variant Omicron, there is no association between specific sublineages (BA.1/BA.1.1 (n = 109) and BA.2 (n = 21)) or any viral genome polymorphisms/mutational profile and 28-day mortality.
The emergence of SARS-CoV-2 variant 20I/501Y.V1 (VOC-202012/1 or GR/501Y.V1) is concerning given its increased transmissibility. We reanalysed 11,916 PCR-positive tests (41% of all positive tests) ...performed on 7-8 January 2021 in France. The prevalence of 20I/501Y.V1 was 3.3% among positive tests nationwide and 6.9% in the Paris region. Analysing the recent rise in the prevalence of 20I/501Y.V1, we estimate that, in the French context, 20I/501Y.V1 is 52-69% more transmissible than the previously circulating lineages, depending on modelling assumptions.
Following a study of predictors of superinfection in viral respiratory tract infections (VRTIs), this study analyzes the predictors of the outcome.
Multicenter retrospective study conducted among ...adults who tested positive for VRTIs with reverse-transcription polymerase chain reaction. We compared characteristics between influenza virus, Paramyxoviridae, and Pneumoviridae and identified predictors of favorable short-term outcome, admission to the intensive care unit (ICU), and mortality.
A total of 590 patients had VRTI, including 347 (59%) influenza infections. Mean (SD) patient age was 71.0 (18.3) years, with a sex ratio of 0.91. In multivariate analyses, predictors of favorable short-term outcome were age ≤75 years (adjusted odds ratio aOR 5.38 95% confidence interval, 1.59-18.2), absence of respiratory disease (4.94 1.01-24.37), and absence of superinfection (aOR 3.91 1.37-11.13). The predictors of ICU admission were age ≤75 years (aOR 3.28 1.71-6.25), chronic respiratory disease (aOR 2.49 1.20-5.19), and procalcitonin level >0.25 ng/mL (aOR 4.25 1.55-11.67). Predictors of mortality were use of inhaled corticosteroids (2.49 1.10-5.63), influenza infection (2.73 1.27-5.85), Charlson score ≥5 (5.35 1.90-15.05), superinfection (2.54 1.05-6.18), and eosinophil count <50/µL (4.39 1.19-16.2). Certainty of superinfection was significantly associated with mortality (2.23 1.15-4.3).
Our study revealed that superinfection was significantly related to the outcome, and that virus species affects mortality. These findings emphasize the need for improving the tools used in daily practice to confirm certainty of superinfection and for broader implementation of vaccination of individuals at risk of VRTIs.
•The first wave of COVID-19 in 2020 had collateral bacteriological effects in French hospitals in the Paris region.•There was a massive increase in blood culturing.•There were higher rates of ...positive blood culture and of blood stream infection.•There was a concomitant increase in antimicrobial resistance (and in antibiotic use).
This study measured the impact of the first wave of COVID-19 pandemic (COVID-19) (March–April 2020) on the incidence of bloodstream infections (BSIs) at Assistance Publique – Hôpitaux de Paris (APHP), the largest multisite public healthcare institution in France.
The number of patient admission blood cultures (BCs) collected, number of positive BCs, and antibiotic resistance and consumption were analysed retrospectively for the first quarter of 2020, and also for the first quarter of 2019 for comparison, in 25 APHP hospitals (ca. 14 000 beds).
Up to a fourth of patients admitted in March–April 2020 in these hospitals had COVID-19. The BSI rate per 100 admissions increased overall by 24% in March 2020 and 115% in April 2020, and separately for the major pathogens (Escherichia coli, Klebsiella pneumoniae, enterococci, Staphylococcus aureus, Pseudomonas aeruginosa, yeasts). A sharp increase in the rate of BSIs caused by microorganisms resistant to third-generation cephalosporins (3GC) was also observed in March–April 2020, particularly in K. pneumoniae, enterobacterial species naturally producing inducible AmpC (Enterobacter cloacae...), and P. aeruginosa. A concomitant increase in 3GC consumption occurred.
The COVID-19 pandemic had a strong impact on hospital management and also unfavourable effects on severe infections, antimicrobial resistance, and laboratory work diagnostics.
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