Spike-Seq: An amplicon-based high-throughput sequencing approach for the sensitive detection and characterization of SARS-CoV-2 genetic variations in environmental samples

Ever since the outbreak of COVID-19 disease in Wuhan, China, different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been identified. Wastewater-based epidemiology (WBE), an approach that has been successfully applied in numerous case studies worldwide, offers a cost-effective and rapid way for monitoring trends of SARS-Cov-2 in the community level without selection bias. Despite being a gold-standard procedure, WBE is a challenging approach due to the sample instability and the moderate efficiency of SARS-CoV-2 concentration in wastewater. In the present study, we introduce Spike-Seq, a custom amplicon-based approach for the S gene sequencing of SARS-CoV-2 in wastewater samples, which enables not only the accurate identification of the existing Spike-related genetic markers, but also the estimation of their frequency in the investigated samples. The implementation of Spike-Seq involves the combination of nested PCR-based assays that efficiently amplify the entire nucleotide sequence of the S gene and next-generation sequencing, which enables the variant detection and the estimation of their frequency. In the framework of the current work, Spike-Seq was performed to investigate the mutational profile of SARS-CoV-2 in samples from the Wastewater Treatment Plant (WWTP) of Athens, Greece, which originated from multiple timepoints, ranging from March 2021 until July 2022. Our findings demonstrate that Spike-Seq efficiently detected major genetic markers of B.1.1.7 (Alpha), B.1.617.2 (Delta) as well as B.1.1.529 (Omicron) variants in wastewater samples and provided their frequency levels, showing similar variant distributions with the published clinical data from the National Public Health organization. The presented approach can prove to be a useful tool for the detection of SARS-CoV-2 in challenging wastewater samples and the identification of the existing genetic variants of S gene.

The overlooked threat of land take from wind energy infrastructures: Quantification, drivers and policy gaps

Wind harnessing is a fast-developing and cost-effective Renewable Energy Source, but the land impacts of wind power stations are often overlooked or underestimated. We digitized land take, i.e., the generation of artificial land, derived from 90 wind power stations in Greece constructed between 2002 and 2020 (1.2 GW). We found substantial land take impacts of 7729 m2/MW (3.5 m2/MWh) of new artificial land, 148 m/MW of new roads and 174 m/MW of widened roads on average. Models showed that the number and size of wind turbines, the absence of other existing infrastructures and the elevational difference across new access roads increased artificial land generation. The elevational difference across new and widened access roads also increased their length. New wind power stations in Greece are planned to be installed at higher elevations and in terrains facing higher risks for soil erosion and soil biodiversity. The general tendency in the European Union is to sit fewer wind power stations in mountainous and forested land. Still, this pattern is inversed in several countries, particularly in Southern Europe. After screening 29 policy and legal documents, we found that land take is indirectly inferred in the global policy but more directly in the European policy through five non-legally binding documents and three Directives. However, the current European energy policies seem to conflict with nature conservation policies, risking land take acceleration. The study provides insights for reducing land take when planning and constructing wind power stations. We underline the need for better quantification of land take and its integration in the complex process of sustainable spatial planning of investments.

COVID-19 and kidney: role of SARS-CoV-2 infection in the induction of renal damage

OBJECTIVE

SARS-CoV-2 causes acute respiratory disease, interstitial and alveolar pneumonia, and involves numerous organs and systems such as the kidney, heart, digestive tract, blood, and nervous system. We aimed to evaluate the incidence of renal manifestations in patients diagnosed with COVID-19 infection.

PATIENTS AND METHODS

We performed a monocentric, cross-sectional, observational study, conducted on 114 patients with SARS-CoV-2. Clinical and laboratory parameters [renal function, serum electrolytes, inflammatory state, blood gas analysis, Interleukin 6 (IL-6) and urinalysis] were evaluated. The same values were checked out after two months (T1), however after negativization.

RESULTS

We enrolled 114 patients (59 males) with a mean age of 63.8 ± 13.9 years. We found hematuria in 48 patients (55.8%), proteinuria in 33 patients (38.4%), leukocyturia in 61 patients (70.9%), acute kidney injury (AKI) in 28 patients (24.6%), AKI in chronic kidney disease (CKD) in 24 patients (21.1%). Moreover, we found a significant increase of inflammatory indexes as C Reactive Protein (CRP), lactic dehydrogenase (LDH), alpha 1 and alpha 2 globulins with a subsequent reduction at T1 (p = 0.016, p < 0.001, p = 0.005, p = 0.007; respectively). Hemoglobin and erythrocyte values significantly decreased (p < 0.001, p = 0.003, respectively), and we found lymphopenia (p < 0.001). Also, we found elevated levels of the D-Dimer (p < 0.001) and a significant increase in the International Normalized Ratio (INR) (p = 0.038). We also showed a significant improvement after negativization in oxygen partial pressure (p = 0.001) and oxygen saturation (p < 0.001) and a significant increase in pH (p = 0.018) and bicarbonate concentration (p = 0.042). Moreover, we found a significant increase in IL-6 (p = 0.004). Also, we reported mild hyponatremia and hypokalemia with subsequent significant recovery (p < 0.001, p < 0.001, respectively) and mild hypochloremia with a recovery to the limits of statistical significance (p = 0.053). At the entrance, we found an increase in serum glucose with a significant reduction during recovery (p < 0.001).

CONCLUSIONS

The prevalence of AKI and/or CKD and/or abnormal urinalysis in patients diagnosed with COVID-19 on admission seems to be high and appears as a negative prognostic factor. Urinalysis appears to be very useful in unveiling the potential kidney impairment of COVID-19 patients; therefore, urinalysis could be used to reflect and predict the disease severity. We also recommend a careful evaluation of metabolic alterations, inflammatory states, and electrolytic disorders in COVID-19 patients.

Assessment of selected pharmaceuticals in Riyadh wastewater treatment plants, Saudi Arabia: Mass loadings, seasonal variations, removal efficiency and environmental risk

Despite increasing interest in pharmaceutical emissions worldwide, studies of environmental contamination with pharmaceuticals arising from wastewater discharges in Saudi Arabia are scarce. Therefore, this study examined occurrence, mass loads and removal efficiency for 15 pharmaceuticals and one metabolite (oxypurinol) from different therapeutic classes in three wastewater treatment plants (WWTPs), in Riyadh city in Saudi Arabia. A total of 144 samples were collected from the influents and effluents between March 2018 and July 2019 and analyzed using Solid Phase Extraction followed by triple quadrupole LC-MS/MS. The average concentrations in the influents and effluents were generally higher than their corresponding concentrations found either in previous Saudi Arabian or global studies. The four most dominant compounds in the influent were acetaminophen, ciprofloxacin, caffeine, and diclofenac, with caffeine and acetaminophen having the highest concentrations ranging between 943 and 2282 μg/L. Metformin and ciprofloxacin were the most frequently detected compounds in the effluents at concentrations as high as 33.2 μg/L. Ciprofloxacin had the highest mass load in the effluents of all three WWTPs, ranging between 0.20 and 20.7 mg/day/1000 inhabitants for different WWTPs. The overall average removal efficiency was estimated high (≥80), with no significant different (p > 0.05) between the treatment technology applied. Acetaminophen and caffeine were almost completely eliminated in all three WWTPs. The samples collected in the cold season generally had higher levels of detected compounds than those from the warm seasons, particularly for NSAID and antibiotic compounds. The estimated environmental risk from pharmaceutical compounds in the studied effluents was mostly low, except for antibiotic compounds. Thus, antibiotics should be considered for future monitoring programmes of the aquatic environment in Saudi Arabia.

Three years of wastewater surveillance for new psychoactive substances from 16 countries

The proliferation of new psychoactive substances (NPS) over recent years has made their surveillance complex. The analysis of raw municipal influent wastewater can allow a broader insight into community consumption patterns of NPS. This study examines data from an international wastewater surveillance program that collected and analysed influent wastewater samples from up to 47 sites in 16 countries between 2019 and 2022. Influent wastewater samples were collected over the New Year period and analysed using validated liquid chromatography - mass spectrometry methods. Over the three years, a total of 18 NPS were found in at least one site. Synthetic cathinones were the most found class followed by phenethylamines and designer benzodiazepines. Furthermore, two ketamine analogues, one plant based NPS (mitragynine) and methiopropamine were also quantified across the three years. This work demonstrates that NPS are used across different continents and countries with the use of some more evident in particular regions. For example, mitragynine has highest mass loads in sites in the United States, while eutylone and 3-methylmethcathinone increased considerably in New Zealand and in several European countries, respectively. Moreover, 2F-deschloroketamine, an analogue of ketamine, has emerged more recently and could be quantified in several sites, including one in China, where it is considered as one of the drugs of most concern. Finally, some NPS were detected in specific regions during the initial sampling campaigns and spread to additional sites by the third campaign. Hence, wastewater surveillance can provide an insight into temporal and spatial trends of NPS use.

Wide-scope target screening characterization of legacy and emerging contaminants in the Danube River Basin by liquid and gas chromatography coupled with high-resolution mass spectrometry

A state-of-the-art wide-scope target screening of 2,362 chemicals and their transformation products (TPs) was performed in samples collected within the Joint Danube Survey 4 (JDS4) performed in 2019. The analysed contaminants of emerging concern (CECs) included three major categories: plant protection products (PPPs), industrial chemicals and pharmaceuticals and personal care products (PPCPs). In total, 586 CECs were detected in the samples including 158 PPPs, 71 industrial chemicals, 348 PPCPs, and 9 other chemicals. A wide-variety of sample matrices were collected including influent and effluent wastewater, groundwater, river water, sediment and biota. Forty-five CECs (19 PPPs, 8 industrial chemicals, 18 PPCPs) were detected at levels above their ecotoxicological thresholds (lowest predicted no-effect concentration (PNEC) values) in one or more of the investigated environmental compartments, indicating potential adverse effects on the impacted ecosystems. Among them 12 are legacy substances; 33 are emerging and qualify as potential Danube River Basin Specific Pollutants (RBSPs). Moreover, the efficiency of the wastewater treatment plants (WWTPs) was evaluated using 20 selected performance indicator chemicals. WWTPs showed effective removal (removal rate ≥80%) and medium removal (removal rate 25-80%) for 6 and 8 of the indicator chemicals, respectively. However, numerous contaminants passed the WWTPs with a lower removal rate. Further investigation on performance of WWTPs is suggested at catchment level to improve their removal efficiency. WWTP effluents are proven to be one of the major sources of contaminants in the Danube River Basin (DRB). Other sources include sewage discharges, industrial and agricultural activities. Continuous monitoring of the detected CECs is suggested to ensure water quality of the studied area.

Delta SARS-CoV-2 variant is entirely substituted by the omicron variant during the fifth COVID-19 wave in Attica region

Wastewater analysis is the most attractive alternative way for the quantification and variant profiling of SARS-CoV-2. Infection dynamics can be monitored by RT-qPCR assays while NGS can provide evidence for the presence of existing or new emerging SARS-CoV-2 variants. Herein, apart from the infection dynamic in Attica since June 1st, 2021, the monitoring of 9 mutations of the omicron and 4 mutations of the delta SARS-CoV-2 variants, utilizing both novel Nested-Seq and RT-PCR, is reported and the substitution of the delta variant (B.1.617.2) by the omicron variant (B.1.1.529) in Attica, Greece within approximately one month is highlighted. The key difference between the two methodologies is discovery power. RT-PCR can only detect known sequences cost-effectively, while NGS is a hypothesis-free approach that does not require prior knowledge to detect novel genes. Overall, the potential of wastewater genomic surveillance for the early discovery and monitoring of variants important for disease management at the community level is underlined. This is the first study, reporting the SARS-CoV-2 infection dynamic for an extended time period and the first attempt to monitor two of the most severe variants with two different methodologies in Greece.

The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Background

The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for "suspect screening" lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.

Results

The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA's CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101).

Conclusions

The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the "one substance, one assessment" approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/).

Supplementary Information

The online version contains supplementary material available at 10.1186/s12302-022-00680-6.

Target and suspect screening of 4777 per- and polyfluoroalkyl substances (PFAS) in river water, wastewater, groundwater and biota samples in the Danube River Basin

Per- and polyfluoroalkyl substances (PFAS) are under regulatory scrutiny since some of them are persistent, bioaccumulative, and toxic. The occurrence of 4777 PFAS was investigated in the Danube River Basin (DRB; 11 countries) using target and suspect screening. Target screening involved investigation of PFAS with 56 commercially available reference standards. Suspect screening covered 4777 PFAS retrieved from the NORMAN Substance Database, including all individual PFAS lists submitted to the NORMAN Suspect List Exchange Database. Mass spectrometry fragmentation patterns and retention time index predictions of the studied PFAS were established for their screening by liquid chromatography - high resolution mass spectrometry using NORMAN Digital Sample Freezing Platform (DSFP). In total, 82 PFAS were detected in the studied 95 samples of river water, wastewater, groundwater, biota and sediments. Suspect screening detected 72 PFAS that were missed by target screening. Predicted no effect concentrations (PNECs) were derived for each PFAS via a quantitative structure-toxicity relationship (QSTR)-based approach and used for assessment of their environmental risk. Risk characterization revealed 18 PFAS of environmental concern in at least one matrix. The presence of PFAS in all studied environmental compartments across the DRB indicates a potentially large-scale migration of PFAS in Europe, which might require their further systematic regulatory monitoring.

SARS-CoV-2 wastewater surveillance data can predict hospitalizations and ICU admissions

We measured SARS-CoV-2 RNA load in raw wastewater in Attica, Greece, by RT-qPCR for the environmental surveillance of COVID-19 for 6 months. The lag between RNA load and pandemic indicators (COVID-19 hospital and intensive care unit (ICU) admissions) was calculated using a grid search. Our results showed that RNA load in raw wastewater is a leading indicator of positive COVID-19 cases, new hospitalization and admission into ICUs by 5, 8 and 9 days, respectively. Modelling techniques based on distributed/fixed lag modelling, linear regression and artificial neural networks were utilized to build relationships between SARS-CoV-2 RNA load in wastewater and pandemic health indicators. SARS-CoV-2 mutation analysis in wastewater during the third pandemic wave revealed that the alpha-variant was dominant. Our results demonstrate that clinical and environmental surveillance data can be combined to create robust models to study the on-going COVID-19 infection dynamics and provide an early warning for increased hospital admissions.

Multidose methotrexate treatment of cornual pregnancy after in vitro fertilization: Two case reports

Background

An ectopic pregnancy, when the gestational sac is implanted outside of the uterine cavity, can be life-threatening. A cornual pregnancy is the most dangerous type of ectopic pregnancy since it can be misdiagnosed easily and has high mortality rate. It is diagnosed when the implantation site is at the junction between the fallopian tube and the uterus. For a successful outcome, early diagnosis and management are critical. The traditional management is surgical, involving cornual resection or hysterectomy, which, however, affects fertility. Thus, conservative management involving administration of methotrexate should always be considered.

Case presentation

The article describes to two women in their early forties with no previous children (G1, P0) and diagnosed with a cornual pregnancy at 7 and 8 weeks of gestation following in vitro fertilization. Given their hemodynamic stability and their desire to conserve fertility they were treated conservatively. The two patients had similar ultrasound findings and blood results. The main difference was the presence of an embryonic heart beat in one case. Successful management was accomplished with multidose methotrexate and leucovorin during hospitalization for 8 days and close monitoring for the next 30 days as outpatients. In addition, the second woman was given a transvaginal injection of potassium chloride (KCL) to stop embryonic cardiac activity.

Conclusion

Conservative management of cornual pregnancies applying multidose therapy of methotrexate and leucovorin is a safe treatment when patients are asymptomatic and preserves fertility.

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Cornual pregnancy is the most dangerous type of ectopic pregnancy.

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Conservative treatment using multiple doses of methotrexate is safe and effective.

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When fetal cardiac activity is present KCL injection should be used.

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If the woman becomes hemodynamically unstable an operation is the only solution.

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With conservative management female fertility remains unaffected.

Change in the chemical content of untreated wastewater of Athens, Greece under COVID-19 pandemic

COVID-19 pandemic spread rapidly worldwide with unanticipated effects on mental health, lifestyle, stability of economies and societies. Although many research groups have already reported SARS-CoV-2 surveillance in untreated wastewater, only few studies evaluated the implications of the pandemic on the use of chemicals by influent wastewater analysis. Wide-scope target and suspect screening were used to monitor the effects of the pandemic on the Greek population through wastewater-based epidemiology. Composite 24 h influent wastewater samples were collected from the wastewater treatment plant of Athens during the first lockdown and analyzed by liquid chromatography mass spectrometry. A wide range of compounds was investigated (11,286), including antipsychotic drugs, illicit drugs, tobacco compounds, food additives, pesticides, biocides, surfactants and industrial chemicals. Mass loads of chemical markers were estimated and compared with the data obtained under non-COVID-19 conditions (campaign 2019). The findings revealed increases in surfactants (+196%), biocides (+152%), cationic quaternary ammonium surfactants (used as surfactants and biocides) (+331%), whereas the most important decreases were estimated for tobacco (-33%) and industrial chemicals (-52%). The introduction of social-restriction measures by the government affected all aspects of life.

Patterns of pharmaceuticals use during the first wave of COVID-19 pandemic in Athens, Greece as revealed by wastewater-based epidemiology

Since 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), impaired public health with considerable morbidity and mortality due to the lack of vaccines and effective treatment. The severe disease mainly harmed adults with predisposing medical comorbidities (such as heart disease, hypertension, chronic lung disease), while it can occur in healthy individuals that may be asymptomatic. Wastewater-based Epidemiology (WBE), a non-invasive, objective, chemical tool was used to monitor and estimate the changes in drug's consumption and prescription patterns under normal conditions (2019) and under COVID-19 pandemic conditions (2020). NSAIDs, antihypertensives, diuretics, antiepileptics, antilipidemics, antibiotics, analgesics, antivirals, anticancer drugs, contrast iodinated drugs, antidiabetics, antiallergic drugs, antiulcers and other pharmaceuticals were studied in wastewater and revealed the application of various treatments during the first wave of the pandemic in Athens, Greece. Data were correlated with COVID-19 infection therapeutical plans. The result of the analysis revealed a remarkable increase for antiviral drugs (170%), hydroxychloroquine (387%), and antibiotics (57%), which were the most applied treatments against COVID-19 during the first wave in Greece. In agreement with related authorities urge, NSAIDs presented decrease (27%) during the first lockdown, while paracetamol demonstrated a remarkable increase (198%). The use levels for Angiotensin II receptor blockers such as valsartan, and co-administrated diuretics, such as hydrochlorothiazide, were reduced during 2020, by 32% and 26% respectively.

Screening of QTc interval and global autonomic activity in autosomal dominant polycystic kidney disease and atherosclerotic renal artery stenosis hypertensive patients

OBJECTIVE

Arterial hypertension (AH) represents a major risk factor for cardiovascular disease and is associated to several complications, such as prolonged corrected QT (QTc) interval and impaired heart rate variability (HRV). Secondary causes of AH include autosomal dominant polycystic kidney disease (ADPKD) and atherosclerotic renal artery stenosis (ARAS), both known to be related to arrhythmic risk and autonomic imbalance. The aim of the study is to evaluate whether global autonomic activity and QTc interval differently affect ADPKD and ARAS hypertensive patients.

PATIENTS AND METHODS

An observational study was performed on 59 patients: 16 ADPKD patients and 19 diagnosed with ARAS, compared to 24 healthy controls (HC). All patients underwent clinical evaluation, biochemical lab tests, 24-hour electrocardiogram (ECG) and renal Doppler ultrasound. HRV was assessed through the analysis of 24-hour ECG to detect standard deviation of normal-to-normal RR intervals (SDNN). QTc interval was defined as prolonged when > 440 msec.

RESULTS

SDNN was significantly lower in ADPKD and ARAS patients than HC (p < 0.0001) and no significant differences were found between ADPKD and ARAS patients (p > 0.05). QTc was found significantly higher in ARAS patients than HC (p = 0.001) and in ARAS patients than ADPKD patients (p = 0.004).

CONCLUSIONS

The pathogenesis of hypertension in ADPKD and ARAS patients is related to the activation of the renin angiotensin aldosterone system (RAAS). In ADPKD, cyst enlargement leads to kidney ischemia and renin release, associated to endothelial dysfunction, low nitric oxide and sympathetic tone activation. Differently, reduction in renal perfusion pressure activates RAAS and renal adrenergic nerves in ARAS patients. We can speculate that prolonged QTc interval is more present in ARAS vs. ADPKD hypertensive patients due to a greater activation of RAAS. We suggest adding 24-hour HRV evaluation in association with traditional risk factors in course of ADPKD and ARAS hypertension to better stratify cardiovascular risk in these groups of patients.

Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater

Considering the lack of effective treatments against COVID-19, wastewater-based epidemiology (WBE) is emerging as a cost-effective approach for real-time population-wide SARS-CoV-2 monitoring. Here, we report novel molecular assays for sensitive detection and mutational/variant analysis of SARS-CoV-2 in wastewater. Highly stable regions of SARS-CoV-2 RNA were identified by RNA stability analysis and targeted for the development of novel nested PCR assays. Targeted DNA sequencing (DNA-seq) was applied for the analysis and quantification of SARS-CoV-2 mutations/variants, following hexamers-based reverse transcription and nested PCR-based amplification of targeted regions. Three-dimensional (3D) structure models were generated to examine the predicted structural modification caused by genomic variants. WBE of SARS-CoV-2 revealed to be assay dependent, and significantly improved sensitivity achieved by assay combination (94%) vs. single-assay screening (30%-60%). Targeted DNA-seq allowed the quantification of SARS-CoV-2 mutations/variants in wastewater, which agreed with COVID-19 patients' sequencing data. A mutational analysis indicated the prevalence of D614G (S) and P323L (RdRP) variants, as well as of the Β.1.1.7/alpha variant of concern, in agreement with the frequency of Β.1.1.7/alpha variant in clinical samples of the same period of the third pandemic wave at the national level. Our assays provide an innovative cost-effective platform for real-time monitoring and early-identification of SARS-CoV-2 variants at community/population levels.

Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater

Considering the lack of effective treatments against COVID-19, wastewater-based epidemiology (WBE) is emerging as a cost-effective approach for real-time population-wide SARS-CoV-2 monitoring. Here, we report novel molecular assays for sensitive detection and mutational/variant analysis of SARS-CoV-2 in wastewater. Highly stable regions of SARS-CoV-2 RNA were identified by RNA stability analysis and targeted for the development of novel nested PCR assays. Targeted DNA sequencing (DNA-seq) was applied for the analysis and quantification of SARS-CoV-2 mutations/variants, following hexamers-based reverse transcription and nested PCR-based amplification of targeted regions. Three-dimensional (3D) structure models were generated to examine the predicted structural modification caused by genomic variants. WBE of SARS-CoV-2 revealed to be assay dependent, and significantly improved sensitivity achieved by assay combination (94%) vs. single-assay screening (30%-60%). Targeted DNA-seq allowed the quantification of SARS-CoV-2 mutations/variants in wastewater, which agreed with COVID-19 patients' sequencing data. A mutational analysis indicated the prevalence of D614G (S) and P323L (RdRP) variants, as well as of the Β.1.1.7/alpha variant of concern, in agreement with the frequency of Β.1.1.7/alpha variant in clinical samples of the same period of the third pandemic wave at the national level. Our assays provide an innovative cost-effective platform for real-time monitoring and early-identification of SARS-CoV-2 variants at community/population levels.

P–578 Human pappiloma virus 16,18 genome methylation patterns in subfertile women

Study question

A comparison between L1 gene and LCR region methylation status of HPV16 and HPV18 viruses in subfertile women, investigating HPV methylation pattern in cervical cancer and asymptomatic HPV infection.

Summary answer

CpG methylation was more frequent in L1 gene compared to LCR in both HPV types. Methylation levels were associated with the grade of cervical dysplasia.

What is known already

HPV infection is a common sexually transmitted disease, related to genital warts and cancer. DNA methylation as a dynamic and strictly controlled process can be involved in numerous cellular processes, cell differentiation, gene expression regulation and genome reprogramming. Human pappiloma virus genome epigenetic alterations may play a key role in HPV life cycle as well as in the oncogenic process in general. However, whether the prevalence of high risk HPV is correlated with female infertility, has yet to be elucidated.

Study design, size, duration

From January 2015 to December 2019, about 2505 infertile couples were referred to the Human Reproduction Unit of Ioannina University Hospital. A total of 212 clinical and laboratory data from female partners were included in the study.

Participants/materials, setting, methods

Cervical smears were studied for HPV DNA methylation. CpG methylation was compared among L1 gene and LCR region in both HPV types. A bisulfite modification assay followed by DNA amplification and sequencing was performed to analyse HPV16 and HPV18 genome.

Main results and the role of chance

In HPV16 types, L1 gene and promoter region indicated high methylation levels in cervical cancer cases. LCR regions methylation levels ranged from 0,5% to 24,2% in asymptomatic HPV16 infection or cervical intraepithelial neoplasia and cervical cancer, respectively. As for L1 gene, the differences between asymptomatic HPV16 infection and cervical cancer cases were statistically significant (P = 0.003). In HPV18 types, L1 gene was methylated in cervical intraepithelial neoplasia and cervical cancer cases. Promoter region methylation levels were high in cervical cancer cases while LCR region methylation levels were low.

Limitations, reasons for caution

Main limitation is the relatively small size of the collected samples.

Wider implications of the findings: HPV genome investigation, as for methylation status, may lead to better understanding and earlier diagnostics of cervical pathology in infertile population. These observations point out the importance of fertility preservation in women at high risk for cervical neoplasia.

Trial registration number

Not applicable

Successful conservative medical management of an interstitial ectopic pregnancy at 10 weeks of gestation: A case report

Background

Interstitial pregnancy is a rare type of ectopic pregnancy, accounting for 2–6% of ectopic pregnancies, but it can be life threatening. There is no clear consensus on management, either surgical or medical, and it depends on hemodynamic stability and whether fertility-sparing treatment is requested.

Case Presentation

We present the case of a 35-year-old woman (G2, P1) who was diagnosed with an interstitial pregnancy at 10 weeks of gestation following in vitro fertilization. She was hemodynamically stable and requested fertility-sparing treatment. She was managed successfully with methotrexate and folinic acid with a hospital stay of 17 days.

Conclusion

Interstitial pregnancy can be managed medically. However, these patients require close monitoring.

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Iterstitial ectopic pregnancy accounts for 2-6% of ectopic pregnancies.

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Management may be either surgical or medical.

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Successful medical management with methotrexate regimen of a 10-week interstital pregnancy is described.

Analytical methodologies for the detection of SARS-CoV-2 in wastewater: Protocols and future perspectives

In March 2020 the World Health Organization announced a pandemic outbreak. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative pathogen for the coronavirus disease-19 (COVID-19) pandemic. The authorities worldwide use clinical science to identify infected people, but this approach is not able to track all symptomatic and asymptomatic cases due to limited sampling capacity of the testing laboratories. This drawback is eliminated by the Wastewater-Based Epidemiology (WBE) approach. In this review, we summarized the peer-reviewed published literature (available as of September 28, 2020), in the field of WBE. The commonly used steps (sampling, storage, concentration, isolation, detection) of the analytical protocols were identified. The potential limitations of each stage of the protocols and good practices were discussed. Finally, new methods for the efficient detection of SARS-CoV-2 were proposed.

Effects of non-invasive ventilation on renal and endothelial function in patients with respiratory failure

OBJECTIVE

Non-invasive positive pressure ventilation (NIV) is now an indispensable safeguard in the management of many pathologies. However, sometimes the positive end-expiratory pressure (PEEP) showed harmful effects on renal function, although effects on renal hemodynamic are unclear. We aimed at evaluating the effects of NIV on renal and endothelial function, in patients with chronic or acute respiratory failure.

PATIENTS AND METHODS

We performed a longitudinal, prospective, interventional study. We enrolled 17 hospitalized and non-hospitalized patients (11 males) with indication to NIV and stable hemodynamic parameters. Patients were treated with NIV and followed up at T0, at T1 (at the end of the NIV cycle) and at T2 (fifteen days after).

RESULTS

17 patients (11 males) with a mean age of 71.94 ± 14.89 years were enrolled. A significant increase in flow mediated dilation (FMD) was found (p = 0.004). We showed a significant improvement, after NIV, in the values of pH (p = 0.0002), pCO2 (p = 0.0001), pO2 (p = 0.04), lactates (p = 0.04), sO2 (p = 0.02) and in the P/F Ratio (p = 0.004). We also showed a significant reduction of serum glucose (p = 0.01) and a significant increase of serum chlorine (p = 0.047), while we did not report a significant increase of creatinine (p = 0.297) or a significant change in diuresis.

CONCLUSIONS

In our study NIV has no significant effects on renal function in patients with respiratory failure. Probably these patients required low PEEP values, which were less harmful to lung parenchyma and not effective on systemic hemodynamic. Furthermore, NIV has improved endothelial function in the short term, likely by reducing oxidative stress, as improvements of the gas-analysis parameters showed. Therefore, NIV could help to reduce cardiovascular risk of patients improving endothelial function.

Evaluation of chemical and biological contaminants of emerging concern in treated wastewater intended for agricultural reuse

The occurrence of chemical and biological contaminants of emerging concern (CECs) was investigated in treated wastewater intended for reuse in agriculture. An agarose hydrogel diffusion-based passive sampler was exposed to the outlet of a wastewater treatment plant (WWTP) located in Cyprus, which is equipped with membrane bioreactor (MBR). Passive samplers in triplicate were exposed according to a time-series exposure plan with maximum exposure duration of 28 days. Composite flow-proportional wastewater samples were collected in parallel with the passive sampling exposure plan and were processed by solid phase extraction using HORIZON SPE-DEX 4790 and the same sorbent material (Oasis HLB) as in the passive sampler. The analysis of passive samplers and wastewater samples enabled (i) the field-scale calibration of the passive sampler prototype by the calculation of in situ sampling rates of target substances, and (ii) the investigation of in silico predicted transformation products of the four most ecotoxicologically hazardous antibiotics (azithromycin, clarithromycin, erythromycin, ofloxacin). Additionally, the wastewater samples were subjected to the analysis of seven preselected antibiotic resistant genes (ARGs) and one mobile resistant element (int1). All extracts were analyzed for chemicals in a single batch using a highly sensitive method for pharmaceuticals, antibiotics and illicit drugs by liquid chromatography tandem MS/MS (LC-QQQ) and for various other target compounds (2316 compounds in total) by liquid chromatography high-resolution mass spectrometry (LC-HRMS). 279 CECs and all investigated ARGs (except for bla_CTX-M-32) were detected, highlighting potential chemical and biological hazards related to wastewater reuse practices. 16 CECs were prioritized following ecotoxicological risk assessment, whereas sul1 and the mobile resistant element (int1) showed the highest abundance. Comprehensive monitoring efforts using novel sampling methods such as passive sampling, wide-scope target screening and molecular analysis are required to assure safe application of wastewater reuse and avoid spread and crop uptake of potentially hazardous chemicals.

Resistant hypertension and obstructive sleep apnea syndrome in therapy with continuous positive airway pressure: evaluation of blood pressure, cardiovascular risk markers and exercise tolerance

OBJECTIVE

Resistant hypertension (RH) may be associated with Obstructive Sleep Apnea (OSA), determining a remarkable increase in cardiovascular risk. The aim of the study was to assess the effect of six months with continuous positive airway pressure (CPAP) treatment on blood pressure (BP) values, cardiovascular risk markers, and exercise tolerance in patients with RH and OSA.

PATIENTS AND METHODS

Twenty-four patients with RH and OSA were recruited and 24-hour ambulatory BP, intima-media thickness (IMT), flow mediated dilation (FMD), renal resistive index (RRI), and endurance cardiopulmonary exercise testing (CPET) were obtained at enrollment and after 6-month treatment.

RESULTS

Significant reduction in clinic systolic and diastolic BP, IMT, and RRI (p = 0.003, p = 0.009, p = 0.020, p = 0.04, respectively) and increase in the left ventricular ejection fraction (p = 0.035) were observed after a 6-month therapy with CPAP. Moreover, improvement in all polysomnographic parameters (number of apneas/hypopneas per hour (p < 0.001), number of episodes of night-time hemoglobin desaturation (ODI) (p = 0.010)), an improvement in Epworth Sleepiness Scale (p < 0.001), as well as in endurance time during constant workload CPET (p = 0.017) were observed too.

CONCLUSIONS

CPAP treatment for six months reduces BP and improves cardiovascular risk and exercise tolerance in patients with RH and OSA. An extended cardiovascular assessment, including exercise testing, might be helpful in this population, given the possible reversibility of some endothelial dysfunction and atherosclerotic markers with CPAP treatment, as reported in our study.

Wide-scope target and suspect screening methodologies to investigate the occurrence of new psychoactive substances in influent wastewater from Athens

Almost all licit and illicit drugs consumed by the society end up either unchanged or as a mixture of metabolites in the sewage systems. The analysis of influent wastewater samples and the estimation of drug consumption is the field of wastewater-based epidemiology (WBE). A new trend of WBE is the estimation of the consumption of New Psychoactive Substances (NPS), which are legal replacements of established narcotic and psychotropic drugs with slightly modified chemical structures and similar or new effects. To investigate the occurrence of NPS, 30 composite daily influent wastewater samples from the wastewater treatment plant (WWTP) of Athens (Greece) were collected in a four-year sampling campaign (2015-2018). A generic four-sorbent solid-phase extraction (SPE) sample preparation protocol able to retain compounds with wide physicochemical properties was used. Extracts were analyzed by liquid-chromatography coupled to quadrupole-time-of-flight mass spectrometry (LC-QTOF-MS) using target screening for 278 NPS and suspect screening for 451 NPS. Target screening method was validated for a subset of 49 representative NPS and illicit drugs with similar structures with the NPS. 24 NPS and related compounds were detected by target screening and two compounds were tentatively identified based on mass accuracy, prediction of retention time using in-house QSRR prediction models, isotopic pattern and HRMS/MS fragmentation, whereas the excreted mass loads were also calculated. The results indicated an occasional and low occurrence of NPS in wastewater during the week and over the years, whereas the estimation of the exact sources and the evaluation of the patterns in wastewater were critically discussed.

Greywater characterization and loadings - Physicochemical treatment to promote onsite reuse

Greywater is the wastewater produced in bathtubs, showers, hand basins, kitchen sinks, dishwashers and laundry machines. Segregation of greywater and blackwater and on site greywater treatment in order to promote its reuse for toilet flushing and/or garden irrigation is an interesting option especially in water deficient areas. The objective of this study was to characterize the different greywater sources in Greek households and to evaluate the performance of alternative physicochemical treatment systems to treat several types of greywater. Based on the results average daily greywater production was equal to 98 L per person per day and accounts for approximately 70-75% of the total household wastewater production (135 L per person per day). Among the different sources, laundry and kitchen sink are the main contributors to the total greywater load of organic carbon, suspended solids and surfactants, whereas dishwasher and bathroom greywater are the main sources of phosphorus and endocrine disrupting chemicals respectively. Depending on sources, greywater accounts for as low as 15% of the total wastewater load of organic carbon (in the case of light greywater sources), to as high as 74% of the total load organic load (in the case of the heavy greywater sources). On the other hand, the nutrients load of greywater is limited. The application of a physical treatment system consisting of coagulation, sedimentation, sand filtration, granular activated carbon filtration and disinfection can provide for a final effluent with high quality characteristics for onsite reuse, especially when treating light greywater.

Effect of personalized dietary intervention on nutritional, metabolic and vascular indices in patients with chronic kidney disease

OBJECTIVE

Patients with chronic kidney disease (CKD) present a markedly increased cardiovascular (CV) morbidity and mortality since the early stages of the disease and a high prevalence of malnutrition, inflammation, and accelerated atherosclerosis. Personalized nutritional intervention, with of a low-protein diet (LPD), since the early stages of CKD should be able to achieve significant metabolic improvements. In our study we have verified the effects of a personalized dietary intervention in patients in the CKD stages 3/4 KDOQI on nutritional, metabolic and vascular indices.

PATIENTS AND METHODS

We have evaluated renal function, lipid profile, mineral metabolism, inflammatory indices, and acid-base balance of 16 patients with CKD (stages 3/4 KDOQI). Assessment of nutritional status, body composition, bone mineral density and muscle mass, using body mass index (BMI), handgrip strength, bioelectrical impedance analysis (BIA), and dual energy X-ray absorptiometry (DEXA) was performed. Vascular indices and endothelial dysfunction such as carotid intima-media thickness (cIMT) and the brachial artery flow-mediated dilation (baFMD) were also analyzed.

RESULTS

After dietary interventions, we observed a significant increase in plasma bicarbonate (p = 0.004) and vitamin D levels (p = 0.03) and a concomitant significant reduction of phosphorus concentration (p = 0.001) and C-reactive protein (CRP) (p = 0.01).

CONCLUSIONS

Nutritional intervention potentially plays a major role in reducing the progression of CKD and systemic complications of predialysis patients. A low-protein diet (LPD) ensuring vegetable protein intake and a reduced amount of specific micronutrients should be recommended to stage 3/4 CKD patients in order to ameliorate metabolic profile, renal outcome, and reduce cardiovascular risk factors.

Uricemia and homocysteinemia: nontraditional risk factors in the early stages of chronic kidney disease--preliminary data

BACKGROUND

Patients with chronic kidney disease (CKD) show a risk of cardiovascular death, which is 10-100 times higher than that in the general population. This increase is not completely explained by the traditional cardiovascular risk factors. Hyperuricemia and hyperhomocysteinemia are highly prevalent in CKD. Patients suffering from these complications present accelerated atherosclerosis, determined mainly from the endothelial dysfunction that carries out a central role in the pathogenesis of cardiovascular diseases.

AIM

The hypothesis was that brachial artery flow mediated dilation (FMD) and carotid intima-media thickness (cIMT) evaluation can be considered as early and systemic markers of atherosclerosis and that nontraditional risk factors, such as hyperhomocysteinemia and hyperuricemia, are associated with early endothelial dysfunction and vascular damage in patients suffering from first- and second-stage CKD.

PATIENTS AND METHODS

The study comprised 50 patients, 10 for each CKD stage, and 15 age- and sex-matched healthy controls. We compared the traditional and nontraditional factors for cardiovascular diseases with alterations of vascular reactivity, such as cIMT, and brachial artery FMD, in patients affected by CKD with those in the control group.

RESULTS

In our study, hyperuricemia was significantly and independently associated with brachial artery FMD reduction (p = 0.007), while hyperhomocysteinemia was significantly and independently associated with carotid intima-media thickening (p = 0.021) in patients at Stage I and II KDOQI (Kidney Disease Outcomes Quality Initiative).

CONCLUSIONS

In our study, we found a progressive increase in the inflammatory indices and endothelial dysfunction at the early stages of CKD. Hyperuricemia and hyperhomocysteinemia were associated with IMT and FMD at Stage I-III KDOQI, and can be used as markers of subclinical atherosclerosis, especially in nephropathic patients with high cardiovascular risk.

Squamous cell carcinoma of the renal pelvis with stones and inferior vena cava infiltration. Case report

We report a rare case of a 50 year old man with renal squamous cell carcinoma (SCC) who first came to our attention with renal colic and fever not responding to antibiotic or analgesic treatment. He had a long history of kidney stones, but had not undergone any imaging in the last 5 years. Physical examination revealed tenderness and a palpable mass in the right flank and lumbar region. A whole body CT scan was performed, revealing an 11 cm mass in the right kidney infiltrating the inferior vena cava. There were areas of calcification within the mass and multiple stones within the renal pelvis. The tumor was considered unsuitable for resection according to radiological and clinical criteria. The mass was biopsied percutaneously under CT guidance and histological examination revealed squamous cell carcinoma of the renal pelvis. The patient was treated with neoadjuvant chemotherapy and embolization of the renal artery. He died one month after diagnosis. To our knowledge this is the second reported case in the world of renal SCC infiltrating the inferior vena cava and with kidney stones.

Subfascial endoscopic perforator surgery (SEPS) in chronic venous insufficiency. A 14 years experience

INTRODUCTION

Subfascial Endoscopic Perforator Surgery (SEPS) enables the direct visualization and section of perforating veins. Morbidity and duration of hospitalization are both less than with conventional open surgery (Linton's or Felder's techniques).

PATIENTS AND METHODS

A total of 322 legs from 285 patients with a mean age of 56 years (range 23-90) were treated at our Department from May 1996 to January 2010. In 309 cases, an endoscope (ETM Endoskopische Technik GmbH, Berlin, Germany) was introduced through a transverse incision approximately 1.5 cm in length and 10 cm from the tibial tuberosity, as with Linton's technique. A spacemaker balloon dissector for SEPS, involving a second incision 6 cm from the first, was used in only 13 cases.

RESULTS

The procedure used in each case was decided on the basis of preoperative evaluation. SEPS and stripping were performed in 238 limbs (73.91%), SEPS and short stripping in 7 limbs (2.17%), SEPS and crossectomy in 51 limbs (15.84%), and SEPS alone in 26 limbs (8.07%). 103 patients presented a total of 158 trophic ulcers; the healing time was between 1 and 3 months, with a healing rate of 82.91% after 1 month and 98.73% after 3 months.

CONCLUSION

Subfascial ligature of perforating veins is superior to sclerotherapy and minimally invasive suprafascial treatment for the treatment of CVI. It is easy to execute, minimally invasive and has few complications.

Ticlopidine-induced aplastic anemia: two new case reports, review, and meta-analysis of 55 additional cases

Ticlopidine-induced aplastic anemia (TIAA) is considered very uncommon. We present two new cases, and we review 55 additional cases from the literature. The first case concerns a 70-year-old man who developed severe aplastic anemia 7 weeks after treatment with 500 mg of ticlopidine daily. The patient sustained a severe septic episode, was treated with antibiotics and GM-CSF, and recovered the 14(th) day after ticlopidine withdrawal. The second was an 82-year-old man receiving ticlopidine for 2 years when, during a febrile episode, he was found neutropenic with marrow aplasia. Ticlopidine withdrawal and treatment with antibiotics, transfusions, and G-CSF helped him to recover. When the data of the 57 patients are evaluated, a reversible direct cytotoxic effect of ticlopidine on the pluripotent/bipotent hematopoietic progenitor stem cell is proposed. It is estimated that the real incidence if TIAA is higher, and many cases, initially presented as agranulocytosis +/- thrombocytopenia, might be true aplastic anemias, not proven by marrow aspiration or trephine biopsy. There is no effective monitoring to prevent this side effect. Recombinant growth factors appear not to help in shortening the neutropenic period.