scholarly journals Alternate primers for whole-genome SARS-CoV-2 sequencing

2021 ◽  
Author(s):  
Matthew Cotten ◽  
Dan Lule Bugembe ◽  
Pontiano Kaleebu ◽  
My V T Phan
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Information Content ◽  
Genome Sequence ◽  
Virus Genome ◽  
Control Measures ◽  
Effective Control ◽  
Whole Genome ◽  
The Novel ◽  
Essential Information ◽  
The World

Abstract As the world is struggling to control the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is an urgency to develop effective control measures. Essential information is encoded in the virus genome sequence with accurate and complete SARS-CoV-2 sequences essential for tracking the movement and evolution of the virus and for guiding efforts to develop vaccines and antiviral drugs. While there is unprecedented SARS-CoV-2 sequencing efforts globally, approximately 19 to 43% of the genomes generated monthly are gapped, reducing their information content. The current study documents the genome gap frequencies and their positions in the currently available data and provides an alternative primer set and a sequencing scheme to help improve the quality and coverage of the genomes.

scholarly journals Alternate primers for whole-genome SARS-CoV-2 sequencing

2020 ◽  
Author(s):  
Matthew Cotten ◽  
Dan Lule Bugembe ◽  
Pontiano Kaleebu ◽  
My V.T. Phan
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Information Content ◽  
Genome Sequence ◽  
Virus Genome ◽  
Control Measures ◽  
Effective Control ◽  
Whole Genome ◽  
The Novel ◽  
Essential Information ◽  
The World

AbstractAs the world is struggling to control the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is an urgency to develop effective control measures. Essential information is encoded in the virus genome sequence with accurate and complete SARS-CoV-2 sequences essential for tracking the movement and evolution of the virus and for guiding efforts to develop vaccines and antiviral drugs. While there is unprecedented SARS-CoV-2 sequencing efforts globally, approximately 19 to 43% of the genomes generated monthly are gapped, reducing their information content. The current study documents the genome gap frequencies and their positions in the currently available data and provides an alternative primer set and a sequencing scheme to help improve the quality and coverage of the genomes.

scholarly journals Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

2021 ◽  
Vol 15 (10) ◽  
pp. e0009835
Author(s):  
Alessandra P. Lamarca ◽  
Luiz G. P. de Almeida ◽  
Ronaldo da Silva Francisco ◽  
Lucymara Fassarella Agnez Lima ◽  
Kátia Castanho Scortecci ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Sharp Increase ◽  
Rio De Janeiro ◽  
Control Measures ◽  
Effective Control ◽  
Whole Genome ◽  
The Novel ◽  
Northeast Region ◽  
Transmission Rates ◽  
Novel Variants

The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed the whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraíba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) in order to monitor the spread of SARS-CoV-2 lineages in Brazil in the first months of 2021. Here, we showed a widespread dispersal of P.1 and P.2 across Brazilian regions and, except for Amazonas, P.2 was the predominant lineage identified in the sampled states. We estimated the origin of P.2 lineage to have happened in February, 2020 and identified that it has differentiated into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December and its origin was inferred to have happened in August 2020. We also confirmed the presence of lineage P.7, recently described in the southernmost region of Brazil, to have spread across the Northeastern states. P.1, P.2 and P.7 are descended from the ancient B.1.1.28 strain, which co-dominated the first phase of the pandemic in Brazil with the B.1.1.33 strain. We also identified the occurrence of a new lineage descending from B.1.1.33 that convergently carries the E484K mutation, N.9. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to identify novel variants of interest and monitor for vaccine effectiveness.

scholarly journals Nations’ Responses and Control Measures in Confrontation with the Novel Coronavirus Disease (COVID-19) Outbreak: A Rapid Review

2020 ◽  
Author(s):  
Parinaz Tabari ◽  
Mitra Amini ◽  
Mohsen Moghadami ◽  
Mahsa Moosavi
Keyword(s):  
Middle East ◽  
Severe Acute Respiratory Syndrome ◽  
Management Strategies ◽  
Control Measures ◽  
Rapid Review ◽  
The Novel ◽  
Rapid Rate ◽  
The World ◽  
Novel Coronavirus ◽  
And Control

The outbreak of Coronavirus disease 2019 (COVID-19) has posed a significant concern in many countries due to the rapid rate of transmission between humans. Taking advantage of the experience of the last epidemics in 2002 Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and 2012 Middle East Respiratory Syndrome Coronavirus (MERS-CoV), some regions of the world were well- prepared for the new outbreak. However, other countries needed to be adapted to the situation promptly. Many management strategies were established, and some restrictions were introduced in some regions. In this review, we aimed to determine countries’ public responses to the epidemic of COVID-19 and how they developed administrative approaches towards the outbreak.

Non-Pharmaceutical Interventions are measures to control coronavirus disease-2019 (COVID-19) transmission in India

Coronaviruses ◽  
2020 ◽  
Vol 01 ◽  
Author(s):  
Ponnuswamy Vijayaraghavan ◽  
Srikrishnan Rajendran Sriramkumar
Keyword(s):  
United States ◽  
Great Britain ◽  
Severe Acute Respiratory Syndrome ◽  
Age Groups ◽  
Viral Disease ◽  
Control Measures ◽  
Whole Genome ◽  
The World ◽  
Chennai City ◽  
Pharmaceutical Interventions

: The coronavirus disease 19 (COVID-19) is a pathogenic and transmittable viral disease cause by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and this disease was emerged on December 2019 in Wuhan, China. It was later spread across the world, including United States, Great Britain, Brazil, Russia, Germany, Spain, Italy, Iran, Pakistan, India and other countries. The whole genome of SARS-CoV-2 shared some similarity with SARS virus, hence bat was suspected to spread this virus in China. However human to human transfer was reported. In India, more than 300 COVID-19 cases were reported on March 21, 2020 and these numbers were increased as 892551 on July 13, 2020. These numbers of COVID-19 cases were detected from a total of 11806256 samples according to the report given by Government of India. As on July 13, Maharashtra state of India recorded a total of 254427 cases and 10289 deaths were registered. Tamilnadu was another state screened more number of COVID-19 cases, followed by Maharashtra. As on July 6, 114978 COVID-19 cases were reported in Tamilnadu and 1571 deaths were recorded. In Tamilnadu alone, over 3000 COVID-19 cases were reported daily from July first week to second week and total cases were 142798 on July 13, 2020. Among these cases, 78573 COVID-19 cases were detected in Chennai city alone accounted about 62% of total COVID-19 cases. It was earlier believed that patients over aged 60 and less than 10 were highly vulnerable to this disease. However, this disease affected all age groups. To prevent COVID-19, no approved antiviral vaccine or drug has yet been discovered. COVID-19 is transmitted through droplets during coughing and sneezing by symptomatic and asymptomatic carriers. Non-pharmaceutical interventions such as washing hands and social distancing are effective measures to control COVID-19 transmission in India. The present study was designed to analyze the control measures of COVID-19 infection and ground reality to control COVID-19 outbreak.

scholarly journals New corona virus: is just a tip of iceberg?

2020 ◽  
Vol 9 (7) ◽  
pp. 1147
Author(s):  
Arvind Narwat ◽  
Seema Rani ◽  
Garima Bhutani ◽  
Rahul Saini ◽  
Kamaldeep Singh
Keyword(s):  
Genome Sequence ◽  
Vaccine Development ◽  
Antiviral Treatment ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
The Novel ◽  
The Past ◽  
Cruise Ships ◽  
The World ◽  
Novel Coronavirus

The world is again experiencing a global viral epidemic of zoonotic origin. As of March 30, 785807 confirmed cases of coronavirus disease 2019 (COVID-19) and 37820 deaths had been reported in more than 120 countries. Strenuous efforts are being made by various countries of the world to halt transmission through shutting down transport, quarantining entire cities and enforcing the use of face masks. International flights have been cancelled and affected cruise ships quarantined. As in all outbreaks, there is an urgent need to develop effective diagnostics, therapeutics and vaccines. Several experimental diagnostic platforms are already in use in China and elsewhere. The whole-genome sequence of SARS-CoV-2 has been obtained and shared widely. Several potential treatments have been proposed, however, no antiviral treatment has been approved for the novel coronavirus, and despite two outbreaks of novel coronaviruses in the past two decades, vaccine development is still in its infancy.

scholarly journals Coronaviruses – a new old menace

2021 ◽  
Author(s):  
Anna Golke ◽  
Karolina Piekarska ◽  
Tomasz Dzieciątkowski
Keyword(s):  
Middle East ◽  
Severe Acute Respiratory Syndrome ◽  
Healthcare Systems ◽  
Middle East Respiratory Syndrome ◽  
Control Measures ◽  
The Novel ◽  
Global Impact ◽  
Infection Control Measures ◽  
The World ◽  
Novel Coronavirus

current pandemic caused by novel coronavirus SARS-CoV-2 pandemic has been described as a global health emergency. The outbreak of this virus has raised a number of questions: what exactly is SARS-CoV-2? How transmissible the novel coronavirus is? How severely affected are patients infected with SARS-CoV-2? What are the risk factors for COVID-19? What are the differences between this novel coronavirus and other coronaviruses? To answer these questions, a comparative study of three pathogenic coronaviruses that primarily invade the human respiratory system and may cause death, namely, severe acute respiratory syndrome (SARS-CoV-1), Middle East respiratory syndrome (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Middle East respiratory syndrome coronavirus (MERS-CoV). This review describes the source of origin, transmission, and pathogenicity of these viruses. Prevention of SARS-CoV-2 spreading entails home isolation of suspected cases and those with mild illnesses and strict infection control measures at hospitals that include contact and droplet precautions. The novel coronavirus spreads faster than its two predecessors – the SARS-CoV-1 and MERS-CoV – but has lower fatality rate. The global impact of this new pandemic is still uncertain, but it is a challenge to healthcare systems around the world.

Characterizing the effectiveness of COVID-19 mitigation measures: A data-centric approach (Preprint)

2020 ◽  
Author(s):  
Lukman Olagoke ◽  
Ahmet E. Topcu
Keyword(s):  
Control Measure ◽  
Control Measures ◽  
World Health ◽  
Mitigation Measures ◽  
Effective Control ◽  
The World ◽  
Decision Making Processes ◽  
And Performance ◽  
Health Organization ◽  
The Impact

BACKGROUND COVID-19 represents a serious threat to both national health and economic systems. To curb this pandemic, the World Health Organization (WHO) issued a series of COVID-19 public safety guidelines. Different countries around the world initiated different measures in line with the WHO guidelines to mitigate and investigate the spread of COVID-19 in their territories. OBJECTIVE The aim of this paper is to quantitatively evaluate the effectiveness of these control measures using a data-centric approach. METHODS We begin with a simple text analysis of coronavirus-related articles and show that reports on similar outbreaks in the past strongly proposed similar control measures. This reaffirms the fact that these control measures are in order. Subsequently, we propose a simple performance statistic that quantifies general performance and performance under the different measures that were initiated. A density based clustering of based on performance statistic was carried out to group countries based on performance. RESULTS The performance statistic helps evaluate quantitatively the impact of COVID-19 control measures. Countries tend show variability in performance under different control measures. The performance statistic has negative correlation with cases of death which is a useful characteristics for COVID-19 control measure performance analysis. A web-based time-line visualization that enables comparison of performances and cases across continents and subregions is presented. CONCLUSIONS The performance metric is relevant for the analysis of the impact of COVID-19 control measures. This can help caregivers and policymakers identify effective control measures and reduce cases of death due to COVID-19. The interactive web visualizer provides easily digested and quick feedback to augment decision-making processes in the COVID-19 response measures evaluation. CLINICALTRIAL Not Applicable

scholarly journals Emerging pandemic COVID-19: myths and facts

2020 ◽  
Vol 6 (7) ◽  
pp. 283
Author(s):  
Rohit Vadala ◽  
Isabella Princess
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Clinical Presentation ◽  
Surface Protein ◽  
Respiratory Viruses ◽  
The Novel ◽  
Nucleocapsid Proteins ◽  
The World ◽  
The Common ◽  
Human Infections ◽  
Relationship Of

<p>The first theory which has established itself across the world is that COVID-19 is a “new virus”. It is rather wise to call it a “new strain” of a pre-existing coronavirus since history clearly denotes cases of coronavirus surfacing the world in past years beginning as early as mid-1960s.Including this novel strain of the virus, seven strains of coronaviruses have been commonly associated with human infections. Coronaviruses are primarily respiratory viruses causing infections ranging from mild to severe involvement of the respiratory tract. The common cold strains of coronavirus are 229E alpha coronavirus, NL63 alpha coronavirus, OC43 beta coronavirus and HKU1 beta coronavirus.The acute respiratory distress causing strains are severe acute respiratory syndrome (SARS) beta CoV causing SARS, MERS beta CoV causing Middle East respiratory syndrome (MERS) and the very novel COVID-19. Researchers and molecular biologists have confirmed phylogenetic relationship of COVID-19 with a 2015 Chinese bat strain of SARS CoV.<sup> </sup>Mutations to the surface protein as well as nucleocapsid proteins were demonstrated. These two mutations predicts the characteristics such as higher ability to infect as well as enhanced pathogenicity of COVID-19 as compared to older SARS strain. For this reason and with similarities in clinical presentation the novel strain has been named as SARS-CoV-2.</p>

scholarly journals Does the novel coronavirus 2019 like heart more than the other family members of coronaviruses?

2020 ◽  
Vol 12 (2) ◽  
pp. 156-157
Author(s):  
Mohammad Mostafa Ansari Ramandi ◽  
Mohammadreza Baay ◽  
Nasim Naderi
Keyword(s):  
Middle East ◽  
Severe Acute Respiratory Syndrome ◽  
Family Members ◽  
Middle East Respiratory Syndrome ◽  
The Other ◽  
The Novel ◽  
The World ◽  
Future Challenges ◽  
Novel Coronavirus ◽  
Coronavirus Infections

The disaster due to the novel coronavirus disease 2019 (COVID-19) around the world has made investigators enthusiastic about working on different aspects of COVID-19. However, although the pandemic of COVID-19 has not yet ended, it seems that COVID-19 compared to the other coronavirus infections (the Middle East Respiratory Syndrome [MERS] and Severe Acute Respiratory Syndrome [SARS]) is more likely to target the heart. Comparing the previous presentations of the coronavirus family and the recent cardiovascular manifestations of COVID-19 can also help in predicting possible future challenges and taking measures to tackle these issues.

scholarly journals Epidemiological perspectives of COVID-19 in Telangana and India: a descriptive study design

2021 ◽  
Vol 8 (4) ◽  
pp. 1817
Author(s):  
Amruta Barhate ◽  
Prakash Bhatia
Keyword(s):  
Data Analysis ◽  
Study Design ◽  
Descriptive Study ◽  
Control Measures ◽  
Data Sources ◽  
Effective Control ◽  
Steady Increase ◽  
The World ◽  
To Come ◽  
Second Wave

Background: The COVID-19 pandemic has made the world to come to a standstill. What started as on 16th March 2020, as 114 confirmed cases of COVID‑19 in the country has now reached worrisome figures. The latest world scenario as per WHO as on 30th November, 2020 is as under-World data: 62,509,444 cases, deaths: 1,458,782; USA: 13,082,877 cases, deaths: 263,946; India: 9,431,691 cases, deaths 137, 139. It is evident that worldwide India is number two in case load and there’s no reason to prevent India from becoming number one unless appropriate corrective steps are taken.Methods: The present study has looked into various data sources available in public domain. The study covered a period of almost nine months i.e., from March 2020 to November 2020. The study revealed a steady increase in the number of COVID-19 cases from March 2020 with peak of pandemic occurring in the mid of September and then a steady decline of cases from October.Results: The data analysis shows that after peaking of cases in September, the epidemic will decline in a phased manner by the end of March 2021. Even though there is a decline seen from the month of October, spike of COVID-19 cases was seen in November in some of the states of India. Therefore, we can’t deny the possibility of a second wave of pandemic to occur in the month of December 2020 and January 2021.Conclusions: Hence appropriate and strict control measures have to be put in place for effective control of the Pandemic and its resurgence.

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