Patient-reported distress at a cancer center during the COVID-19 pandemic.

Assessments of health-related quality of life (HRQOL) are conducted by health systems to improve patient-centered care. Studies have shown that the COVID-19 pandemic poses unique stressors for patients with cancer. This study investigates change in self-reported global health scores in patients with cancer before and during the COVID-19 pandemic. In this single-institution retrospective cohort study, patients who completed the Patient-Reported Outcomes Measurement Information System (PROMIS) at a comprehensive cancer center before and during the COVID-19 pandemic were identified. Surveys were analyzed to assess change in the global mental health (GMH) and global physical health (GPH) scores at different time periods (pre-COVID: 3/1/5/2019-3/15/2020, surge1: 6/17/2020-9/7/2020, valley1: 9/8/2020-11/16/2020, surge2: 11/17/2020-3/2/2021, and valley2: 3/3/2021-6/15/2021). A total of 25,192 surveys among 7209 patients were included in the study. Mean GMH score for patients before the COVID-19 pandemic (50.57) was similar to those during various periods during the pandemic: surge1 (48.82), valley1 (48.93), surge2 (48.68), valley2 (49.19). Mean GPH score was significantly higher pre-COVID (42.46) than during surge1 (36.88), valley1 (36.90), surge2 (37.33) and valley2 (37.14). During the pandemic, mean GMH (49.00) and GPH (37.37) scores obtained through in-person were similar to mean GMH (48.53) and GPH (36.94) scores obtained through telehealth. At this comprehensive cancer center, patients with cancer reported stable mental health and deteriorating physical health during the COVID-19 pandemic as indicated by the PROMIS survey. Modality of the survey (in-person versus telehealth) did not affect scores.

Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings.

COVID-19 resulted in extensive morbidity and mortality worldwide. SARS-CoV-2 evolved rapidly, with increasing transmission due to Variants of Concern (VOC). Identifying VOC became important but genome submissions from low-middle income countries (LMIC) remained low leading to gaps in genomic epidemiology. We demonstrate the use of a specific mutation RT-PCR based approach to identify VOC in SARS-CoV-2 positive samples through the pandemic in Pakistan. We selected 2150 SARS-CoV-2 PCR positive respiratory specimens tested between April 2021 and February 2022, at the Aga Khan University Hospital Clinical Laboratories, Karachi, Pakistan. Commercially available RT-PCR assays were used as required for mutations in Spike protein (N501Y, A570D, E484K, K417N, L452R, P681R and deletion69_70) to identify Alpha, Beta, Gamma, Delta, and Omicron variants respectively. Three pandemic waves associated with Alpha, Delta and Omicron occurred during the study period. Of the samples screened, VOC were identified in 81.7% of cases comprising mainly; Delta (37.2%), Alpha (29.8%) and Omicron (17.1%) variants. During 2021, Alpha variants were predominant in April and May; Beta and Gamma variants emerged in May and peaked in June; the Delta variant peaked in July and remained predominant until November. Omicron (BA.1) emerged in December 2021 and remained predominant until February 2022. The CT values of Alpha, Beta, Gamma and Delta were all significantly higher than that of Omicron variants (p<0.0001). We observed VOC through the pandemic waves using spike mutation specific RT-PCR assays. We show the spike mutation specific RT-PCR assay is a rapid, low-cost and adaptable for the identification of VOC as an adjunct approach to NGS to effectively inform the public health response. Further, by associating the VOC with CT values of its diagnostic PCR we gain information regarding the viral load of samples and therefore the level of transmission and disease severity in the population.

The effect of the global supply chain and oil prices on the inflation rates in advanced economies and emerging markets

This study investigates the effect of global supply chain pressures and crude oil prices on the consumer price index from October 1997 to February 2022 using panel linear and nonlinear autoregressive distributed lags (ARDLs, NARDLs). The results showed that the asymmetric effect of the global supply chain on the inflation rate is stronger when the supply chain increases than when it decreases in the long run for advanced economies and vice versa in emerging markets. A one standard deviation of the supply chain pressures has rebounded the inflation rate by about 1.7% and 0.71% for advanced economies and emerging markets, respectively. The findings establish that a 10 U.S. dollar increase in oil prices leads the inflation rate to rise by 0.1%–0.6% for all countries in the short run. However, the impact of the global supply chain index fits much better with the inflation rate than the oil prices in the short and long run, including the subprime crisis, such as the COVID‐19 outbreak, and the beginning of the Russo–Ukrainian conflict. Thus, the empirical results of the current study provide acumens for policymakers of advanced economies and emerging markets to consume green energy and make use of green technology and environmental innovations for counterbalancing the inflation issues induced by the higher rates of oil prices without halting the economic growth and sustainable development. [ABSTRACT FROM AUTHOR] Copyright of Geological Journal is the property of John Wiley & Sons, Inc. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Sequential viral introductions and spread of BA.1 drove the Omicron wave across Pakistani provinces (preprint)

Background: COVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan. Methods: We studied 276,525 COVID-19 cases and 1,041 genomes sequenced from December 2021 to August 2022. Sequences were analyzed and visualized using phylogenetic trees. Results: The highest case numbers and deaths were recorded in Sindh and Punjab, the most populous provinces in Pakistan. Omicron variants comprised 95% of all genomes, with BA.2 (34.2%) and BA.5 (44.6%) predominating. The first Omicron wave was associated with the sequential identification of BA.1 in Sindh, then Islamabad Capital Territory, Punjab, Khyber Pakhtunkhwa (KP), Azad Jammu Kashmir (AJK), Gilgit-Baltistan (GB) and Balochistan. Phylogenetic analysis revealed Sindh to be the source of BA.1 and BA.2 introductions into Punjab and Balochistan during early 2022. BA.4 was first introduced in AJK and BA.5 in Punjab. Most recent common ancestor (MRCA) analysis revealed relatedness between the earliest BA.1 genome from Sindh with Balochistan, AJK, Punjab and ICT, and that of first BA.1 from Punjab with strains from KPK and GB. Conclusions: Phylogenetic analysis provides insights into the introduction and transmission dynamics of the Omicron variant in Pakistan, identifying Sindh as a hotspot for viral dissemination. Such data linked with public health efforts can help limit surges of new infections.

Clinical Characteristics, Racial Inequities, and Outcomes in Patients with Breast Cancer and COVID-19: A COVID-19 and Cancer Consortium (CCC19) Cohort Study (preprint)

Title: Clinical Characteristics, Racial Inequities, and Outcomes in Patients with Breast Cancer and COVID-19: A COVID-19 and Cancer Consortium (CCC19) Cohort Study Background: Limited information is available for patients with breast cancer (BC) and coronavirus disease 2019 (COVID-19), especially among underrepresented racial/ethnic populations. Methods: This is a COVID-19 and Cancer Consortium (CCC19) registry-based retrospective cohort study of females with active or history of BC and laboratory-confirmed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection diagnosed between March 2020 and June 2021 in the US. Primary outcome was COVID-19 severity measured on a five-level ordinal scale, including none of the following complications, hospitalization, intensive care unit admission, mechanical ventilation, and all-cause mortality. Multivariable ordinal logistic regression model identified characteristics associated with COVID-19 severity. Results: 1,383 female patient records with BC and COVID-19 were included in the analysis, the median age was 61 years, and median follow-up was 90 days. Multivariable analysis revealed higher odds of COVID-19 severity for older age (aOR per decade, 1.48 [95% CI, 1.32 - 1.67]); Black patients (aOR 1.74; 95 CI 1.24-2.45), Asian Americans and Pacific Islander patients (aOR 3.40; 95 CI 1.70 - 6.79) and Other (aOR 2.97; 95 CI 1.71-5.17) racial/ethnic groups; worse ECOG performance status (ECOG PS [≥]2: aOR, 7.78 [95% CI, 4.83 - 12.5]); pre-existing cardiovascular (aOR, 2.26 [95% CI, 1.63 - 3.15])/pulmonary comorbidities (aOR, 1.65 [95% CI, 1.20 - 2.29]); diabetes mellitus (aOR, 2.25 [95% CI, 1.66 - 3.04]); and active and progressing cancer (aOR, 12.5 [95% CI, 6.89 - 22.6]). Hispanic ethnicity, timing and type of anti-cancer therapy modalities were not significantly associated with worse COVID-19 outcomes. The total all-cause mortality and hospitalization rate for the entire cohort was 9% and 37%, respectively however, it varied according to the BC disease status. Conclusions: Using one of the largest registries on cancer and COVID-19, we identified patient and BC related factors associated with worse COVID-19 outcomes. After adjusting for baseline characteristics, underrepresented racial/ethnic patients experienced worse outcomes compared to Non-Hispanic White patients. Funding: This study was partly supported by National Cancer Institute grant number P30 CA068485 to Tianyi Sun, Sanjay Mishra, Benjamin French, Jeremy L. Warner; P30-CA046592 to Christopher R. Friese; P30 CA023100 for Rana R McKay; P30-CA054174 for Pankil K. Shah and Dimpy P. Shah; and the American Cancer Society and Hope Foundation for Cancer Research (MRSG-16-152-01 -CCE) and P30-CA054174 for Dimpy P. Shah. REDCap is developed and supported by Vanderbilt Institute for Clinical and Translational Research grant support (UL1 TR000445 from NCATS/NIH). The funding sources had no role in the writing of the manuscript or the decision to submit it for publication. Clinical trial number: CCC19 registry is registered on ClinicalTrials.gov, NCT04354701.

E-learning in higher education during COVID-19: evidence from blackboard learning system

Purpose>The blackboard learning system is an online platform designed for e-learning employed by higher education institutes like universities that facilities students to continue learning and educational activities. This study explores the determinants that affect students' acceptance and use of Blackboard learning system (BLS) in Pakistan utilizing the modified UTAUT framework with social isolation as an additional variable.Design/methodology/approach>A questionnaire survey was conducted, and the study gathered 494 university students' responses in Pakistan as participants. The collected data were interpreted applying PLS-SEM version 3.2.3 software.Findings>The study's findings exhibited that PE, EE, FC and SI are the prime determinants influencing the intention and use of BLS in Pakistani universities. Hedonic motivation and social isolation interact differently between UTAUT variables and use intention. The results verify the suitability of the applied theory in the background of the study.Research limitations/implications>However, the findings highlight the present understanding of BLS use from the learners' aspect, but the study's limitation cannot be evaded. The study respondents belonged to a specific region of Pakistan (Karachi) that might influence the usefulness of the outcomes. Other factors categorized as the environmental, system and organizational elements were not part of the study that may also differentiate the BLS acceptance. The model was extended by including the social isolation, but the effect is insignificant yet positive;therefore, it is required to evaluate the model differently, such as the organizational aspect, for future research. Moreover, the ethnic factors that vary in emerging and developed economies may provide different explanations;therefore, they can be incorporated in future studies. Likewise, the variables such as hedonic motivation need to be emphasized more by examining and evaluating its effect on students' education performance in the future.Practical implications>The outcome of the study suggests some implications. At first, being the modified framework UTAUT2 application makes the collaboration appropriate according to the current phenomena of the COVID-19 pandemic and its contribution to the higher education region to analyze the acceptance of e-learning systems. Educational institutions within Pakistan would emphasize enhancing students' accomplishment by improving the interface and the blackboard learning system workability. Hence, learners' effectiveness in learning would be escalated;they would be encouraged to accomplish study objectives using BLS, particularly when they consider it easy to use and a useful platform for e-learning during the pandemic. Furthermore, enhancing the e-learning system in the context of the effort demands to be required to utilize BLS should be the foremost objective as learners would be motivated to accept the technology if they consider it simple, convenient, and user-friendly to adopt. Thus, the benefits of using BLS during this situation when universities are not operational will make students adaptable to change in the prospect. Learners will accept the model of online education, even if the universities become operational. However, it can increase the rate of earnings and revenue for universities as they can enroll in online and regular classes. Therefore, it is suggested that higher education management should create a resilient online platform by which facilitators can communicate with learners without any obstacles.Social implications>Hence, it is recommended to introduce the online short course, qualification, certified courses and integrated coursework with international ventures and ongoing classes. Numerous learners continue their studies along with the job. Therefore, it is suggested to introduce online programs for those learners. Another benefit would be that it offers an integrated platform for sharing knowledge. BLS offers to maintain the complete information in one place, and learners can see them as per their conve ience based on their availability. This reduces the burden on administration related to keeping the educational material and resource in various files. Thus, it also reduces the expense of universities. It is suggested to emphasize encouraging the use of BLS through an effective plan that can assist in execution and help learners identify the technology features rather than to face difficultly to accept the change. Moreover, the acceptance of BLS for educational purposes verifies that other learning events can occur on the online platform. Thus, it is recommended to promote the origin of the online atmosphere and the initiation of other events. Globally, dynamics are changing frequently and continuously and are moving towards artificial intelligence systems;the circumstances are suitable for promoting online educational platforms' acceptance by incorporating it with the current educational arrangement.Originality/value>The study provides recommendations for the research to be conducted to explore the modified framework in different regions and boundaries to evaluate the effect of other factors on adopting e-learning platforms.

Demographics, Outcomes, and Risk Factors for Patients with Sarcoma and COVID-19: A CCC19-Registry Based Retrospective Cohort Study.

BACKGROUND: Patients with sarcoma often require individualized treatment strategies and are likely to receive aggressive immunosuppressive therapies, which may place them at higher risk for severe COVID-19. We aimed to describe demographics, risk factors, and outcomes for patients with sarcoma and COVID-19. METHODS: We performed a retrospective cohort study of patients with sarcoma and COVID-19 reported to the COVID-19 and Cancer Consortium (CCC19) registry (NCT04354701) from 17 March 2020 to 30 September 2021. Demographics, sarcoma histologic type, treatments, and COVID-19 outcomes were analyzed. RESULTS: of 281 patients, 49% (n = 139) were hospitalized, 33% (n = 93) received supplemental oxygen, 11% (n = 31) were admitted to the ICU, and 6% (n = 16) received mechanical ventilation. A total of 23 (8%) died within 30 days of COVID-19 diagnosis and 44 (16%) died overall at the time of analysis. When evaluated by sarcoma subtype, patients with bone sarcoma and COVID-19 had a higher mortality rate than patients from a matched SEER cohort (13.5% vs 4.4%). Older age, poor performance status, recent systemic anti-cancer therapy, and lung metastases all contributed to higher COVID-19 severity. CONCLUSIONS: Patients with sarcoma have high rates of severe COVID-19 and those with bone sarcoma may have the greatest risk of death.

Patient-reported distress at a cancer center during the COVID-19 pandemic (preprint)

Background: Assessments of health-related quality of life (HRQOL) are conducted by health systems to improve patient-centered care. Studies have shown that the COVID-19 pandemic poses unique stressors for patients with cancer. This study investigates change in self-eported global health scores in patients with cancer before and during the COVID-19 pandemic. Methods and Materials: In this single-institution retrospective cohort study, patients who completed the Patient-Reported Outcomes Measurement Information System (PROMIS) at a comprehensive cancer center before and during the COVID-19 pandemic were identified. Surveys were analyzed to assess change in the global mental health (GMH) and global physical health (GPH) scores at different time periods (pre-COVID: 3/1/5/2019-3/15/2020, surge1: 6/17/2020-9/7/2020, valley1: 9/8/2020-11/16/2020, surge2: 11/17/2020-3/2/2021, and valley2: 3/3/2021-6/15/2021). Results: A total of 25,192 surveys among 7,209 patients were included in the study. Mean GMH score for patients before the COVID-19 pandemic (50.57) was similar to those during various periods during the pandemic: surge1 (48.82), valley1 (48.93), surge2 (48.68), valley2 (49.19). Mean GPH score was significantly higher pre-COVID (42.46) than during surge1 (36.88), valley1 (36.90), surge2 (37.33) and valley2 (37.14). During the pandemic, mean GMH (49.00) and GPH (37.37) scores obtained through in-person were similar to mean GMH (48.53) and GPH (36.94) scores obtained through telehealth. Conclusion: At this comprehensive cancer center, patients with cancer reported stable mental health and deteriorating physical health during the COVID-19 pandemic as indicated by the PROMIS survey. Modality of the survey (in-person versus telehealth) did not affect scores.

Staging Laparoscopy in Oesophago-gastric cancers;A highly selective approach and its impact on patient outcome during COVID 19

Background Staging laparoscopy is performed in all Oesophago-gastric cancer patients suitable for radical treatment with tumour staged ≥T2 prior to neoadjuvant chemotherapy. In response to COVID 19 pandemic, on 25th March 2020, the joint statement issued by the Royal College of Surgeons and AUGIS advised all laparoscopic procedures should be avoided due to the risk of virus transmission associated with aerosol-generating procedures. In accordance with the guidance, a more selective approach on who underwent a staging laparoscopy was followed. This audit explores its impact on patient outcome comparing data from pre COVID period with the COVID period. Methods Retrospective and prospective data was collected for 24months on all OG cancer patients from 25th March2019 to 24th March2021. ‘Pre COVID’ period was defined as 25th March 2019 to 24th March 2020 and ‘COVID’ period was defined as 25th March 2020 to 24th March 2021. All patients with Oesophago-gastric cancer with MDT cancer staged ≥T2, suitable for neoadjuvant chemotherapy were included. Patients with tumour staged <T2 and or diagnosed with squamous cell carcinoma involving upper or middle third of oesophagus were excluded. Fishers Exact model using SPSS V24 was used to identify any statistically significant differences between the 2 groups. Results Pre-COVID Period: 80patients underwent staging laparoscopy. Of these, 9patients(11.6%) with tumour staged as ≥T3 were declined curative surgery due to advanced disease(n = 2), metastatic disease(n = 3) or both(n = 4). In total, 40patients underwent curative surgery and there were 0 open/close laparotomies. COVID Period: Of the 79patients suitable for staging laparoscopy, only 7patients(8.7%) underwent laparoscopy. Of these, 3patients(3.8%) with tumour staged as ≥T3 were declined curative surgery due to advanced disease(n = 2) and metastatic disease(n = 1). In total, 33patients underwent curative surgery and only 1patient had an open/close laparotomy due to a liver metastases. No statistically significant difference was found p = 0.0913 Conclusions Staging laparoscopy is a useful tool for accurate staging of Oesophago-gastric cancers. It helps avoid unnecessary open and close laparotomy due to advanced disease and also allows us to assess patient fitness to major surgery. During the pandemic, the number of staging laparoscopies performed declined significantly but with no statistically significant difference to patient outcome. Thus we conclude,  the COVID 19 pandemic has enabled us to have a selective approach to performing staging laparoscopy in Oesophago-gastric patients with advanced disease staged ≥T3 only.

To diagnose histopathological alterations in respiratory system through radiological analysis

Histopathological alteration in the respiratory system of COVID-19 patient is mainly caused due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). HRCT is a highly diagnostic tool to detect COVID-19, as chest computerized tomography (CT) describes pre and post effect of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the respiratory system by radiological findings such as Ground-glass opacity, Pleural effusion, bilateral consolidation, and Interlobular septal thickening. [ FROM AUTHOR] Copyright of Professional Medical Journal is the property of Professional Medical Journal and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

ASSESSMENT OF DETERMINANTS OF PRACTICES REGARDING USE OF PERSONAL PROTECTIVE EQUIPMENT (PPE) AMONG MEDICAL STUDENTS

Objective: To assess the knowledge, attitudes regarding hygienic and personal protective practices and to evaluate the factors associated with the knowledge regarding use of PPE among medical college students. Study Design: A descriptive cross-sectional study. Place and Duration of Study: Foundation University, Islamabad Pakistan, from Mar to May 2021. Methodology: Using non-probability consecutive sampling, a self-administered questionnaire will be given to students. Questions will be asked about their knowledge of the types of PPE and its correct use and analyzed in SPSS-20. Results: Out of 289 respondents, one hundred and sixty-eight (58%) belongs to 1st - 3rd year of MBBS and one hundred and twenty-one (42%) were in 4th and final year. Majority (68%) were females and ninety-two (32%) males. Two hundred and forty-three (84%) of them agreed that main goal of infection control is to prevent infection among patients and health care workers. Two hundred and twenty-eight (79%) of them had knowledge regarding correct duration of hand washing and ninety-eight (34%) agreed that use of gloves replaced the need of hand washing. More than half (78%) had knowledge that hand washing is indicated after removal of gloves. Majority (92%) knows that PPE provides barrier against infection. About half (53%) and (48%) had correct knowledge regarding donning and doffing of PPE respectively. Regarding attitudes, half of the respondent (50%) strongly agrees towrds correct use of PPE and hand hygiene. Conclusion: The levels of self-reported PPE information and Infection prevention and control training are sub-optimal in medical students of FFH which significantly correlates to COVID-19 and other infectious diseases-related anxiety.

ASSESSING BARRIERS TO ADOPTION OF SUSTAINABLE PERSONAL HYGIENE BEHAVIOUR AND LIFESTYLE CHANGE IN COMMUNITIES IN RAWALPINDI DURING COVID-19 PANDEMIC

Objective: To assess the current habits of personal hygiene practices, to determine the role of demographic characteristics in personal hygiene practices and to identify barriers to sustainable behavioral change during COVID-19 pandemic in general communities of Rawalpindi. Study Design: A cross sectional mixed method study. Place and Duration of Study: Different communities of Rawalpindi city, from Aug 2020 to Apr 2021. Methodology: Non-probability consecutive sampling was used. Both qualitative and quantitative data (sample size;n=400) was collected for understanding of the barriers in sustainability of modified behaviour during and after COVID-19. Results: Out of 400 respondents, 43% were in the age group of 15-30 years while 30% were between 31-45 years. More than half 65% of them were males and 35% females. About 98% of the respondents practice frequent hand washing, 87% uses hand sanitizers, 75% wear masks, 67% practice social distancing and 95% cover their mouth during coughing and sneezing. The educational and occupational status of the respondents was significantly associated with personal hygiene and lifestyle change behaviour. About 391 respondents 391 (97%) were used to practice hand washing, 350 (87.3%) hand sanitizer 301 (75%) wear masks outside home. About 269 (67%) practice social distancing and 382 (95%) cover their mouth while coughing/sneezing. Conclusion: Sustainable behaviour change for positive health and reduced transmission of communicable diseases is possible, if the nature of human beings and the cultural and religious beliefs that define them are taken into account.

SARS-CoV-2 Variants of Concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron coincident with consecutive pandemic waves in Pakistan (preprint)

Identification and monitoring of SARS-CoV-2 Variants of Concern/Interest (VOC/VOIs) is essential to guide public health measures. We report the surveillance of VOCs circulating in Karachi during the pandemic between April 2021 and February 2022. We screened 2150 SARS-CoV-2 PCR positive samples received at the AKUH Clinical Laboratories. VOC was identified using a PCR-based approach targeting lineage-specific mutations using commercially available assays. Of the SARS-CoV-2 PCR positive samples, 81.7% had VOC/VOI, while 18.3% were undetermined. Alpha variants were predominant at 82.5% and 40.3% of the cases in April and May 2021. Beta variants increased in May (29%) and June (42%) and then reduced to 6% by July. Gamma variant cases were at 14.5% and 9% in May and June, respectively. Delta variants first detected in May, increased to comprise 66% of all variants by July, remaining dominant in August, September, October, and November 2021 at 88%, 91%, 91% and 85% respectively. Omicron (BA.1) variants emerged in December, rising to 42% of cases with an increase to 81% by January 2022 and then reducing to 45% in February 2022. Delta variant prevalence was coincident with increased hospital admissions and mortality. The Omicron variant surge was associated with increased daily infections but limited COVID-19 severity. We highlight the predominance of the VOCs identified through a rapid PCR based approach. As this is important to inform a public health response, we propose that a mutation targeted approach can be a rapid, lower cost solution to aid tracking of known VOCs during pandemic waves.

Covid 19 Make us Confident to Perform ESWL Sessions for Treatment of Ureteric Stone (preprint)

The clinicians prefer URS as a first-line line treatment of upper ureteric stones but with COVID-19 restrictions and considering the patient's benefit, ESWL sessions to remove ureteric stones were preferred as first-line treatment of upper ureteric stones. The aims of this study was to compare the level of stone clearance with EWSL sessions during COVID-19 pandemic as a first-line treatment. A longitudinal study was conducted at the Department of Urology, Liaquat University Hospital for the duration of 6 months. Total thirty patients of age more than 15 years who presented with an upper ureteric stone of 0. Patients were managed for upper ureteric stone with ESWL and complete stone clearance was considered a satisfactory outcome. The mean age of patients enrolled in the study was 31 10. 82 years with a preponderance of males that is 55%. The mean size of the stone observed was 1.10 0. Upon exposure to EWSL sessions, 68% of patients showed complete clearance of stones whereas 10% of patients had no clearance and 16% of patients showed partial clearance. The comparison of different variables among the level of stone clearance showed that complete removal of stone was carried out by a maximum of 4 EWSL sessions having a mean stone size of 1.09 0. 22 cm whereas maximum of 3 sessions were given to patients that resulted in incomplete stone clearance. In conclusion, the decision for carrying out EWSL sessions for ureteric stone clearance was successful in the majority of patients during a pandemic.

Evolutionary history and introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan through international travelers.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge, and their identification is important for the public health response to coronavirus disease 2019 (COVID-19). Genomic sequencing provides robust information but may not always be accessible, and therefore, mutation-based polymerase chain reaction (PCR) approaches can be used for rapid identification of known variants. International travelers arriving in Karachi between December 2020 and February 2021 were tested for SARS-CoV-2 by PCR. A subset of positive samples was tested for S-gene target failure (SGTF) on TaqPathTM COVID-19 (Thermo Fisher Scientific) and for mutations using the GSD NovaType SARS-CoV-2 (Eurofins Technologies) assays. Sequencing was conducted on the MinION platform (Oxford Nanopore Technologies). Bayesian phylogeographic inference was performed integrating the patients' travel history information. Of the thirty-five COVID-19 cases screened, thirteen had isolates with SGTF. The travelers transmitted infection to sixty-eight contact cases. The B.1.1.7 lineage was confirmed through sequencing and PCR. The phylogenetic analysis of sequence data available for six cases included four B.1.1.7 strains and one B.1.36 and B.1.1.212 lineage isolate. Phylogeographic modeling estimated at least three independent B.1.1.7 introductions into Karachi, Pakistan, originating from the UK. B.1.1.212 and B.1.36 were inferred to be introduced either from the UK or the travelers' layover location. We report the introduction of SARS-CoV-2 B.1.1.7 and other lineages in Pakistan by international travelers arriving via different flight routes. This highlights SARS-CoV-2 transmission through travel, importance of testing, and quarantine post-travel to prevent transmission of new strains, as well as recording detailed patients' metadata. Such results help inform policies on restricting travel from destinations where new highly transmissible variants have emerged.

Blocking key mutated hotspot residues in the RBD of the omicron variant (B.1.1.529) with medicinal compounds to disrupt the RBD-hACE2 complex using molecular screening and simulation approaches† † Electronic supplementary information (ESI) available. See DOI: 10.1039/d2ra00277a

A new variant of SARS-CoV-2 known as the omicron variant (B.1.1.529) reported in South Africa with 30 mutations in the whole spike protein, among which 15 mutations are in the receptor-binding domain, is continuously spreading exponentially around the world. The omicron variant is reported to be highly contagious with antibody-escaping activity. The emergence of antibody-escaping variants is alarming, and thus the quick discovery of small molecule inhibitors is needed. Hence, the current study uses computational drug screening and molecular dynamics simulation approaches (replicated) to identify novel drugs that can inhibit the binding of the receptor-binding domain (RBD) with hACE2. Screening of the North African, East African and North-East African medicinal compound databases by employing a multi-step screening approach revealed four compounds, namely (−)-pipoxide (C1), 2-(p-hydroxybenzyl) benzofuran-6-ol (C2), 1-(4-hydroxy-3-methoxyphenyl)-2-{4-[(E)-3-hydroxy-1-propenyl]-2-methoxyphenoxy}-1,3-propanediol (C3), and Rhein (C4), with excellent anti-viral properties against the RBD of the omicron variant. Investigation of the dynamics demonstrates stable behavior, good residue flexibility profiles, and structural compactness. Validation of the top hits using computational bioactivity analysis, binding free energy calculations and dissociation constant (KD) analysis also indicated the anti-viral properties of these compounds. In conclusion, this study will help in the design and discovery of novel drug therapeutics, which may be used against the emerging omicron variant of SARS-CoV-2. A new variant of SARS-CoV-2 known as the omicron variant (B.1.1.529) reported in South Africa with 30 mutations in the whole spike protein, among which 15 mutations are in the receptor-binding domain, is continuously spreading exponentially around the world.

Novel Coronavirus (SARS-CoV-2) in Water and Environment-A Scoping Review.

A pneumonia outbreak was primarily reported in the fall of 2019 in Wuhan, Hubei province, China, with the identity SARS-CoV-2, a novel coronavirus. It quickly grew from a local epidemic to a global pandemic and was declared a public health emergency by the WHO. A total of three prominent waves were identified across the globe, with a slight temporal variability as per the geographical locations, and has impacted several sectors which connect the world. By March 2022, the coronavirus had infected 444.12 million people and claimed 6.01 million human lives worldwide, and these numbers have not yet stabilized. Our paper enlightens readers on the seven strains of human coronaviruses, with special emphasis on the three severe deadliest outbreaks (SARS-2002, MERS-2012, and COVID-19). This work attempts a comprehensive understanding of the coronavirus and its impact on the possible sectors that link the world through the economic chain, climate conditions, SDGs, recycling of the event, and mitigations. There are many points that are raised by the authors in the possible sectors, which are emerging or are as yet unnoticed and thus have not been taken into consideration. This comprehension will leave sets of new challenges and opportunities for the researchers in various streams, especially in earth sciences. Science-integrated research may help to prevent upcoming disasters as a by-product of (existing) epidemics in the form of coronavirus.

Investigation and forecast of COVID-19 Wave-II: a case study of Pakistan

This study has investigated and forecasted the number of confirmed, deaths, active, and recovered cases of COVID-19 for Wave-II using the ARIMA model in Pakistan. An exponential growth forecast for all the series has been observed under the fitted model for 1 October 2020 to 19 December 2020. Based on our empirical results of forecasted models, the numeral COVID-19 confirmed cases will increase by 1.26 times with a 95% confidence interval at the end of January 2021. Similarly, the number of deaths due to COVID-19 will increase by 1.34 times with a 95% confidence interval until January 2021. Moreover, the number of active cases of COVID-19 will increase by 0.11 times with a 95% confidence interval till the end of January 2021. Besides these, Pakistan has an 89.2% rate of recoveries which will increase by 1.38 times until January 2021. Finally, results show an alarming situation for January 2021 in Pakistan.

Geriatric risk factors for serious COVID-19 outcomes among older adults with cancer: a cohort study from the COVID-19 and Cancer Consortium.

BACKGROUND: Older age is associated with poorer outcomes of SARS-CoV-2 infection, although the heterogeneity of ageing results in some older adults being at greater risk than others. The objective of this study was to quantify the association of a novel geriatric risk index, comprising age, modified Charlson comorbidity index, and Eastern Cooperative Oncology Group performance status, with COVID-19 severity and 30-day mortality among older adults with cancer. METHODS: In this cohort study, we enrolled patients aged 60 years and older with a current or previous cancer diagnosis (excluding those with non-invasive cancers and premalignant or non-malignant conditions) and a current or previous laboratory-confirmed COVID-19 diagnosis who reported to the COVID-19 and Cancer Consortium (CCC19) multinational, multicentre, registry between March 17, 2020, and June 6, 2021. Patients were also excluded for unknown age, missing data resulting in unknown geriatric risk measure, inadequate data quality, or incomplete follow-up resulting in unknown COVID-19 severity. The exposure of interest was the CCC19 geriatric risk index. The primary outcome was COVID-19 severity and the secondary outcome was 30-day all-cause mortality; both were assessed in the full dataset. Adjusted odds ratios (ORs) and 95% CIs were estimated from ordinal and binary logistic regression models. FINDINGS: 5671 patients with cancer and COVID-19 were included in the analysis. Median follow-up time was 56 days (IQR 22-120), and median age was 72 years (IQR 66-79). The CCC19 geriatric risk index identified 2365 (41·7%) patients as standard risk, 2217 (39·1%) patients as intermediate risk, and 1089 (19·2%) as high risk. 36 (0·6%) patients were excluded due to non-calculable geriatric risk index. Compared with standard-risk patients, high-risk patients had significantly higher COVID-19 severity (adjusted OR 7·24; 95% CI 6·20-8·45). 920 (16·2%) of 5671 patients died within 30 days of a COVID-19 diagnosis, including 161 (6·8%) of 2365 standard-risk patients, 409 (18·5%) of 2217 intermediate-risk patients, and 350 (32·1%) of 1089 high-risk patients. High-risk patients had higher adjusted odds of 30-day mortality (adjusted OR 10·7; 95% CI 8·54-13·5) than standard-risk patients. INTERPRETATION: The CCC19 geriatric risk index was strongly associated with COVID-19 severity and 30-day mortality. Our CCC19 geriatric risk index, based on readily available clinical factors, might provide clinicians with an easy-to-use risk stratification method to identify older adults most at risk for severe COVID-19 as well as mortality. FUNDING: US National Institutes of Health National Cancer Institute Cancer Center.