Household transmission dynamics of COVID-19 among residents of Delhi, India: a prospective case-ascertained study.

Objective: The aim of this study was to observe the secondary infection rate and transmission dynamics of COVID-19 among household contacts, and their associations with various factors across four dimensions of interaction. Methods: This was a case-ascertained study among unvaccinated household contacts of a laboratory-confirmed COVID-19 case in New Delhi between December 2020 and July 2021. For this study, 99 index cases and their 316 household contacts were interviewed and sampled (blood and oro-nasal swab) on days 1, 7, 14, and 28. Results: The secondary infection rate among unvaccinated household contacts was 44.6% (95% confidence interval (CI) 39.1-50.1). The predictors of secondary infection among individual contact levels were: being female (odds ratio (OR) 2.13), increasing age (OR 1.01), symptoms at baseline (OR 3.39), and symptoms during follow-up (OR 3.18). Among index cases, age of the primary case (OR 1.03) and symptoms during follow-up (OR 6.29) were significantly associated with secondary infection. Among household-level and contact patterns, having more rooms (OR 4.44) and taking care of the index case (OR 2.02) were significantly associated with secondary infection. Conclusion: A high secondary infection rate highlights the need to adopt strict measures and advocate COVID-19-appropriate behaviors. A targeted approach for higher-risk household contacts would efficiently limit infections among susceptible contacts.

SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19.

The global spread of the SARS coronavirus 2 (SARS-CoV-2), its manifestation in human hosts as a contagious disease, and its variants have induced a pandemic resulting in the deaths of over 6,000,000 people. Extensive efforts have been devoted to drug research to cure and refrain the spread of COVID-19, but only one drug has received FDA approval yet. Traditional drug discovery is inefficient, costly, and unable to react to pandemic threats. Drug repurposing represents an effective strategy for drug discovery and reduces the time and cost compared to de novo drug discovery. In this study, a generic drug repurposing framework (SperoPredictor) has been developed which systematically integrates the various types of drugs and disease data and takes the advantage of machine learning (Random Forest, Tree Ensemble, and Gradient Boosted Trees) to repurpose potential drug candidates against any disease of interest. Drug and disease data for FDA-approved drugs (n = 2,865), containing four drug features and three disease features, were collected from chemical and biological databases and integrated with the form of drug-disease association tables. The resulting dataset was split into 70% for training, 15% for testing, and the remaining 15% for validation. The testing and validation accuracies of the models were 99.3% for Random Forest and 99.03% for Tree Ensemble. In practice, SperoPredictor identified 25 potential drug candidates against 6 human host-target proteomes identified from a systematic review of journals. Literature-based validation indicated 12 of 25 predicted drugs (48%) have been already used for COVID-19 followed by molecular docking and re-docking which indicated 4 of 13 drugs (30%) as potential candidates against COVID-19 to be pre-clinically and clinically validated. Finally, SperoPredictor results illustrated the ability of the platform to be rapidly deployed to repurpose the drugs as a rapid response to emergent situations (like COVID-19 and other pandemics).

Effectiveness of BBV152/Covaxin and AZD1222/Covishield vaccines against severe COVID-19 and B.1.617.2/Delta variant in India, 2021: a multi-centric hospital-based case-control study.

OBJECTIVES: India introduced BBV152/Covaxin and AZD1222/Covishield vaccines in January 2021. We estimated the effectiveness of these vaccines against severe COVID-19 among individuals aged ≥45 years. METHODS: We did a multi-centric, hospital-based, case-control study between May and July 2021. Cases were severe COVID-19 patients, and controls were COVID-19 negative individuals from 11 hospitals. Vaccine effectiveness (VE) was estimated for complete (2 doses ≥ 14 days) and partial (1 dose ≥ 21 days) vaccination; interval between two vaccine doses and vaccination against the Delta variant. We used the random effects logistic regression model to calculate the adjusted odds ratios (aOR) with a 95% confidence interval (CI) after adjusting for relevant known confounders. RESULTS: We enrolled 1143 cases and 2541 control patients. The VE of complete vaccination was 85% (95% CI: 79-89%) with AZD1222/Covishield and 71% (95% CI: 57-81%) with BBV152/Covaxin. The VE was highest for 6-8 weeks between two doses of AZD1222/Covishield (94%, 95% CI: 86-97%) and BBV152/Covaxin (93%, 95% CI: 34-99%). The VE estimates were similar against the Delta strain and sub-lineages. CONCLUSION: BBV152/Covaxin and AZD1222/Covishield were effective against severe COVID-19 among the Indian population during the period of dominance of the highly transmissible Delta variant in the second wave of the pandemic. An escalation of two-dose coverage with COVID-19 vaccines is critical to reduce severe COVID-19 and further mitigate the pandemic in the country.

SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19

Illustration of SperoPredictor repurposing framework. It starts with data collection followed by machine learning models training, model deployment, literature, and molecular docking-based validation.

A comprehensive review of artificial intelligence and network based approaches to drug repurposing in Covid-19.

Conventional drug discovery and development is tedious and time-taking process; because of which it has failed to keep the required pace to mitigate threats and cater demands of viral and re-occurring diseases, such as Covid-19. The main reasons of this delay in traditional drug development are: high attrition rates, extensive time requirements, and huge financial investment with significant risk. The effective solution to de novo drug discovery is drug repurposing. Previous studies have shown that the network-based approaches and analysis are versatile platform for repurposing as the network biology is used to model the interactions between variety of biological concepts. Herein, we provide a comprehensive background of machine learning and deep learning in drug repurposing while specifically focusing on the applications of network-based approach to drug repurposing in Covid-19, data sources, and tools used. Furthermore, use of network proximity, network diffusion, and AI on network-based drug repurposing for Covid-19 is well-explained. Finally, limitations of network-based approaches in general and specific to network are stated along with future recommendations for better network-based models.

Acceptance, perception and awareness regarding COVID-19 vaccination among general population in Karachi, Pakistan

Introduction: Even though the coronavirus disease 2019 (COVID-19) outbreak was first reported in late 2019 in Wuhan, China, it is still prevalent across the globe and continues to create mayhem. According to WHO, on March 26, 2021, SARS-CoV-2 virus has infected a total of 125 million people worldwide and caused 3 million casualties. There have been 14.5 million confirmed cases in Southeast Asia, out of which 6.5 lac confirmed cases of COVID-19 are from Pakistan alone, with 14,028 deaths. In Sindh, Pakistan, there have been 2.6 lac confirmed cases of COVID-19 out of which 2 lac 56 thousand have recovered while 4,487 died. Since the outbreak, countless research has been undertaken pertaining to the virus transmission cycle and different countries have strived to come up with a vaccine to protect the masses. The continued dissemination of this coronavirus vaccine emphasizes the role of international collaboration in the development of vaccines and therapeutics. Factors contributing towards vaccine hesitancy include unknown adverse effects of the vaccine, perceived threats, lack of awareness, religious beliefs, myths surrounding the pandemic and vaccine, lack of confidence in the health system and lack of community awareness about vaccine-preventable diseases. Moreover, since the vaccine is new and there is a lack of research pertaining to its efficacy and detrimental effects, people are reluctant to get vaccinated. The findings of this study might help the government figure out the best way to introduce mass vaccination programs in Pakistan and other South Asian countries. Moreover, lockdowns and social distancing may be eased if a COVID-19 vaccination offers immune defense, which will be beneficial for the country's economy. Objective: To gauge the percentage of citizens who are willing to become vaccinated, their overall attitude towards the vaccination programs and the factors contributing towards vaccine hesitancy at the COVID Vaccination Center, Jinnah Post Graduate Medical Center, Karachi, Pakistan. Methodology: A cross sectional study from May 2021 to August 2021 was conducted at the COVID Vaccination Center, Jinnah Post Graduate Medical Center in Karachi. The study was conducted on 400 persons who were either the vaccination staff of the COVID Vacination Center or the persons coming for COVID vaccination. The sampling technique was non probability purposive sampling. The data was collected by rotating a structured questionnaire. The questionnaire was given to the data collectors who distributed them to the vaccination staff and the visitors. Written consent was taken from the participants and all ethical considerations and research protocols were observed. Data was collected in the form of pre-tested self-administered questionnaires. In order to standardize the questionnaires, a pilot study was conducted among research participants for the purpose of examining content validity. Data collected was analyzed using SPSS software version 20. The statistical analysis was conducted with 95% confidence interval and a pvalue of <0.05 was taken as threshold of statistical significance. Results: 400 subjects were approached to fill in the questionnaires. The age group of participants was less than 25 years were 48.2%(n=204), 25 to 50 years were 38.8% (n=164) and more than 50 years were 7.6%(n=32) Males were 40.%(n=169) while females were 54.5%(n=231). Among the participants 40.4% (n=171) were married and 54.1%(n=229) were unmarried. Coming to the educational background, the majority had a bachelor's degree or beyond. Not Formally educated were 1.7%(n=7), those who studied till fifth grade or below were 1.2%(n=5), those educated up until matriculation were 3.3%(n=14), those who were intermediate educated were 14.3%(n=63), Diploma holders were 31%(n=131) and those who were university educated were 42.5%(n=180. When the participants were asked about their opinion regarding their health status, 21.5%(n=91) said it was excellent, 47.8%(n=202) said it was good, 21.3%(n=90) said it was fair, while 4%(n=17) said it was poor. Whe the participants were asked whether they were they suffering from any illness (e.g: asthma, high BP, diabetes mellitus), 16.3%(n=69) said yes while 78.3%(n=331) said no. When the participants were asked whether COVID-19 existed, 86.5% (n=366) said yes while 8%(n=34) said no. When asked if COVID-19 was dangerous, 82.7%(n=350) said yes while 11.8% (n=50) said no. Replying to the question had the participants ever been infected by COVID in past, 13.9%(n=59) said yes while 54.8%(n=274) said no. When asked whether any members of their family, friends or neighbours had been affected by COVID-19, 61.9%(n=262) said yes and 32.6%(n=138) said no. When asked had they ever heard about COVID-19 vaccination, 39%(n=165) said yes and 55%(n=235) said no. 92.7%(n=392) said yes while 1.9%(n=8) said when asked whether had they received COVID-19 vaccination, 39%(n=165) said yes while 61 %(n=235) said no. When those who had not taken the vaccine were asked the reasons for not doing so, 6.5%(n=28) said that the COVID-19vaccine was not effective, 9.5%(n=40) said that it had side effects, 4.7%(n=20) believed that they had alternate protection against COVID-19 while 36.9%(n=156) gave other reasons. When the participants were asked whether they considered themselves at risk of getting COVID-19,43.7%(n=185) said yes, 27.2%(n=115) said no and 23.6%(n=100) said that they were not sure. Replying to the question would they prefer a vaccine with lower efficacy for the time being, 50.6%(n=214) said yes and 44%(n=186) said no. When asked which vaccine would they prefer, 35.5%(n=150) said Sinopharm/Sinovac (China), 5.2%(n=22) said Sputnik-V (Russia), 3.1%(n=13) said AstraZeneca(United Kingdom), 17.5%(n=74) said Pfizer(USA), 18.9%(n=80) said any vaccine and 14.4(n=61) were not in favour of any vaccine. When asked in detail regarding the participants' major concerns and reservations regarding COVID 19 vaccine, about 29.6%(n=125) participants did not trust a vaccine made in such a short period of time, 35.7%(n=151) trusted the vaccine and 29.3%(n=124) were not sure. When asked whether the Vaccine's contents were not permissible in their religion, 7.1%(n=30) agreed, 60.3%(n=255) disagreed and 27.2%(n=115) were not sure. When asked whether they did not need a vaccine as they had already contracted COVID-19, 8%(n=34) agreed, 70.7%(n=299) disagreed and 15.8%(n=57) were not sure, Replying to the question whether the Vaccine could cause infertility, 7.8%(n=33) agreed, 49.9%(n=211) disagreed and 36.9%(n=156) were not sure. When the participants were asked whether COVID-19 vaccine was a conspiracy of the West, 17%(n=72) agreed, 52.2%(n=221) disagreed while 25.3%(n=107) were not sure. Responding to the question whether the participants would wait and see vaccine outcomes on other recipients, 38.8%(n=154) agreed, 45.4%(n=132) disagreed while 10.4%(n=44) were not sure. Responding to the question that vaccination would not be effective for different mutated forms, 34.3%(n=145) agreed, 23.9%(n=121) disagreed and 36.4%(n=154) were not sure. When asked whether they suspected that Vaccine inserts a chip inside the body, 6.9%(n=19) agreed, 59.8%(n=253) disagreed while 27.9%(n=118) were not sure. When the participants were asked whether they would get a booster dose if required, 49.4%(n=209) said yes and 22.7%(n=96) said no. When asked what were their reason/s for getting vaccinated, 51.1%(n=216) said that they wanted to protect their family and friends, 21.7%(n=92) said that they were at high risk of contracting COVID 19, 1.9%(n=8) said that they were suffering from co-morbidities while 15.4%(n=65) gave other reasons and 4.5%(n=19) said that they did not want to get vaccinated. Conclusion: The population's acceptance rate for COVID-19 vaccine is only thirty nine percent according to this study. In this research, key characteristics are emphasized that have significant consequences for formulating vaccine policy that maximizes vaccine uptake. Religious leaders should be involved in developing successful communication strategies, particularly for low-income families. Public me saging should dispel any worries about the vaccine's safety and efficacy, as well as emphasize the vaccine's potential for containing the pandemic. [ABSTRACT FROM AUTHOR] Copyright of Middle East Journal of Family Medicine is the property of Medi+WORLD International Pty. Ltd 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.)

Could COVID-19's Aftermath on Children's Health Be Felt into the 22nd Century?

The COVID-19 pandemic has massively affected people's health, societies, and the global economy. Our lives are no longer as they were before COVID-19, and, most likely, will never be the same again. We hypothesize that the effect of the COVID-19 pandemic on population health and the economy will last for a very long time and will still be felt in the 22nd century. Our hypothesis is based on evidence from the 1918-1919 influenza pandemic, the Dutch famine during the Second World War, and the 2007-2008 economic crisis, as well as from the rationally predicted impact of COVID-19 on human development. We expect that the COVID-19 pandemic, including the mitigation measures taken against it, will affect children's development in multiple ways, including obesity, both while in utero and during critical and sensitive windows of development, including the early childhood years and those of puberty and adolescence. The psychosocial and biological impact of this effect will be considerable and unequally distributed. The implications will last at least a lifetime, and, through inter-generational transmission, will likely take us to future generations, into the 22nd century. We argue for the urgent need of designing and initiating comprehensive longitudinal cohort studies to closely monitor the long-term effects of COVID-19 on children conceived, born, and raised during the pandemic. Such an approach requires a close and effective collaboration between scientists, healthcare providers, policymakers, and the younger generations, and it will hopefully uncover evidence necessary to understand and mitigate the impact of the pandemic on people's lives in the 21st and 22nd centuries.

COVID-19 Pandemic and Vaccines Update on Challenges and Resolutions.

The coronavirus disease (COVID-19) is caused by a positive-stranded RNA virus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), belonging to the Coronaviridae family. This virus originated in Wuhan City, China, and became the cause of a multiwave pandemic that has killed 3.46 million people worldwide as of May 22, 2021. The havoc intensified with the emergence of SARS-CoV-2 variants (B.1.1.7; Alpha, B.1.351; Beta, P.1; Gamma, B.1.617; Delta, B.1.617.2; Delta-plus, B.1.525; Eta, and B.1.429; Epsilon etc.) due to mutations generated during replication. More variants may emerge to cause additional pandemic waves. The most promising approach for combating viruses and their emerging variants lies in prophylactic vaccines. Several vaccine candidates are being developed using various platforms, including nucleic acids, live attenuated virus, inactivated virus, viral vectors, and protein-based subunit vaccines. In this unprecedented time, 12 vaccines against SARS-CoV-2 have been phased in following WHO approval, 184 are in the preclinical stage, and 100 are in the clinical development process. Many of them are directed to elicit neutralizing antibodies against the viral spike protein (S) to inhibit viral entry through the ACE-2 receptor of host cells. Inactivated vaccines, to the contrary, provide a wide range of viral antigens for immune activation. Being an intracellular pathogen, the cytotoxic CD8+ T Cell (CTL) response remains crucial for all viruses, including SARS-CoV-2, and needs to be explored in detail. In this review, we try to describe and compare approved vaccines against SARS-CoV-2 that are currently being distributed either after phase III clinical trials or for emergency use. We discuss immune responses induced by various candidate vaccine formulations; their benefits, potential limitations, and effectiveness against variants; future challenges, such as antibody-dependent enhancement (ADE); and vaccine safety issues and their possible resolutions. Most of the current vaccines developed against SARS-CoV-2 are showing either promising or compromised efficacy against new variants. Multiple antigen-based vaccines (multivariant vaccines) should be developed on different platforms to tackle future variants. Alternatively, recombinant BCG, containing SARS-CoV-2 multiple antigens, as a live attenuated vaccine should be explored for long-term protection. Irrespective of their efficacy, all vaccines are efficient in providing protection from disease severity. We must insist on vaccine compliance for all age groups and work on vaccine hesitancy globally to achieve herd immunity and, eventually, to curb this pandemic.

COVID-19 and ethnicity: A novel pathophysiological role for inflammation.

INTRODUCTION: There have been recent mounting concerns regarding multiple reports stating a significantly elevated relative-risk of COVID-19 mortality amongst the Black and Minority Ethnic (BAME) population. An urgent national enquiry investigating the possible reasons for this phenomenon has been issued in the UK. Inflammation is at the forefront of COVID-19 research as disease severity appears to correlate with pro-inflammatory cytokine dysregulation. This narrative review aims to shed light on the novel, pathophysiological role of inflammation in contributing towards the increased COVID-19 mortality risk amongst the BAME population. METHODS: Searches in PubMed, Medline, Scopus, medRxiv and Google Scholar were performed to identify articles published in English from inception to 18th June 2020. These databases were searched using keywords including: 'COVID-19' or 'Black and Minority Ethnic' or 'Inflammation'. A narrative review was synthesized using these included articles. RESULTS: We suggest a novel pathophysiological mechanism by which acute inflammation from COVID-19 may augment existing chronic inflammation, in order to potentiate a 'cytokine storm' and thus the more severe disease phenotype observed in the BAME population. Obesity, insulin resistance, cardiovascular disease, psychological stress, chronic infections and genetic predispositions are all relevant factors which may be contributing to elevated chronic systemic inflammation amongst the BAME population. CONCLUSION: Overall, this review provides early insights and directions for ongoing research regarding the pathophysiological mechanisms that may explain the severe COVID-19 disease phenotype observed amongst the BAME population. We suggest 'personalization' of chronic disease management, which can be used with other interventions, in order to tackle this.