Wastewater-based SARS-CoV-2 airport surveillance: key trends at the Cape Town International Airport.

Monitoring of SARS-CoV-2 RNA in wastewater has revealed the role of mobility in the transmission of coronavirus disease (COVID-19), and the surveillance of airport wastewater in cities across the world has demonstrated how travel entry points can give an indication of trends in transmission. This study undertook wastewater surveillance at the Cape Town International Airport (CTIA) to assess the use of a WBE approach to provide supplementary information on the presence of COVID-19 at a key air travel entry point in South Africa. Grab wastewater samples (n = 55) were collected from the CTIA wastewater pump station and analysed using quantitative real-time polymerase chain reaction (qRT-PCR) method. The study found a correlation between the wastewater data and clinical cases reported in the City of Cape Town during various time periods and during the peak of a COVID-19 wave. Highly elevated viral loads in the wastewater were observed at times there was increased mobility through the airport. The study also revealed elevated viral load levels at the airport despite the stricter restrictions and through the lower restrictions. The study findings indicate wastewater surveillance and airports can provide supplementary information to airport authorities to assess the impacts of imposed travel restrictions.

Using Wastewater Surveillance to Compare COVID-19 Outbreaks during the Easter Holidays over a 2-Year Period in Cape Town, South Africa.

Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown to be an important approach to determine early outbreaks of infections. Wastewater-based epidemiology (WBE) is regarded as a complementary tool for monitoring SARS-CoV-2 trends in communities. In this study, the changes in the SARS-CoV-2 RNA levels in wastewater during Easter holidays in 2021 and 2022 in the City of Cape Town were monitored over nine weeks. Our findings showed a statistically significant difference in the SARS-CoV-2 RNA viral load between the study weeks over the Easter period in 2021 and 2022, except for study week 1 and 4. During the Easter week, 52% of the wastewater treatment plants moved from the lower (low viral RNA) category in 2021 to the higher (medium to very high viral RNA) categories in 2022. As a result, the median SARS-CoV-2 viral loads where higher during the Easter week in 2022 than Easter week in 2021 (p = 0.0052). Mixed-effects model showed an association between the SARS-CoV-2 RNA viral loads and Easter week over the Easter period in 2021 only (p < 0.01). The study highlights the potential of WBE to track outbreaks during the holiday period.

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1-BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa.

This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive correlation between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA in wastewater samples and clinical cases (r = 0.7749, P < .0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven third wave, was significantly higher than during the Omicron-driven fourth wave. Whole-genome sequencing confirmed presence of Omicron lineage defining mutations in wastewater with the first occurrence reported 23 November 2021 (BA.1 predominant). The variant spread rapidly, with prevalence of Omicron-positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sublineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. These findings demonstrate the value of wastewater-based epidemiology to monitor the spatiotemporal spread and potential origin of new Omicron sublineages.

Cardiovascular Complications of Pregnancy-Associated COVID-19 Infections.

Cardiovascular complications are frequently present in coronavirus-2019 (COVID-19) infection. These include microvascular and macrovascular thrombotic complications such as arterial and venous thromboembolism, myocardial injury or inflammation resulting in infarction, heart failure, and arrhythmias. Data suggest increased risk of adverse outcomes in pregnant compared with nonpregnant women of reproductive age with COVID-19 infection, including need for intensive care unit admission, mechanical ventilation, and extracorporeal membrane oxygenation utilization. Current statements addressing COVID-19-associated cardiac complications do not include pregnancy complications that may mimic COVID-19 complications such as peripartum cardiomyopathy, spontaneous coronary artery dissection, and preeclampsia. Unique to pregnancy, COVID-19 complications can result in preterm delivery and modify management of the pregnancy. Moreover, pregnancy has often been an exclusion criterion for enrollment in research studies. In this review, we summarize what is known about pregnancy-associated COVID-19 cardiovascular complications.

Mechanisms of Immune Dysregulation in COVID-19 Are Different From SARS and MERS: A Perspective in Context of Kawasaki Disease and MIS-C.

Coronaviruses have led to three major outbreaks to date-Severe Acute Respiratory Syndrome (SARS; 2002), Middle East Respiratory Syndrome (MERS; 2012) and the ongoing pandemic, Coronavirus Disease (COVID-19; 2019). Coronavirus infections are usually mild in children. However, a few children with MERS had presented with a severe phenotype in the acute phase resulting in progressive pneumonic changes with increasing oxygen dependency and acute respiratory distress requiring ventilatory support. A subset of children with a history of SARS-CoV-2 infection develops a multisystem hyper-inflammatory phenotype known as Multisystem Inflammatory Syndrome in Children (MIS-C). This syndrome occurs 4-6 weeks after infection with SARS-CoV-2 and has been reported more often from areas with high community transmission. Children with MIS-C present with high fever and often have involvement of cardiovascular, gastrointestinal and hematologic systems leading to multiorgan failure. This is accompanied by elevation of pro-inflammatory cytokines such as IL-6 and IL-10. MIS-C has several similarities with Kawasaki disease (KD) considering children with both conditions present with fever, rash, conjunctival injection, mucosal symptoms and swelling of hands and feet. For reasons that are still not clear, both KD and MIS-C were not reported during the SARS-CoV and MERS-CoV outbreaks. As SARS-CoV-2 differs from SARS-CoV by 19.5% and MERS by 50% in terms of sequence identity, differences in genomic and proteomic profiles may explain the varied disease immunopathology and host responses. Left untreated, MIS-C may lead to severe abdominal pain, ventricular dysfunction and shock. Immunological investigations reveal reduced numbers of follicular B cells, increased numbers of terminally differentiated CD4+T lymphocytes, and decreased IL-17A. There is still ambiguity about the clinical and immunologic risk factors that predispose some children to development of MIS-C while sparing others. Host-pathogen interactions in SARS, MERS and COVID-19 are likely to play a crucial role in the clinical phenotypes that manifest. This narrative review focuses on the immunological basis for development of MIS-C syndrome in the ongoing SARS-CoV-2 pandemic. To the best of our knowledge, these aspects have not been reviewed before.

Policy Response to Post Covid-19: An Analytical Study of Indian Monetary and Fiscal Policies

The Covid-19 pandemic has emerged as a traumatic experience worldwide. It has impacted economic activities adversely, and led to health crisis, job losses, affected trade & transport, market selloff, collapse of export revenues and financial ambiguity. The Indian economy has also reeled under the brunt of Covid-19 which impelled the government to fight by initiating community awareness programs, social distancing measures, lockdown, testing and quarantine plans & actions and support packages for the public etc. Government of India also introduced stimulus packages to revitalize the financial system and amended fiscal and monetary policies such as Atmanirbhar Bharat Mission, Pradhan Mantri Garib Kalyan Yojana, PSU policy, deregulation of the agricultural sector, commercialisation of coal mining, etc to reduce the impact of the pandemic. Overall, the proactive measures undertaken during the pandemic have laid the foundations for economic recovery to gain momentum going ahead. But on the contrary all packages increased the capital expenditure of the country and increased economic hardship. Therefore, it is suggested that government should focus on measures that lead to decline in the expenditure and yield high revenues by raising the tax revenue buoyancy through improved compliance and increasing receipts from monetisation of assets and strategic disinvestments.

Deciphering the Interactions of SARS-CoV-2 Proteins with Human Ion Channels Using Machine-Learning-Based Methods.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is accountable for the protracted COVID-19 pandemic. Its high transmission rate and pathogenicity led to health emergencies and economic crisis. Recent studies pertaining to the understanding of the molecular pathogenesis of SARS-CoV-2 infection exhibited the indispensable role of ion channels in viral infection inside the host. Moreover, machine learning (ML)-based algorithms are providing a higher accuracy for host-SARS-CoV-2 protein-protein interactions (PPIs). In this study, PPIs of SARS-CoV-2 proteins with human ion channels (HICs) were trained on the PPI-MetaGO algorithm. PPI networks (PPINs) and a signaling pathway map of HICs with SARS-CoV-2 proteins were generated. Additionally, various U.S. food and drug administration (FDA)-approved drugs interacting with the potential HICs were identified. The PPIs were predicted with 82.71% accuracy, 84.09% precision, 84.09% sensitivity, 0.89 AUC-ROC, 65.17% Matthews correlation coefficient score (MCC) and 84.09% F1 score. Several host pathways were found to be altered, including calcium signaling and taste transduction pathway. Potential HICs could serve as an initial set to the experimentalists for further validation. The study also reinforces the drug repurposing approach for the development of host directed antiviral drugs that may provide a better therapeutic management strategy for infection caused by SARS-CoV-2.

Science Diplomacy and COVID-19: Future Perspectives for South-South Cooperation.

Apart from economic, political, and cultural cooperation for an equal growth of all developing countries, science and technology are an integral significant component in these levels of engagement for leveraging mutual gains. The current pandemic not only brought about an 1800 shift in the relationship between the government, policy makers, and the scientific community but highlights the importance of South-South Cooperation (SSC). SSC may serve as a mode of cooperation to foster the transfer of need-based technologies among developing and least developing countries and open many fronts for mutual sharing in terms of geopolitical, available resources, and expertise. The cooperation under the SSC does not substitute but complements North-South development cooperation to achieve the Sustainable Development Goals (SDGs). The use of science diplomacy would be an effective tool to bring all the stakeholders of the Global South to a common platform to combat future global challenges. Science policy instruments would need to incorporate scope for international collaborations as a means of furthering the national and global imperatives.

Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology.

This study uses wastewater-based epidemiology (WBE) to rapidly and, through targeted surveillance, track the geographical distribution of SARS-CoV-2 variants of concern (Alpha, Beta and Delta) within 24 wastewater treatment plants (WWTPs) in the Western Cape of South Africa. Information obtained was used to identify the circulating variant of concern (VOC) within a population and retrospectively trace when the predominant variant was introduced. Genotyping analysis of SARS-CoV-2 showed that 50% of wastewater samples harbored signature mutations linked to the Beta variant before the third wave, with the Delta variant absent within the population. Over time, the prevalence of the beta variant decreased steadily. The onset of the third wave resulted in the Delta variant becoming the predominant variant, with a 100% prevalence supporting the theory that the Delta variant was driving the third wave. In silico molecular docking analysis showed that the signature mutations of the Delta variant increased binding to host proteins, suggesting a possible molecular mechanism that increased viral infectivity of the Delta variant.

Surgical Diseases Management during COVID-19 Crisis at a Tertiary Care Hospital of India: Our Institutional Strategy.

Introduction In response to the national coronavirus disease 2019 (COVID-19) pandemic, all hospitals and medical institutes gave priority to COVID-19 screening and to the management of patients who required hospitalization for COVID-19 infection. Surgical departments postponed all elective operative procedures and provided only essential surgical care to patients who presented with acute surgical conditions or suspected malignancy. Ample literature has emerged during this pandemic regarding the guidelines for safe surgical care. We report our experience during the lockdown period including the surgical procedures performed, the perioperative care provided, and the specific precautions implemented in response to the COVID-19 crisis. Materials and Methods We extracted patient clinical data from the medical records of all surgical patients admitted to our tertiary care hospital between the March 24th, 2020 and May 31st, 2020. Data collected included: patient demographics, surgical diagnoses, surgical procedures, nonoperative management, and patient outcomes. Results Seventy-seven patients were included in this report: 23 patients were managed medically, 28 patients underwent a radiologic intervention, and 23 patients required an operative procedure. In total eight of the 77 patients died due to ongoing sepsis, multiorgan failure, or advanced malignancy. Conclusion During the COVID-19 lockdown period, our surgical team performed many lifesaving surgical procedures and appropriately selected cancer operations. We implemented and standardized essential perioperative measures to reduce the spread of COVID-19 infection. When the lockdown measures were phased out a large number of patients remained in need of delayed elective and semi-elective operative treatment. Hospitals, medical institutes, and surgical leadership must adjust their priorities, foster stewardship of limited surgical care resources, and rapidly implement effective strategies to assure perioperative safety for both patients and operating room staff during periods of crisis.

Impact of COVID-19 Pandemic on Cancer Surgical Services-AIIMS, New Delhi Experience.

COVID pandemic has impacted cancer care delivery and cancer surgical services globally. There is an urgent need to study the extent of the impact of COVID on cancer surgery and individual institutional response and strategies adopted to counter the adverse impact. A review of administrative and clinical policy changes adopted at the tertiary cancer center to combat COVID pandemic and resume cancer surgical services were performed. A retrospective comparative analysis of cancer out-patient census during COVID pandemic affected year and the preceding normal year along with cancer surgery data audit for the same periods was performed to assess the impact of the pandemic on cancer surgery. In addition, COVID infection rates among cancer surgery patients and healthcare workers were evaluated. There was approximately a 50% reduction in cancer outpatient registrations during COVID pandemic affected year. A trend of increasing footfalls was noted with decreasing COVID intensity and opening of lockdowns. There was a 33% reduction in major elective surgery and a 41% reduction in emergency surgery performed during the COVID period. As far as cancer surgeries are concerned, there was a 12-50% reduction in volumes involving different subsites. Overall COVID positivity rates among cancer surgery patients was low (8.17%), and approximately 30% of healthcare workers involved in cancer surgery were tested positive for COVID during the study period. Results of the current study indicate a significant impact of COVID pandemic on cancer surgical services. There was a significant impact on outpatient visits and cancer surgery volumes. However, a multidisciplinary-coordinated team approach, effective administrative and policy implementation, adoption of revised surgical safety and anesthesia protocols, COVID screening, and testing protocols facilitated resumption of cancer surgical services without adverse impact on surgical outcomes.

Spatial and Temporal Trends of SARS-CoV-2 RNA from Wastewater Treatment Plants over 6 Weeks in Cape Town, South Africa.

Recent scientific trends have revealed that the collection and analysis of data on the occurrence and fate of SARS-CoV-2 in wastewater may serve as an early warning system for COVID-19. In South Africa, the first COVID-19 epicenter emerged in the Western Cape Province. The City of Cape Town, located in the Western Cape Province, has approximately 4 million inhabitants. This study reports on the monitoring of SARS-CoV-2 RNA in the wastewater of the City of Cape Town's wastewater treatment plants (WWTPs) during the peak of the epidemic. During this period, the highest overall median viral RNA signal was observed in week 1 (9200 RNA copies/mL) and declined to 127 copies/mL in week 6. The overall decrease in the amount of detected viral SARS-CoV-2 RNA over the 6-week study period was associated with a declining number of newly identified COVID-19 cases in the city. The SARS-CoV-2 early warning system has now been established to detect future waves of COVID-19.

A pathway map of signaling events triggered upon SARS-CoV infection.

Severe acute respiratory syndrome coronaviruses (SARS-CoVs) caused worldwide epidemics over the past few decades. Extensive studies on various strains of coronaviruses provided a basic understanding of the pathogenesis of the disease. Presently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is leading a global pandemic with unprecedented challenges. This is the third coronavirus outbreak of this century. A signaling pathway map of signaling events induced by SARS-CoV infection is not yet available. In this study, we present a literature-annotated signaling pathway map of reactions induced by SARS-CoV infected cells. Multiple signaling modules were found to be orchestrated including PI3K-AKT, Ras-MAPK, JAK-STAT, Type 1 IFN and NFκB. The signaling pathway map of SARS-CoV consists of 110 molecules and 101 reactions mediated by SARS-CoV proteins. The pathway reaction data are available in various community standard data exchange formats including Systems Biology Graphical Notation (SBGN). The pathway map is publicly available through the GitHub repository and data in various formats can be freely downloadable.

Effect of coronavirus lockdowns on the ambient seismic noise levels in Gujarat, northwest India.

The Covid-19 pandemic created havoc and forced lockdowns in almost all the countries worldwide, to inhibit social spreading. In India as well, as a precautionary measure, complete and partial lockdowns were announced in phases during March 25 to May 31, 2020. The restricted human activities led to a drastic reduction in seismic background noise in the high frequency range of 1-20 Hz, representative of cultural noise. In this study, we analyse the effect of anthropogenic activity on the Earth vibrations, utilizing ambient noise recorded at twelve broadband seismographs installed in different environmental and geological conditions in Gujarat. We find that the lockdowns caused 1-19 dB decrease in seismic noise levels. The impact of restricted anthropogenic activities is predominantly visible during the daytime in urban areas, in the vicinity of industries and/or highways. A 27-79% reduction in seismic noise ground displacement (drms) is observed in daytime during the lockdown, in populated areas. However, data from station MOR reveals a drastic decrease in drms amplitude both during the day (79%) and night times (87%) since factories in this area operate round the clock. The noise at stations located in remote areas and that due to microseisms, shows negligible variation.

Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications.

SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. Here, we have presented global viewpoint on implications of emerging SARS-CoV-2 variants based on structural-function impact of crucial mutations occurring in its spike (S), ORF8 and nucleocapsid (N) proteins. While the N501Y mutation was observed in all three lineages, the 501Y.V1 and P.1 accumulated a different set of mutations in the S protein. The missense mutational effects were predicted through a COVID-19 dedicated resource followed by atomistic molecular dynamics simulations. Current findings indicate that some mutations in the S protein might lead to higher affinity with host receptors and resistance against antibodies, but not all are due to different antibody binding (epitope) regions. Mutations may, however, result in diagnostic tests failures and possible interference with binding of newly identified anti-viral candidates against SARS-CoV-2, likely necessitating roll out of recurring "flu-like shots" annually for tackling COVID-19. The functional relevance of these mutations has been described in terms of modulation of host tropism, antibody resistance, diagnostic sensitivity and therapeutic candidates. Besides global economic losses, post-vaccine reinfections with emerging variants can have significant clinical, therapeutic and public health impacts.

COVID-19 in children treated with immunosuppressive medication for kidney diseases.

BACKGROUND: Children are recognised as at lower risk of severe COVID-19 compared with adults, but the impact of immunosuppression is yet to be determined. This study aims to describe the clinical course of COVID-19 in children with kidney disease taking immunosuppressive medication and to assess disease severity. METHODS: Cross-sectional study hosted by the European Rare Kidney Disease Reference Network and supported by the European, Asian and International paediatric nephrology societies. Anonymised data were submitted online for any child (age <20 years) with COVID-19 taking immunosuppressive medication for a kidney condition. Study recruited for 16 weeks from 15 March 2020 to 05 July 2020. The primary outcome was severity of COVID-19. RESULTS: 113 children were reported in this study from 30 different countries. Median age: 13 years (49% male). Main underlying reasons for immunosuppressive therapy: kidney transplant (47%), nephrotic syndrome (27%), systemic lupus erythematosus (10%). Immunosuppressive medications used include: glucocorticoids (76%), mycophenolate mofetil (MMF) (54%), tacrolimus/ciclosporine A (58%), rituximab/ofatumumab (11%). 78% required no respiratory support during COVID-19 illness, 5% required bi-level positive airway pressure or ventilation. Four children died; all deaths reported were from low-income countries with associated comorbidities. There was no significant difference in severity of COVID-19 based on gender, dialysis status, underlying kidney condition, and type or number of immunosuppressive medications. CONCLUSIONS: This global study shows most children with a kidney disease taking immunosuppressive medication have mild disease with SARS-CoV-2 infection. We therefore suggest that children on immunosuppressive therapy should not be more strictly isolated than children who are not on immunosuppressive therapy.