scholarly journals Sequencing of SARS-CoV-2 in local transmission cases through Oxford Nanopore MinION platform from Karachi Pakistan

2021 ◽  
Vol 15 (10) ◽  
pp. 1376-1383
Author(s):  
Samina Naz Mukry ◽  
Shariq Ahmed ◽  
Ali Raza Bukhari ◽  
Aneeta Shahni ◽  
Gul Sufaida ◽  
...  
Keyword(s):  
Transmission Rate ◽  
Spike Protein ◽  
Effective Vaccine ◽  
First Case ◽  
Viral Adaptation ◽  
Oxford Nanopore ◽  
Potential Vaccine ◽  
Second Wave ◽  
Virus Isolates ◽  
Local Transmission

Introduction: The first case of severe acute respiratory syndrome 2 (SARS-CoV-2) was imported to Pakistan in February 2020, since then 8,260 deaths have been witnessed. The virus has been constantly mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS-CoV-2 have been defined globally. In this study, the epidemiology of SARS-CoV-2 was studied and locally transmitted SARS-CoV-2 isolates from Karachi were sequenced to compared and identify any possible variants. Methodology: The real time PCR was performed on nasopharyngeal specimen to confirm SARS-CoV-2 with Orf 1ab and E gene as targets. The virus isolates were sequenced through oxford nanopore technology MinION platform. Isolates from the first and second wave of COVID-19 outbreak in Karachi were compared. Results: The overall positivity rate for PCR was 26.24% with the highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. Another spike protein mutation A222V coexisted with D614G in the virus from the second wave of COVID-19. Conclusions: Based on the present findings it is suggested that the locally transmitted virus from Karachi varies from those reported from other parts of Pakistan. Slight variability was also observed between viruses from the first and second wave. Variability in any potential vaccine target may result in failed trials, therefore information on any local viral variants is always useful for effective vaccine design and/or selection.

scholarly journals Sequencing of SARS CoV2 in local transmission cases through oxford nanopore MinION platform from Karachi Pakistan

2021 ◽  
Author(s):  
Samina Naz Mukry ◽  
Shariq Ahmed ◽  
Ali Raza Bukhari ◽  
Aneeta Shahni ◽  
Gul Sufaida ◽  
...  
Keyword(s):  
Transmission Rate ◽  
Spike Protein ◽  
Effective Vaccine ◽  
First Case ◽  
Viral Adaptation ◽  
Oxford Nanopore ◽  
Potential Vaccine ◽  
Viral Sequencing ◽  
Second Wave ◽  
Local Transmission

The first case of severe acute respiratory syndrome 2 (SARS CoV2) was imported to Pakistan in February 2020 since then 8,260 deaths have been witnessed. The virus has been mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS CoV2 have been defined globally. In this study, the epidemiology of SARS CoV2 was studied and locally transmitted SARS CoV2 isolates from Karachi were sequenced to compared and identify any possible variants.The real time PCR was performed on nasopharyngeal specimen to confirm SARSCoV2 with Orf 1ab and E gene as targets. The viral sequencing was performed through oxford nanopore technology MinION platform. Isolates from first and second wave of COVID-19 outbreak in Karachi were compared. The overall positivity rate for PCR was 26.24% with highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. Another spike protein mutation A222V coexisted with D614G in the virus from second wave of COVID-19. Based on the present findings it is suggested that the locally transmitted virus from Karachi vary from those reported from other parts of Pakistan. Slight variability was also observed between viruses from first and second wave. Variability in any potential vaccine target may result in failed trials therefore information on any local viral variants is always useful for effective vaccine design and/or selection.

scholarly journals Synthesis and immunological evaluation of synthetic peptide based anti-SARS-CoV-2 vaccine candidates

2021 ◽  
Author(s):  
Qingyu Zhao ◽  
Yanan Gao ◽  
Min Xiao ◽  
Xuefei Huang ◽  
Xuanjun Wu
Keyword(s):  
Synthetic Peptide ◽  
Spike Protein ◽  
Effective Vaccine ◽  
The Novel ◽  
Vaccine Candidates ◽  
Peptide Epitopes ◽  
Novel Coronavirus ◽  
Immunological Evaluation

For prevention of the coronavirus disease 2019 caused by the novel coronavirus SARS-CoV-2, an effective vaccine is critical. Herein, several potential peptide epitopes from the spike protein of SARS-CoV-2 have...

Nanovaccine: A hope to triumph the battle against novel Coronavirus disease 2019 (COVID-19)

2021 ◽  
Vol 15 ◽  
Author(s):  
Anurag Singh ◽  
Anand Maurya ◽  
Gaurav Mishra ◽  
Rajendra Awasthi ◽  
Kamal Dua ◽  
...  
Keyword(s):  
Subunit Vaccine ◽  
Goblet Cells ◽  
Spike Protein ◽  
Effective Vaccine ◽  
The Novel ◽  
Infection Site ◽  
Peptide Vaccines ◽  
Ciliated Cells ◽  
Novel Coronavirus ◽  
Major Target

Background: The novel coronavirus 2019 (COVID-19) infection has caused the global emergence of coronavirus in humans during the last 12 months. Till May 11, 2021, the confirmed global COVID-19 cases and deaths reached 158551526 and 3296855, respectively. Methods: Goblet cells and ciliated cells in the nose act as the initial infection site of SARS-CoV-2. Thus, mucus immunity is important to protect from infection. The outburst of SARS-CoV-2 infection can be halted only when an effective vaccine will be developed. Results: Globally, over 100 different vaccines are under investigation, including DNA vaccines, RNA vaccines, inactivated virus vaccines, adenovirus-based vaccines, recombinant/ subunit protein vaccines, peptide vaccines, and virus-like particles etc. Inactivated virus vaccines and mRNA, and adenovirus-based vaccines have moved fast into clinical trials. Conclusion: : Vaccines containing spike protein of SARS-CoV as subunit could effectively prevent binding of coronavirus to the host cell and membrane fusion. Thus, spike protein can be used as a major target for subunit vaccine preparation.

scholarly journals Rhino-orbital COVID-19 associated mucormycosis- A case report

2021 ◽  
Vol 7 (4) ◽  
pp. 304-307
Author(s):  
Shanmuga Vadivoo Natarajan ◽  
B Usha
Keyword(s):  
Diabetes Mellitus ◽  
Infectious Disease ◽  
Case Report ◽  
Tertiary Care ◽  
Notifiable Disease ◽  
Health Ministry ◽  
First Case ◽  
Uncontrolled Diabetes ◽  
History Of ◽  
Second Wave

COVID-19 Associated Mucormycosis (CAM) is an emerging infectious disease that has caused increased mortality & morbidity in India during this second wave of the pandemic. The country has reported more than 30,000 cases and over 2,000 deaths by Mucormycosis so far, according to sources from Union Health Ministry. CAM is now a notifiable disease. At our Tertiary care teaching hospital, which caters for COVID 19 management, we are reporting the first case of Rhino orbital CAM, which was caused by Rhizopus spp. Our patient had a history of contact with a suspected COVID 19 patient and was recently diagnosed with uncontrolled diabetes mellitus. A direct KOH microscopic examination of purulent material aspirated from the sinonasal polyp of the patient revealed fungal elements, and Rhizopus spp was isolated. Due to a shortage of Amphotericin B, the patient was referred to a government higher speciality centre for further management. The patient was followed up & was noted that he was treated with antifungal and discharged following recovery.

scholarly journals Web Application for Statistical Tracking and Predicting the Evolution of Active Cases with the Novel Coronavirus (SARS-CoV-2)

2021 ◽  
pp. 70-74
Author(s):  
Iulia Clitan ◽  
◽  
Adela Puscasiu ◽  
Vlad Muresan ◽  
Mihaela Ligia Unguresan ◽  
...  
Keyword(s):  
Neural Network ◽  
Mathematical Model ◽  
Web Application ◽  
Point Of View ◽  
The Novel ◽  
End User ◽  
First Case ◽  
Novel Coronavirus ◽  
Second Wave ◽  
Over Time

Since February 2020, when the first case of infection with SARS COV-2 virus appeared in Romania, the evolution of COVID-19 pandemic continues to have an ascending allure, reaching in September 2020 a second wave of infections as expected. In order to understand the evolution and spread of this disease over time and space, more and more research is focused on obtaining mathematical models that are able to predict the evolution of active cases based on different scenarios and taking into account the numerous inputs that influence the spread of this infection. This paper presents a web responsive application that allows the end user to analyze the evolution of the pandemic in Romania, graphically, and that incorporates, unlike other COVID-19 statistical applications, a prediction of active cases evolution. The prediction is based on a neural network mathematical model, described from the architectural point of view.

scholarly journals HiSpike Method for High-Throughput Cost Effective Sequencing of the SARS-CoV-2 Spike Gene

2022 ◽  
Vol 8 ◽  
Author(s):  
Ephraim Fass ◽  
Gal Zizelski Valenci ◽  
Mor Rubinstein ◽  
Paul J. Freidlin ◽  
Shira Rosencwaig ◽  
...  
Keyword(s):  
Real Time ◽  
High Throughput ◽  
Cost Effective ◽  
Developed Countries ◽  
Spike Protein ◽  
Medical Community ◽  
Effective Vaccine ◽  
Gene Variants ◽  
Spike Gene ◽  
Field Samples

The changing nature of the SARS-CoV-2 pandemic poses unprecedented challenges to the world's health systems. Emerging spike gene variants jeopardize global efforts to produce immunity and reduce morbidity and mortality. These challenges require effective real-time genomic surveillance solutions that the medical community can quickly adopt. The SARS-CoV-2 spike protein mediates host receptor recognition and entry into the cell and is susceptible to generation of variants with increased transmissibility and pathogenicity. The spike protein is the primary target of neutralizing antibodies in COVID-19 patients and the most common antigen for induction of effective vaccine immunity. Tight monitoring of spike protein gene variants is key to mitigating COVID-19 spread and generation of vaccine escape mutants. Currently, SARS-CoV-2 sequencing methods are labor intensive and expensive. When sequence demands are high sequencing resources are quickly exhausted. Consequently, most SARS-CoV-2 strains are sequenced in only a few developed countries and rarely in developing regions. This poses the risk that undetected, dangerous variants will emerge. In this work, we present HiSpike, a method for high-throughput cost effective targeted next generation sequencing of the spike gene. This simple three-step method can be completed in < 30 h, can sequence 10-fold more samples compared to conventional methods and at a fraction of their cost. HiSpike has been validated in Israel, and has identified multiple spike variants from real-time field samples including Alpha, Beta, Delta and the emerging Omicron variants. HiSpike provides affordable sequencing options to help laboratories conserve resources for widespread high-throughput, near real-time monitoring of spike gene variants.

scholarly journals COVID-19 Vaccine Acceptance: We Need to Start Now

2021 ◽  
Author(s):  
Krutika Kuppalli ◽  
David M Brett-Major ◽  
Tara C Smith
Keyword(s):  
Public Attitudes ◽  
Effective Vaccine ◽  
Approval Process ◽  
Government Officials ◽  
Vaccine Acceptance ◽  
The Public ◽  
Present Information ◽  
Attitudes And Perceptions ◽  
Potential Vaccine ◽  
Health Experts

Abstract In this perspective, we discuss the importance of developing a vaccine to help curb transmission of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). The question remains: once a safe and effective vaccine is developed, will the public be willing to get it? We present information from one of the first tracking polls to assess public attitudes and perceptions towards a possible Coronavirus Disease 2019 (COVID-19) vaccine that suggests public hesitancy over a potential vaccine, concern regarding accelerating clinical trials, and unease over the vaccine approval process. Public health experts, government officials, advocates, and others in the scientific community should respect the signals of hesitancy and communicate sensitivity, applying lessons not only to how we message, but also in how we build this urgently needed vaccine if we are to have successful uptake once available.

scholarly journals China's Policy to Close Borders to Prevent the Spread of the Second Wave of Covid-19 Virus

2021 ◽  
Vol 5 (1) ◽  
pp. 163-178
Author(s):  
Elyta Elyta ◽  
Syarifah Ema Rahmaniah ◽  
Hendra Ramdani
Keyword(s):  
Data Collection ◽  
Cell Phones ◽  
Border Region ◽  
Knowing How ◽  
Data Collection Methods ◽  
The World ◽  
Internet Searches ◽  
Second Wave ◽  
Local Transmission ◽  
Collection Methods

At the beginning of 2020, the world was shocked by the outbreak of Covid-19, which was known to have originated from Wuhan. The increase in cases of local transmission in China's border region with Russia has sparked new concerns. In writing this paper, the author uses data collection methods with literature studies from journals and electronic books, including data from trusted websites through internet searches in the form of soft files that can support the paper's explanation. From the results of this paper, the reader can see that it is divided into several essential points explaining how China's policy to close the border in Russia to prevent the spread of the Covid-19 Virus in their country, first, how the procedures carried out by China in tightening checks on Russian borders. And Second, knowing how China monitors its citizens by using cell phones.

scholarly journals An Exploration of Fractal Based Prognostic Model and Comparative Analysis for Second Wave of COVID-19 Diffusion

2021 ◽  
Author(s):  
Easwaramoorthy D. ◽  
Gowrisankar A. ◽  
Manimaran A. ◽  
Nandhini S. ◽  
Santo Banerjee ◽  
...  
Keyword(s):  
Fractal Dimension ◽  
Death Rate ◽  
Transmission Rate ◽  
The United States ◽  
Fractal Interpolation ◽  
Interpolation Function ◽  
Statistical Tool ◽  
Dimension Estimate ◽  
Fractal Interpolation Function ◽  
Second Wave

Abstract The coronavirus disease 2019 (COVID-19) pandemic has fatalized 216 countries across the world and has claimed the lives of millions of people globally. Researches are being carried out worldwide by scientists to understand the nature of this catastrophic virus and find a potential vaccine for it. The most possible efforts have been taken to present this paper as a form of contribution to the understanding of this lethal virus in the first and second wave. This paper presents a unique technique for the methodical comparison of disastrous virus dissemination in two waves amid five most infested countries and the death rate of the virus in order to attain a clear view on the behaviour of the spread of the disease. For this study, the dataset of the number of deaths per day and the number of infected cases per day of the most affected countries, The United States of America, Brazil, Russia, India, and The United Kingdom have been considered in first and second wave. The correlation fractal dimension has been estimated for the prescribed datasets of COVID-19 and the rate of death has been compared based on the correlation fractal dimension estimate curve. The statistical tool, analysis of variance has also been used to support the performance of the proposed method. Further, the prediction of the daily death rate has been demonstrated through the autoregressive moving average model. In addition, this study also emphasis a feasible reconstruction of the death rate based on the fractal interpolation function. Subsequently, the normal probability plot is portrayed for the original data and the predicted data, derived through the fractal interpolation function to estimate the accuracy of the prediction. Finally, this paper neatly summarized with the comparison and prediction of epidemic curve of the first and second waves of COVID-19 pandemic to picturize the transmission rate in the both times.

scholarly journals Proposed Design of Walk-Through Gate (WTG): Mitigating the Effect of COVID-19

2020 ◽  
Vol 3 (3) ◽  
pp. 41
Author(s):  
Saddam Hussain ◽  
Muhammad Jehanzeb Masud Cheema ◽  
Saad Motahhir ◽  
Muhammad Mazhar Iqbal ◽  
Arfan Arshad ◽  
...  
Keyword(s):  
Transmission Rate ◽  
Face Mask ◽  
Shopping Mall ◽  
Effective Vaccine ◽  
Public And Private ◽  
Transmission Chain ◽  
Economic Survival ◽  
The World ◽  
Precautionary Measures ◽  
Fast Transmission

The world is facing a new challenge to overcome the pandemic disease of Coronavirus (COVID-19). An outbreak of COVID-19 to more than 213 countries and territories caused damage to the economy of every country. The proper vaccine to combat this pandemic disease is not invented yet. Due to the lockdown situation, there is a shortage of daily used products globally. To overcome the issue of food shortage and economic survival, the world has to ease the lockdown rules and become operational with the precautionary measures. COVID-19 has a fast transmission rate, therefore, while living with COVID-19, breaking the fast transmission chain of COVID-19 is the only vital solution. Furthermore, there is a dire need to disinfect every individual and his luggage at the entrance of every shopping mall, hospital, public and private institutions, bus stops, metro stations, and railway stations. Hence, the proposed walk-through gate (WTG) with different sensors, i.e., infrared thermal camera, UV disinfectant sensor, disinfectant spraying system, touch-less hand sanitizer, and box having a face mask with a dustbin to discard the previous mask can provide an effective and efficient relief. The world cannot stop working and cannot survive for more than 3–6 months in a lockdown, hence the proposed idea is to install the disinfectant automated spraying WTG with a security walk-through gate at every possible entrance to conform living with the COVID-19 disease such as many other diseases. Breaking the transmission chain is the only solution to win the battle against COVID-19 until an effective vaccine invention.

Sign in / Sign up

Export Citation Format

Share Document