COVID-19 vaccination campaign in Nepal, emerging UK variant and futuristic vaccination strategies to combat the ongoing pandemic

Predicting onset risk of COVID-19 symptom to support healthy travel route planning in the new normal of long-term coexistence with SARS-CoV-2

Due to the increased outdoor transmission risk of new SARS-COV-2 variants, the health of urban residents in daily travel is being threatened. In the new normal of long-term coexistence with SARS-CoV-2, how to avoid being infected by SARS-CoV-2 in daily travel has become a key issue. Hence, a spatiotemporal solution has been proposed to assist healthy travel route planning. Firstly, an enhanced urban-community-scale geographic model was proposed to predict daily COVID-19 symptom onset risk by incorporating the real-time effective reproduction numbers, and daily population variation of fully vaccinated. On-road onset risk predictions in the next following days were then extracted for searching healthy routes with the least onset risk values. The healthy route planning was further implemented in a mobile application. Hong Kong, one of the representative highly populated cities, has been chosen as an example to apply the spatiotemporal solution. The application results in the four epidemic waves of Hong Kong show that based on the high accurate prediction of COVID-19 symptom onset risk, the healthy route planning could reduce people's exposure to the COVID-19 symptoms onset risk. To sum, the proposed solution can be applied to support the healthy travel of residents in more cities in the new normalcy.

Introductory Chapter: Lessons from SARS-CoV-2/COVID-19 after Two Years of Pandemic

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Effect of religious fatalism and concern about new variants on the acceptance of COVID-19 vaccines

Introduction

To protect public health, it is important that the population be vaccinated against COVID-19; however, certain factors can affect vaccine acceptance.

Objective

The objective of this study was to determine whether religious fatalism and concern about new variants have a significant effect on the acceptance of COVID-19 vaccines.

Methodology

An explanatory study was conducted with 403 adults of legal age captured through non-probabilistic convenience sampling in vaccination centers in the 13 health networks of the Regional Health Directorate of Puno, Peru. Data were collected through a brief scale of religious fatalism, a scale of acceptance of vaccines against COVID-19 and a scale of concern about a new variant of COVID-19.

Results

The proposed model obtained an adequate fit. There was a negative effect of religious fatalism on vaccine acceptance, a positive effect of fatalism on vaccine rejection, a positive effect of concern about new variants on the acceptance of vaccines, and a positive effect of concern about new variants on vaccine rejection.

Conclusion

These findings provide evidence for the usefulness of considering both religious fatalism and concern about new variants affect the intention to receive the COVID-19 vaccine in adults in southern Peru.

In Silico Analysis Reveals the Inhibitory Potential of Madecassic Acid against Entry Factors of SARS-CoV-2

Coronavirus disease 19 (COVID-19) is the ongoing global health emergency caused by SARS-CoV-2 infection. The virus is highly contagious, affecting millions of people worldwide. SARS-CoV-2, with its trimeric spike glycoprotein, interacts with the angiotensin-converting enzyme 2 (ACE2) receptor and other co-receptors like basigin to invade the host cell. Moreover, certain host proteases like transmembrane serine proteases, furin, neuropilin 1 (NRP1), and endosomal cathepsins are involved in the priming of spike glycoproteins at the S1/S2 interface. This is critical for the entry of viral genome and its replication in the host cytoplasm. Vaccines and anti-SARS-CoV-2 drugs have been developed to overcome the infection. Nonetheless, the frequent emergence of mutant variants of the virus has imposed serious concerns regarding the efficacy of therapeutic agents, including vaccines that were developed for previous strains. Thus, screening and development of pharmaceutical agents with multi-target potency could be a better choice to restrain SARS-CoV-2 infection. Madecassic acid (MDCA) is a pentacyclic triterpenoid found in Centella asiatica. It has multiple medicinal properties like anti-oxidative, anti-inflammatory, and anti-diabetic potential. However, its implication as an anti- SARS-CoV-2 agent is still obscure. Hence, in the present in silico study, the binding affinities of MDCA for spike proteins, their receptors, and proteases were investigated. Results indicated that MDCA interacts with ligand-binding pockets of the spike receptor binding domain, ACE2, basigin, and host proteases, viz. transmembrane serine proteinase, furin, NRP1, and endosomal cathepsins, with greater affinities. Moreover, the MDCA-protein interface was strengthened by prominent hydrogen bonds and several hydrophobic interactions. Therefore, MDCA could be a promising multi-target therapeutic agent against SARS-CoV-2 infection.

Management of COVID-19 and vaccination in Nepal: A qualitative study

OBJECTIVE

The aim of this research is to investigate the perspective of citizens of Nepal on the management COVID-19, the roll-out of the vaccine, and to gain an understanding of attitudes towards the governments' handling of the COVID-19 pandemic.

METHOD

A qualitative methodology was used. In-depth interviews were conducted with 18 males and 23 females aged between 20 and 86 years old from one remote and one urban district of Nepal. Interviews were conducted in November and December 2021. A thematic approach was used to analyse the data, utilising NVivo 12 data management software.

RESULT

Three major themes were identified: (1) Peoples' perspective on the management of COVID-19, (2) people's perception of the management of COVID-19 vaccination and (3) management and dissemination of information. It was found that most participants had heard of COVID-19 and its mitigation measures, however, the majority had limited understanding and knowledge about the disease. Most participants expressed their disappointment concerning poor testing, quarantine, vaccination campaigns and poor accountability from the government towards the management of COVID-19. Misinformation and stigma were reported as the major factors contributing to the spread of COVID-19. People's knowledge and understanding were mainly shaped by the quality of the information they received from various sources of communication and social media. This heavily influenced their response to the pandemic, the preventive measures they followed and their attitude towards vaccination.

CONCLUSION

Our study concludes that the study participants' perception was that testing, quarantine centres and vaccination campaigns were poorly managed in both urban and rural settings in Nepal. Since people's knowledge and understanding of COVID-19 are heavily influenced by the quality of information they receive, we suggest providing contextualised correct information through a trusted channel regarding the pandemic, its preventive measures and vaccination. This study recommends that the government proactively involve grassroots-level volunteers like Female Community Health Volunteers to effectively prepare for future pandemics.

PATIENT AND PUBLIC CONTRIBUTION

This study was based on in-depth interviews with 41 people from diverse socioeconomic backgrounds. This study would not have been possible without their participation.

Variant-specific RT-qPCR for rapid screening of B.1.617 mutations in SARS-CoV-2

The continuous emergence of new SARS-CoV-2 variants required rapid and reliable diagnostic methods for early detection and monitoring of the spread of the virus, especially in low-resource countries where whole genome sequencing is not available. We aimed to evaluate and compare the performance of two different RT-qPCR screening assays for the detection of B.1.617 lineage mutations. A total of 85 SARS-CoV-2 positive samples were collected between 9^th August and 10 September 2021 and screened by two mutation-specific RT-qPCR assays for simultaneous detection of B.1.617.1 and B.1.617.2 lineage mutations. VIASURE Variant II PCR assay identified 2 Delta variant-specific mutations (L452R, and P681 R) in 80% of tested samples, while the PKamp™ Variant Detect™ assay was only able to detect one Delta variant specific mutation (L452R) in 75% of tested samples. This is the first report to show the Delta variant as the cause of the third wave in Libya. The use of multiplex RT-qPCR assays has allowed the identification of new variants for rapid screening. However, RT-qPCR results should be confirmed by whole genome sequencing of SARS-COV-2.

Mass vaccinations against COVID-19 through the use of technologies for the management of appointment scheduling and data of large volumes of vaccinated

Mass vaccination against COVID-19 using technologies to manage appointment scheduling and data in large volumes of vaccinated people Abstract Mass vaccination poses a challenge for health authorities due to the high volume of people who need to be vaccinated in a short period of time. Manual processes in vaccination centres to record and control vaccinations where the data is entered on paper result in delays in the timely input of information rendering the vaccination process inefficient. The proposed prototype, as a strategy for mass COVID-19 vaccination, to generate appointments, record, and control entry to vaccination centres, uses mobile technology, QR codes, and cloud computing to automate these data-driven processes. Technology-based processes help people by giving them the flexibility to choose the most convenient vaccination centre and provide health authorities with data-driven tools for management, control, and real-time decision-making.

Factors influencing the acceptability of COVID-19 vaccination: A cross-sectional study from Malaysia

Background

With the surge of COVID-19 cases worldwide, vaccines against COVID-19 are also developing across the countries. However, the acceptability of COVID-19 vaccination among general people is questionable. The availability of several vaccines’ options against COVID-19 has perplexed people regarding individual vaccines’ efficacy and safety. Therefore, we aim to determine the acceptance, preferences, impact factors of future COVID-19 vaccines in Malaysia and the factors influencing the COVID-19 vaccination acceptance among vaccine demand and vaccine delay groups.

Material and methods

An online-based cross-sectional survey was conducted among Malaysian residents 18 years and above of either gender using the snowball sampling technique. A self-administered questionnaire was made available to participants through various social media networks, email, and telegram. The data obtained from the survey were analyzed using SPSS version 25.0. Association between background characteristics and respondents were analyzed using the Chi-square test in the vaccine delay group and vaccine acceptance group.

Results

Total of 1282 responses were considered for the study, mainly from male respondents (71%). Among the respondents, 95.9% thought that vaccination would be an effective way to prevent and control COVID-19, and 96% would accept vaccination if the COVID-19 vaccine were successfully developed and approved for listing in the future. Essential factors influencing vaccination decisions were vaccine convenience (95.7%) and doctor's recommendation (97.3%). Bivariate analysis revealed that age less than 24 years, Malay race, living in urban areas, tertiary education, students, single marital status, family income (Malaysian ringgits) RM 4,850 to RM 10,959 and >RM 10,960 were significantly associated with vaccine acceptance of COVID19 vaccination.

Conclusion

All the factors influencing COVID-19 vaccine acceptance rates throughout the country should be studied on a larger scale, and appropriate steps to ensure vaccine acceptance among the public should be meticulously devised by the government and related authorities.

How an Outbreak of COVID-19 Circulated Widely in Nepal: A Chronological Analysis of the National Response to an Unprecedented Pandemic

Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The first COVID-19 case was reported in Wuhan, China, in December 2019. In March 2020, the World Health Organization (WHO) declared COVID-19 a global pandemic. The first COVID-19 case in Nepal was reported in January 2020 in a Nepalese man who had returned from Wuhan to Nepal. This study aims to evaluate the government of Nepal’s (GoN) response to the COVID-19 pandemic and explore ways to prevent COVID-19 and other pandemic diseases in the future. As of May 2022, a total of 979,140 cases and 11,951 deaths associated with COVID-19 have been reported in Nepal. To prevent the spread of the virus, the GoN initiated various preventive and control measures, including lockdown strategies. The effects of COVID-19 are expected to persist for many years; the best strategies a resource-limited country such as Nepal can implement to control pandemic diseases such as COVID-19 in the pre-vaccine stage are to increase testing, tracing, and isolation capacity.

Computational studies on potential new anti-Covid-19 agents with a multi-target mode of action

A compound that could inhibit multiple targets associated with SARS-CoV-2 infection would prove to be a drug of choice against the virus. Human receptor-ACE2, receptor binding domain (RBD) of SARS-CoV-2 S-protein, Papain-like protein of SARS-CoV-2 (PLpro), reverse transcriptase of SARS-CoV-2 (RdRp) were chosen for in silico study. A set of previously synthesized compounds (1-5) were docked into the active sites of the targets. Based on the docking score, ligand efficiency, binding free energy, and dissociation constants for a definite conformational position of the ligand, inhibitory potentials of the compounds were measured. The stability of the protein-ligand (P-L) complex was validated in silico by using molecular dynamics simulations using the YASARA suit. Moreover, the pharmacokinetic properties, FMO and NBO analysis were performed for ranking the potentiality of the compounds as drug. The geometry optimizations and electronic structures were investigated using DFT. As per the study, compound-5 has the best binding affinity against all four targets. Moreover, compounds 1, 3 and 5 are less toxic and can be considered for oral consumption.

Medical laboratory staff satisfaction and their perspective on the role of health institutions to combat COVID-19 pandemic

Objective

To assess the facilities and challenges encountered in the clinical laboratories, satisfaction of the medical laboratory staff (MLS) toward their profession and their views on the role of related health institutions during the first wave of the Coronavirus Disease 2019 (COVID-19) pandemic in Nepal.

Methods

A web-based cross-sectional study was conducted among registered MLS in Nepal. Data were collected using a structured self-reported questionnaire on the Google Docs platform.

Results

A total of 301 respondents were enrolled in the study; of which 180 were male and 121 were female. Of the 301 respondents, a lack of infrastructure was reported by 241 (80.1%), a lack of skill development training by 204 (67.8%), limited availability of diagnostics kits by 151 (50.2%), overburdened by the workload by 142 (47.2%) and difficulty in sample management by 129 (42.9%). A total of 244 of 301 respondents (81.1%) believed that stakeholder institutions should collaborate with the government during the pandemic. The level of satisfaction during the pandemic (130 of 301; 43.19%) was found to have decreased compared with before the pandemic (203 of 301; 67.4%).

Conclusion

MLS were not fully satisfied with the available resources during the pandemic.

Prevention and Control Measures for Imported SARS-CoV-2 Transmission During the Postpandemic Period in Shenzhen, China

In China, most cities have gradually controlled the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and brought coronavirus disease 2019 (COVID-19) under control locally. This means that crucial work has shifted from internal management of the pandemic to external prevention and control, especially management of international travelers and imported goods. There is much uncertainty about variants of concern for SARS-CoV-2, which pose challenges to the steady resumption of social and economic life once the mutant strains begin to spread. The sporadic outbreaks of COVID-19 in different provinces of China caused by these mutant strains emphasizes the need for both prevention and control measures. Therefore, we introduce China's experience with preventing and controlling COVID-19 in the postpandemic period, which may serve as a reference in various settings.

Perceived COVID-19 vaccine effectiveness, acceptance, and drivers of vaccination decision-making among the general adult population: A global survey of 20 countries

Background

Mass vaccination campaigns have significantly reduced the COVID-19 burden. However, vaccine hesitancy has posed significant global concerns. The purpose of this study was to determine the characteristics that influence perceptions of COVID-19 vaccine efficacy, acceptability, hesitancy and decision making to take vaccine among general adult populations in a variety of socioeconomic and cultural contexts.

Methods

Using a snowball sampling approach, we conducted an online cross-sectional study in 20 countries across four continents from February to May 2021.

Results

A total of 10,477 participants were included in the analyses with a mean age of 36±14.3 years. The findings revealed the prevalence of perceptions towards COVID-19 vaccine’s effectiveness (78.8%), acceptance (81.8%), hesitancy (47.2%), and drivers of vaccination decision-making (convenience [73.3%], health providers’ advice [81.8%], and costs [57.0%]). The county-wise distribution included effectiveness (67.8–95.9%; 67.8% in Egypt to 95.9% in Malaysia), acceptance (64.7–96.0%; 64.7% in Australia to 96.0% in Malaysia), hesitancy (31.5–86.0%; 31.5% in Egypt to 86.0% in Vietnam), convenience (49.7–95.7%; 49.7% in Austria to 95.7% in Malaysia), advice (66.1–97.3%; 66.1% in Austria to 97.3% in Malaysia), and costs (16.0–91.3%; 16.0% in Vietnam to 91.3% in Malaysia). In multivariable regression analysis, several socio-demographic characteristics were identified as associated factors of outcome variables including, i) vaccine effectiveness: younger age, male, urban residence, higher education, and higher income; ii) acceptance: younger age, male, urban residence, higher education, married, and higher income; and iii) hesitancy: male, higher education, employed, unmarried, and lower income. Likewise, the factors associated with vaccination decision-making including i) convenience: younger age, urban residence, higher education, married, and lower income; ii) advice: younger age, urban residence, higher education, unemployed/student, married, and medium income; and iii) costs: younger age, higher education, unemployed/student, and lower income.

Conclusions

Most participants believed that vaccination would effectively control and prevent COVID-19, and they would take vaccinations upon availability. Determinant factors found in this study are critical and should be considered as essential elements in developing COVID-19 vaccination campaigns to boost vaccination uptake in the populations.

This large-scale multi-country study explores perceived COVID-19 vaccine effectiveness, acceptability, and hesitancy rates and their related factors among the general adult populations from 20 countries. We found that a considerable proportion of the participants has an intention to receive the COVID-19 vaccine. However, more than half still expressed their hesitancy to receive the vaccines. Countries where the majority of respondents responded that they would accept COVID-19 vaccination included Malaysia (96.0%), Bangladesh (93.6%), and Iraq (91.8%). The majority of the participants from Vietnam (86.0%) and Turkey (74.7%) expressed hesitance to receive COVID-19 vaccine. Perceived vaccine effectiveness ranged from 67.8% in Egypt to 95.9% in Malaysia. The participants believed that convenience, health providers’ advice, and costs of vaccines are important for people to decide whether to accept COVID-19 vaccines. Country of residence, age, sex, level of education, area of residence, marital status, and family economic status were significantly associated with tendency to undergo COVID-19 vaccination and the perception that COVID-19 vaccine decision-making is influenced by convenience. The findings of this study provide useful guidance for tailored interventions to enhance the acceptance of COVID-19 vaccine. Promotional program addressed on detected socioeconomic factors is warranted.

In silico studies on phytochemicals to combat the emerging COVID-19 infection

The current COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its variants, remains a serious health hazard globally. The SARS-CoV-2 Mpro and spike proteins, as well as the human ACE2 receptor, have previously been reported as good targets for the development of new drug leads to combat COVID-19. Various ligands, including synthetic and plant-derived small molecules, can interact with the aforementioned proteins. In this study, we investigated the interaction of eight phytochemicals, from selected medicinal plants (Aegle marmelos, Azadirachta indica, and Ocimum sanctum) commonly used in Indian traditional medicine, with SARS-CoV-2 Mpro (PDBID: 6LU7), SARS-CoV-2S spike protein (PDB ID: 6M0J) and the human ACE2 receptor (PDB ID: 6M18). All compounds were subjected to density functional theory (DFT) and frontier molecular orbitals (FMO) analysis to determine their geometry, and key electronic and energetic properties. Upon examining the interactions of the phytochemicals with the human ACE2 receptor and the SARS-CoV-2 Mpro, spike protein targets, two compounds (C-5 and C-8) were identified as the best binding ligands. These were further examined in MD simulation studies to determine the stability of the ligand–protein interactions. QSAR, pharmacokinetic and drug-likeness properties studies revealed that C-5 may be the best candidate to serve as a template for the design and development of new drugs to combat COVID-19.

Repurposing benzimidazole and benzothiazole derivatives as potential inhibitors of SARS-CoV-2: DFT, QSAR, molecular docking, molecular dynamics simulation, and in-silico pharmacokinetic and toxicity studies

Density Functional Theory (DFT) and Quantitative Structure-Activity Relationship (QSAR) studies were performed on four benzimidazoles (compounds 1-4) and two benzothiazoles (compounds 5 and 6), previously synthesized by our group. The compounds were also investigated for their binding affinity and interactions with the SARS-CoV-2 M^pro (PDB ID: 6LU7) and the human angiotensin-converting enzyme 2 (ACE2) receptor (PDB ID: 6 M18) using a molecular docking approach. Compounds 1, 2, and 3 were found to bind with equal affinity to both targets. Compound 1 showed the highest predictive docking scores, and was further subjected to molecular dynamics (MD) simulation to explain protein stability, ligand properties, and protein-ligand interactions. All compounds were assessed for their structural, physico-chemical, pharmacokinetic, and toxicological properties. Our results suggest that the investigated compounds are potential new drug leads to target SARS-CoV-2.

Clinical features and laboratory findings first case of B. 1.617.2 (delta) variant concern (VOC) in Iraq

Since the initial report of the severe acute respiratory syndrome (SARS CoV-2) in Wuhan, China, in 2019, the virus has constantly mutated, resulting in the appearance of novel variants. In December 2020, the B.1.617.2 (delta) variant concern (VOC) was first reported in India, and rapidly spread around the globe, is now the main brand in the United Kingdom, and it has grown dramatically. Here we present the clinical features and laboratory findings of the first case of B. 1.617.2 (delta) variant concern (VOC) in Iraq. A 6-year-old female child presented with severe abdominal pain, headache, severe vomiting, and diarrhea, runny nose, alerted mental status, loss of appetite, and fever. The patient was diagnosed with COVID-19 delta variant B.1.617.2 by RT-PCR. The patient was treated by administration of glucose saline 4% for 3 days, ceftriaxone vial 1 mg every 12 h for 6 days, and an acetaminophen bottle on a need to prevent fever followed by a Flagyl bottle every 24 h for 3 days. Vaccination and prevention the spread of the virus and against it are important preventive approaches for delta variant. Sore throat, runny nose, headache, and vomiting, diarrhea are the major clinical features of the delta variant. This was followed by an elevation of the leukocyte WBC, and blood platelets. To reduce the impact of new delta variant B.1.617.2 infection; handwashing, wearing a double mask, avoiding crowded and closed settings, social distancing, lockdown, and ensuring good ventilation are major significant options against this variant.

Factors influencing the acceptability of COVID-19 vaccination: A cross-sectional study from Malaysia

Background

With the surge of COVID-19 cases worldwide, vaccines against COVID-19 are also developing across the countries. However, the acceptability of COVID-19 vaccination among general people is questionable. The availability of several vaccines’ options against COVID-19 has perplexed people regarding individual vaccines’ efficacy and safety. Therefore, we aim to determine the acceptance, preferences, impact factors of future COVID-19 vaccines in Malaysia and the factors influencing the COVID-19 vaccination acceptance among vaccine demand and vaccine delay groups.

Material and methods

An online-based cross-sectional survey was conducted among Malaysian residents 18 years and above of either gender using the snowball sampling technique. A self-administered questionnaire was made available to participants through various social media networks, email, and telegram. The data obtained from the survey were analyzed using SPSS version 25.0. Association between background characteristics and respondents were analyzed using the Chi-square test in the vaccine delay group and vaccine acceptance group.

Results

Total of 1282 responses were considered for the study, mainly from male respondents (71%). Among the respondents, 95.9% thought that vaccination would be an effective way to prevent and control COVID-19, and 96% would accept vaccination if the COVID-19 vaccine were successfully developed and approved for listing in the future. Essential factors influencing vaccination decisions were vaccine convenience (95.7%) and doctor's recommendation (97.3%). Bivariate analysis revealed that age less than 24 years, Malay race, living in urban areas, tertiary education, students, single marital status, family income (Malaysian ringgits) RM 4,850 to RM 10,959 and >RM 10,960 were significantly associated with vaccine acceptance of COVID19 vaccination.

Conclusion

All the factors influencing COVID-19 vaccine acceptance rates throughout the country should be studied on a larger scale, and appropriate steps to ensure vaccine acceptance among the public should be meticulously devised by the government and related authorities.