scholarly journals Omicron strain spreads with the doubling time of 3.2-3.6 days in South Africa province of Gauteng that achieved herd immunity to Delta variant

2021 ◽  
Author(s):  
Frederic Grabowski ◽  
Marek Kochańczyk ◽  
Tomasz Lipniacki
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
Linear Regression ◽  
Doubling Time ◽  
Herd Immunity ◽  
The Novel ◽  
Gauteng Province ◽  
The World ◽  
Log Linear ◽  
Short Doubling Time

Omicron, the novel, highly mutated SARS-CoV-2 Variant of Concern (belonging to the Pango lineage B.1.1.529), was first collected on November 8, 2021, in Gauteng province of South Africa. By the end of November 2021 it has spread towards fixation in Gauteng and was detected on all continents. Based on data collected till December 7, 2021, we showed the exponential growth of the Omicron variant over the four-week period in Gauteng (November 8-December 5, 2021) with the doubling time equal 3.38 day [CI 95%: 3.18-3.61 day]. Log-linear regression suggests that the spread began around October 10, 2021, however due to stochasticity in the initial spread this estimate is likely inaccurate. Phylogenetic analysis indicates that the Omicron strain started to diverge in between October 28 and November 5, 2021. This implies that the hidden spread of Omicron before October 10, 2021 (which would suggest slower strain growth) is unlikely. The very short doubling time of Omicron in Gauteng, a province that has reached herd immunity to the Delta variant (implied by the decrease of the weekly number of cases between July and October, 2021, at no significant mobility restrictions), suggests that Omicron will cause abrupt outbreaks of COVID-19 epidemics across the world, and will become the (temporarily) dominant strain.

scholarly journals Genome-wide data inferring the evolution and population demography of the novel pneumonia coronavirus (SARS-CoV-2)

2020 ◽  
Author(s):  
Bin Fang ◽  
Linlin Liu ◽  
Xiao Yu ◽  
Xiang Li ◽  
Guojun Ye ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Sliding Window ◽  
The Novel ◽  
Population Demography ◽  
Short Term ◽  
Genome Wide ◽  
The World ◽  
Genome Wide Data ◽  
Neutrality Tests

AbstractAs the highly risk and infectious diseases, the outbreak of coronavirus disease 2019 (COVID-19) poses unprecedent challenges to global health. Up to March 3, 2020, SARS-CoV-2 has infected more than 89,000 people in China and other 66 countries across six continents. In this study, we used 10 new sequenced genomes of SARS-CoV-2 and combined 136 genomes from GISAID database to investigate the genetic variation and population demography through different analysis approaches (e.g. Network, EBSP, Mismatch, and neutrality tests). The results showed that 80 haplotypes had 183 substitution sites, including 27 parsimony-informative and 156 singletons. Sliding window analyses of genetic diversity suggested a certain mutations abundance in the genomes of SARS-CoV-2, which may be explaining the existing widespread. Phylogenetic analysis showed that, compared with the coronavirus carried by pangolins (Pangolin-CoV), the virus carried by bats (bat-RaTG13-CoV) has a closer relationship with SARS-CoV-2. The network results showed that SARS-CoV-2 had diverse haplotypes around the world by February 11. Additionally, 16 genomes, collected from Huanan seafood market assigned to 10 haplotypes, indicated a circulating infection within the market in a short term. The EBSP results showed that the first estimated expansion date of SARS-CoV-2 began from 7 December 2019.

scholarly journals Nested PCR Detection and Phylogenetic Analysis of Babesia bovis and Babesia bigemina in Cattle from Peri-Urban Localities in Gauteng Province, South Africa

2014 ◽  
Vol 76 (1) ◽  
pp. 145-150 ◽  
Author(s):  
Phillip Senzo MTSHALI ◽  
Ana Mbokeleng TSOTETSI ◽  
Matlhahane Molifi Oriel THEKISOE ◽  
Moses Sibusiso MTSHALI
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
Nested Pcr ◽  
Pcr Detection ◽  
Babesia Bovis ◽  
Babesia Bigemina ◽  
Gauteng Province

scholarly journals Phylogenetic analysis to define feline immunodeficiency virus subtypes in 31 domestic cats in South Africa

2006 ◽  
Vol 77 (3) ◽  
Author(s):  
R. Kann ◽  
J. Seddon ◽  
M. Kyaw-Tanner ◽  
J.P. Schoeman ◽  
T. Schoeman ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Feline Immunodeficiency Virus ◽  
Envelope Gene ◽  
Domestic Cats ◽  
Blood Samples ◽  
Immunodeficiency Virus ◽  
The World ◽  
Subtype A

Feline immunodeficiency virus (FIV), a lentivirus, is an important pathogen of domestic cats around the world and has many similarities to human immunodeficiency virus (HIV). A characteristic of these lentiviruses is their extensive genetic diversity, which has been an obstacle in the development of successful vaccines. Of the FIV genes, the envelope gene is the most variable and sequence differences in a portion of this gene have been used to define 5 FIV subtypes (A, B, C, D and E). In this study, the proviral DNA sequence of the V3-V5 region of the envelope gene was determined in blood samples from 31 FIV positive cats from 4 different regions of South Africa. Phylogenetic analysis demonstrated the presence of both subtypes A and C, with subtype A predominating. These findings contribute to the understanding of the genetic diversity of FIV.

scholarly journals Mild Symptomatic SARS-CoV-2 P.1 (B.1.1.28) Infection in a Fully Vaccinated 83-Year-Old Man

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 614
Author(s):  
Marco Fabiani ◽  
Katia Margiotti ◽  
Antonella Viola ◽  
Alvaro Mesoraca ◽  
Claudio Giorlandino
Keyword(s):  
South Africa ◽  
Severe Acute Respiratory Syndrome ◽  
Vaccine Efficacy ◽  
Therapeutic Antibody ◽  
The Novel ◽  
The World ◽  
The Uk

The novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) and the associated coronavirus disease 2019 (COVID-19) continue to spread throughout the world, causing more than 120 million infections. Several variants of concern (VOCs) have emerged and spread with implications for vaccine efficacy, therapeutic antibody treatments, and possible reinfections. On 17 March 2021, several VOCs were detected, including lineage B.1.1.7, first identified in the UK, B.1.351 in South Africa, Lineage P.1 (B.1.1.28.1) in Brazil, and novel Sub-Lineage A (A.23.1), reported in Uganda, and B.1.525, reported in Nigeria. Here, we describe an 83-year-old man infected with the SARS-CoV-2 P.1 variant after two doses of the BNT162b2 mRNA COVID-19 vaccine.

scholarly journals Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

2021 ◽  
Author(s):  
Raquel Viana ◽  
Sikhulile Moyo ◽  
Daniel Gyamfi Amoako ◽  
Houriiyah Tegally ◽  
Cathrine Scheepers ◽  
...  
Keyword(s):  
South Africa ◽  
Southern Africa ◽  
Transmission Dynamics ◽  
World Health ◽  
Genomic Profile ◽  
Gauteng Province ◽  
Population Immunity ◽  
Rapid Spread ◽  
The World ◽  
Health Organization

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants respectively. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

scholarly journals A statistical analysis of the novel coronavirus (COVID-19) in Italy and Spain

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0249037
Author(s):  
Jeffrey Chu
Keyword(s):  
Linear Regression ◽  
Regression Model ◽  
Basic Reproduction Number ◽  
Linear Regression Model ◽  
Reproduction Number ◽  
Early Stage ◽  
The Novel ◽  
Novel Coronavirus ◽  
Log Linear ◽  
The Basic Reproduction Number

The novel coronavirus (COVID-19) that was first reported at the end of 2019 has impacted almost every aspect of life as we know it. This paper focuses on the incidence of the disease in Italy and Spain—two of the first and most affected European countries. Using two simple mathematical epidemiological models—the Susceptible-Infectious-Recovered model and the log-linear regression model, we model the daily and cumulative incidence of COVID-19 in the two countries during the early stage of the outbreak, and compute estimates for basic measures of the infectiousness of the disease including the basic reproduction number, growth rate, and doubling time. Estimates of the basic reproduction number were found to be larger than 1 in both countries, with values being between 2 and 3 for Italy, and 2.5 and 4 for Spain. Estimates were also computed for the more dynamic effective reproduction number, which showed that since the first cases were confirmed in the respective countries the severity has generally been decreasing. The predictive ability of the log-linear regression model was found to give a better fit and simple estimates of the daily incidence for both countries were computed.

scholarly journals COVID-19: Threat or Opportunity?

2020 ◽  
Vol 38 (3) ◽  
Author(s):  
Mozhgan Rivaz ◽  
Seyed Mojtaba Kazemi ◽  
Mina Mosallanezhad
Keyword(s):  
Herd Immunity ◽  
Healthcare Providers ◽  
The Novel ◽  
Social Psychological ◽  
Mortality And Morbidity ◽  
Cultural Aspects ◽  
The World ◽  
Distribution Of Resources ◽  
The Face ◽  
Novel Coronavirus

The COVID-19 pandemic is spreading quickly. Despite scientists’ best efforts all over the world, there is not a vaccine or definite treatment for it and the novel coronavirus remains a threat to humanity with far-reaching, and in many cases, irredeemable consequences for the economic, political, social-psychological , and cultural aspects of humans’ lives.(1)The quick transmission and fatality of the disease, absence of herd immunity, lack of or inequitable distribution of resources, e.g. Personal Protective Equipment ( PPE), and the existing challenges in the implementation of social distancing result in a daily increase in the number of victims and, consequently, an ever-expanding workload in healthcare systems worldwide. Moreover, the increasing mortality and morbidity of COVID-19 and lack of hospital beds and ventilators have led to healthcare provider’s exhaustion and burnout.(1,2) Healthcare providers, especially nurses are the most vulnerable group in the face of the current disaster. Unfortunately, In the world, many front-line experts have lost their lives.(3)

scholarly journals Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains

2020 ◽  
Author(s):  
Aditi Joshi ◽  
Sushmita Paul
Keyword(s):  
Phylogenetic Analysis ◽  
Positive Selection ◽  
Whole Genome Sequence ◽  
Special Focus ◽  
The Novel ◽  
Genome Sequences ◽  
Travel History ◽  
The World ◽  
Viral Sequences ◽  
Nsp3 Gene

AbstractRecently classified as a pandemic by WHO, novel Corononavirus 2019 has affected almost every corner of the globe causing human deaths in a range of hundred thousands. The virus having its roots in Wuhan (China) has been spread over the world by its own property to change itself accordingly. These changes correspond to its transmission and pathogenicity due to which the concept of social distancing appeared into the picture. In this paper, a few findings from the whole genome sequence analysis of viral genome sequences submitted from India are presented. The data used for analysis comprises 440 collective genome sequences of virus submitted in GenBank, GISAID, and SRA projects, from around the world as well as 28 viral sequences from India. Multiple sequence alignment of all genome sequences was performed and analysed. A novel non-synonymous mutation 4809C>T (S1515F) in NSP3 gene of SARS-CoV2 Indian strains is reported along with other frequent and important changes from around the world: 3037C>T, 14408C>T, and 23403A>G. The novel change was observed in samples collected in the month of March, whereas was found to be absent in samples collected in January with the respective persons’ travel history to China. Phylogenetic analysis clustered the sequences with this change as one separate clade. Mutation was predicted as stabilising change by insilco tool DynaMut. A second patient in the world to our knowledge with multiple (Wuhan and USA) strain contraction was observed in this study. The infected person is among the two early infected patients with travel history to China. Strains sequenced in Iran stood out to have different variants, as most of the reported frequent variants were not observed. The objective of this paper is to highlight the similarities and changes observed in the submitted Indian viral strains. This helps to keep track on the activity, that how virus is changing into a new subtype. Major strains observed were European with the novel change in India and other being emergent clade of Iran. Its important to observe the changes in NSP3 gene, as this gene has been reported with extensive positive selection as well as potential drug target. Extensive Positive Selection Drives the Evolution of Nonstructural Proteins. With the limited number of sequences this was the only frequent novel non-synonymous change observed from Indian strains, thereby making this change vulnerable for investigation in future. This paper has a special focus on tracking of Indian viral sequences submitted in public domain.

Invasive Shot Hole Borers Euwallacea fornicatus, E. kuroshio, and E. perbrevis (Coleoptera: Curculionidae: Scolytinae)

EDIS ◽  
2020 ◽  
Vol 2020 (1) ◽  
pp. 7
Author(s):  
Demian F. Gomez ◽  
Jiri Hulcr ◽  
Daniel Carrillo
Keyword(s):  
South Africa ◽  
Invasive Species ◽  
Prevention And Control ◽  
Economic Impacts ◽  
Forest Resources ◽  
Economic Damage ◽  
Ambrosia Beetles ◽  
Invasive Insects ◽  
The World ◽  
And Control

Invasive species, those that are nonnative and cause economic damage, are one of the main threats to ecosystems around the world. Ambrosia beetles are some of the most common invasive insects. Currently, severe economic impacts have been increasingly reported for all the invasive shot hole borers in South Africa, California, Israel, and throughout Asia. This 7-page fact sheet written by Demian F. Gomez, Jiri Hulcr, and Daniel Carrillo and published by the School of Forest Resources and Conservation describes shot hole borers and their biology and hosts and lists some strategies for prevention and control of these pests. http://edis.ifas.ufl.edu/fr422

The World Economic Forum Principles on "Climate Governance on Corporate Boards": can soft law help to face climate change around the world?

2020 ◽  
pp. 37-55
Author(s):  
Sabrina Bruno
Keyword(s):  
Climate Change ◽  
South Africa ◽  
Comparative Analysis ◽  
Boards Of Directors ◽  
Soft Law ◽  
Corporate Boards ◽  
World Economic Forum ◽  
Financial Factor ◽  
The World ◽  
World Economic

Climate change is a financial factor that carries with it risks and opportunities for companies. To support boards of directors of companies belonging to all jurisdictions, the World Economic Forum issued in January 2019 eight Principlescontaining both theoretical and practical provisions on: climate accountability, competence, governance, management, disclosure and dialogue. The paper analyses each Principle to understand scope and managerial consequences for boards and to evaluate whether the legal distinctions, among the various jurisdictions, may undermine the application of the Principles or, by contrast, despite the differences the Principles may be a useful and effective guidance to drive boards' of directors' conduct around the world in handling climate change challenges. Five jurisdictions are taken into consideration for this comparative analysis: Europe (and UK), US, Australia, South Africa and Canada. The conclusion is that the WEF Principles, as soft law, is the best possible instrument to address boards of directors of worldwide companies, harmonise their conduct and effectively help facing such global emergency.

Sign in / Sign up

Export Citation Format

Share Document