scholarly journals PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern

2021 ◽  
Author(s):  
Chantal B.F. Vogels ◽  
Mallery Breban ◽  
Tara Alpert ◽  
Mary E. Petrone ◽  
Anne E. Watkins ◽  
...  
Keyword(s):  
South Africa ◽  
Immune Responses ◽  
Open Source ◽  
Primary Target ◽  
Pcr Assay ◽  
Gene Target ◽  
Spike Gene ◽  
The World ◽  
The Uk

AbstractWith the emergence of SARS-CoV-2 variants that may increase transmissibility and/or cause escape from immune responses1–3, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant first detected in the UK4,5 could be serendipitously detected by the ThermoFisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a “spike gene target failure” (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern that lack spike Δ69-70, such as B.1.351 (also 501Y.V2) detected in South Africa6 and P.1 (also 501Y.V3) recently detected in Brazil7. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all three variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open source PCR assay to detect SARS-CoV-2 variants of concern8. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence spread of B.1.1.7, B.1.351, and P.1.

scholarly journals Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

PLoS Biology ◽  
2021 ◽  
Vol 19 (5) ◽  
pp. e3001236
Author(s):  
Chantal B. F. Vogels ◽  
Mallery I. Breban ◽  
Isabel M. Ott ◽  
Tara Alpert ◽  
Mary E. Petrone ◽  
...  
Keyword(s):  
South Africa ◽  
United Kingdom ◽  
Severe Acute Respiratory Syndrome ◽  
Immune Responses ◽  
Primary Target ◽  
Pcr Assay ◽  
Gene Target ◽  
Spike Gene ◽  
The United Kingdom ◽  
The World

With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath Coronavirus Disease 2019 (COVID-19) PCR assay because a key deletion in these viruses, spike Δ69–70, would cause a “spike gene target failure” (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69–70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675–3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675–3677 as the primary target and spike Δ69–70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.

International Listening Post report summary: the world at the dawn of 2019

2019 ◽  
Vol 19 (1) ◽  
pp. 121-124
Author(s):  
Sandy Henderson ◽  
Ulrike Beland ◽  
Dimitrios Vonofakos
Keyword(s):  
South Africa ◽  
Faroe Islands ◽  
The South ◽  
The World ◽  
The Uk

On or around 9 January 2019, twenty-two Listening Posts were conducted in nineteen countries: Canada, Chile, Denmark, Faroe Islands, Finland, Germany (Frankfurt and Berlin), Hungary, India, Ireland, Israel, Italy (two in Milan and one in the South), Peru, Serbia, South Africa, Spain, Sweden, Taiwan, Turkey, and the UK. This report synthesises the reports of those Listening Posts and organises the data yielded by them into common themes and patterns.

scholarly journals Strome van lewende water: Nuwe-Testamentiese perspektiewe op die missionêre karakter van die kerk

2013 ◽  
Vol 47 (1) ◽  
Author(s):  
Flip P.J. Buys
Keyword(s):  
South Africa ◽  
North America ◽  
Missional Church ◽  
The World ◽  
God's Mission ◽  
Reformed Churches ◽  
The Uk ◽  
Missional Churches ◽  
The Church ◽  
International Phenomenon

Oor ’n wye front word besorgdheid uitgespreek oor die stagnering en kwynende getallegroei van hoofstroom-reformatoriese kerke in Suid-Afrika. Die besorgdheid word egter ook uitgespreek dat predikante en kerke in hulle ywer om kerklike vernuwing teweeg te bring, soveel kompromieë maak dat die kerk sy eie aard as heilge volk van God in die wêreld verloor. Daar is ’n internasionale tendens te bespeur by reformatoriese kerke, in Suid-Afrika, Noord Amerika, Australië, Nederland, Duitsland en die Verenige Koninkryk om die na-binne-gerigtheid van kerke om te draai om werklik missionêre kerke te kan wees. Daar is ook tekens van ’n groeiende ontwakende passie om die onbereikte taalgroepe tot by die uithoeke van die aarde te bereik met die evangelie. Daar is oor ’n wye front lewendige debatte aan die gang wat vra vir ’n herevaluering van oorgeërfde ekklesiologiese tradisies en gebruike en ’n herbesinning oor Bybelse beginsels. In die lig van hierdie ontwikkelings is die doel van hierdie artikel om Nuwe-Testamentiese beginsels op te som en te onderstreep en as boustene aan te bied om die profiel van ’n missionêre kerk te skets. Grave concerns are expressed about the decline of mainline reformed churches in South Africa, especially the Reformed Churches in South Africa. At the same time fears are expressed that efforts to facilitate renewal in churches in order to become healthy and more effective missional churches, are making too many compromises with the gospel, so that the church is in danger of losing its very character as God’s holy people in the world. There is also an international phenomenon of reformed and evangelical type churches in North America, the Netherlands, Germany, the UK and Australia endeavouring to outgrow their ingrown vision and become part of God’s mission to reach unreached people groups in every corner of the world. There are lively debates on reviewing and rethinking inherited ecclesiological theological traditions and practices in churches. This article endeavours to gather basic building bricks by summarising and emphasising the most basic New Testament principles for outlining the profile of a missional church.

BS449 to EC3 via BS5950: The Process, the Pitfalls and the Preparations

2005 ◽  
Vol 8 (3) ◽  
pp. 275-285 ◽  
Author(s):  
David A. Nethercot
Keyword(s):  
South Africa ◽  
Hong Kong ◽  
Design Codes ◽  
Personal View ◽  
The Past ◽  
The World ◽  
Direct Association ◽  
The Uk ◽  
Steel Design ◽  
The Eu

For more than 35 years the author has been directly involved with the preparation of Structural Steel Design Codes – both in the UK and, more widely, in the EU. This activity has also extended to include direct association with Code developments in several other countries around the world e.g. South Africa, Hong Kong etc. plus observation of the process in many places. Utilising the UK position as the timeline, this paper presents a largely personal view of developments over the past 100 years, beginning in the pre-code era and culminating in today's age of international cooperation.

scholarly journals Naturally-acquired immunity in Syrian Golden Hamsters provides protection from re-exposure to emerging heterosubtypic SARS-CoV-2 variants B.1.1.7 and B.1.351

2021 ◽  
Author(s):  
Jordan J. Clark ◽  
Parul Sharma ◽  
Eleanor G. Bentley ◽  
Adam C. Harding ◽  
Anja Kipar ◽  
...  
Keyword(s):  
South Africa ◽  
Immune Responses ◽  
Clinical Signs ◽  
Acquired Immunity ◽  
Hamster Model ◽  
Syrian Golden Hamsters ◽  
Subsequent Exposure ◽  
Acquired Immune Responses ◽  
The Uk ◽  
Prior Infection

AbstractThe ability of acquired immune responses against SARS-CoV-2 to protect after subsequent exposure to emerging variants of concern (VOC) such as B1.1.7 and B1.351 is currently of high significance. Here, we use a hamster model of COVID-19 to show that prior infection with a strain representative of the original circulating lineage B of SARS-CoV-2 induces protection from clinical signs upon subsequent challenge with either B1.1.7 or B1.351 viruses, which recently emerged in the UK and South Africa, respectively. The results indicate that these emergent VOC may be unlikely to cause disease in individuals that are already immune due to prior infection, and this has positive implications for overall levels of infection and COVID-19 disease.

scholarly journals Molecular analysis and new records of the invasive polychaete Boccardia proboscidea (Annelida: Spionidae)

2019 ◽  
Vol 20 (2) ◽  
Author(s):  
VASILY I. RADASHEVSKY ◽  
VICTORIA V. PANKOVA ◽  
VASILY V. MALYAR ◽  
TATYANA V. NERETINA ◽  
ROBIN S. WILSON ◽  
...  
Keyword(s):  
South Africa ◽  
16S Rdna ◽  
Sequence Data ◽  
Haplotype Diversity ◽  
The North ◽  
Rdna Sequences ◽  
The World ◽  
The Usa ◽  
Asian Pacific ◽  
The Uk

The spionid polychaete Boccardia proboscidea Hartman, 1940 is a tube-dweller and shell/stone-borer widely occurring in temperate waters across the world and considered invasive in many areas. It was originally described from California, USA, and later reported from Pacific Canada, the Asian Pacific, Australia, New Zealand, Argentina, South Africa, and northern Europe. The Bayesian inference analysis of sequence data of three gene fragments (836 bp in total) of the mitochondrial 16S rDNA, nuclear 28S rDNA, and Histone 3 has shown that individuals from the Pacific coasts of Canada and the USA, Argentina, Australia, South Africa, the United Kingdom, and Mediterranean France were genetically very similar (maximal average p-distance value, 0.49%, was between 16S rDNA sequences). We consider these individuals to be conspecific and report the earliest records of B. proboscidea from the UK and a possible first Mediterranean record in the Gulf of Lion. The high 16S haplotype diversity of B. proboscidea detected in the north-eastern Pacific suggests a native distribution for the species in the northern Pacific and subsequent introductions through human activities to other parts of the world. The histories of these introductions are reviewed and the hypotheses about times and places of introductions are updated.

scholarly journals Reliability of Spike Gene Target Failure for ascertaining SARS-CoV-2 lineage B.1.1.7 prevalence in a hospital setting

2021 ◽  
Author(s):  
José Afonso Guerra-Assunção ◽  
Paul A. Randell ◽  
Florencia A. T. Boshier ◽  
Michael A. Crone ◽  
Juanita Pang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Lower Cost ◽  
Hospital Setting ◽  
Qpcr Assay ◽  
Spike Protein ◽  
Whole Genome ◽  
Gene Target ◽  
Spike Gene ◽  
The Uk

AbstractThe appearance of the SARS-CoV-2 lineage B.1.1.7 in the UK in late 2020, associated with faster transmission, sparked the need to find effective ways to monitor its spread. The set of mutations that characterise this lineage include a deletion in position 69 and 70 of the spike protein, which is known to be associated with Spike Gene Target Failure (SGTF) in a commonly used three gene diagnostic qPCR assay. The lower cost and faster turnaround times compared to whole genome sequencing make the use of qPCR for monitoring of the variant spread an attractive proposition. However, there are several potential issues with this approach. Here we use 826 SARS-CoV-2 samples collected in a hospital setting as part of the Hospital Onset COVID Infection (HOCI) study where qPCR was used for viral detection, followed by whole genome sequencing (WGS), to identify the factors to consider when using SGTF to infer lineage B.1.1.7 prevalence in a hospital setting, with potential implications for locations where this variant has recently been introduced.

scholarly journals Screening, Prevention and Treatment of COVID-19 with Special Reference to African-Americans

2021 ◽  
Vol 2 (3) ◽  
pp. 01-06
Author(s):  
Prabir Mandal
Keyword(s):  
South Africa ◽  
Immune Responses ◽  
Severe Illness ◽  
The Novel ◽  
Novel Variants ◽  
Prevention And Treatment ◽  
Previous Infection ◽  
Flu Virus ◽  
The Uk ◽  
Over Time

Viruses mutate all the time, and the coronavirus that causes COVID-19 is no exception. As new variants of the COVID-19 emerge, a slew of new studies suggest that some may be able to evade immune responses triggered by a previous infection or by a vaccine. The novel variants of SARS-CoV-2 including those seen in the UK (2OI/5O1Y.V1/B.1.1.7), South Africa (2OH/5O1Y.V2/B.1.351), Brazil (P.1/2OJ/5O1Y.V3/B.1.1.248) have emerged with the concern of increased infectivity and virulence. Scientists are working to learn more about the characteristics of these strains whether they could cause more severe illness, and whether currently authorized vaccines will protect people against them. All viruses naturally mutate and evolve over time. For example, flu virus change often, which is why doctors recommend that you get a flu shot every year. Various mRNA vaccine platforms have been developed in recent years and validated in studies of immunogenicity and efficacy.

scholarly journals COVID-19 Modelling: The Effects of Social Distancing

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Oliva Bendtsen Cano ◽  
Sabrina Cano Morales ◽  
Claus Bendtsen
Keyword(s):  
South Africa ◽  
Open Source ◽  
Source Code ◽  
Stochastic Simulations ◽  
Middle Income ◽  
Open Source Code ◽  
Social Distancing ◽  
Middle Income Countries ◽  
The Uk

The purpose of this article is to reach all those who find it difficult to become well informed about the steps that have been implemented to tackle the COVID-19 pandemic and to spark discussion and thought. Here, we use simple stochastic simulations to evaluate different approaches taken to manage the crisis. We then compare these results with updated data of what really happened in the UK and in South Africa. The initial simulations aligned well with how the pandemic has evolved throughout five months following lockdown. The models are, as expected, not fully accurate, but exact enough to be used as a guideline to the evolution of the disease in both high- and middle-income countries. This is shown through simulations formed by an open source code, which allows evaluation of the outcomes from different intervention scenarios or conditions.

Positive Action to Promote Women in Politics: Some European Comparisons

2003 ◽  
Vol 52 (3) ◽  
pp. 587-614 ◽  
Author(s):  
Meg Russell ◽  
Colm O'Cinneide
Keyword(s):  
South Africa ◽  
Developed Countries ◽  
Women In Politics ◽  
Women's Representation ◽  
Women’S Representation ◽  
The Us ◽  
Positive Action ◽  
The World ◽  
The Uk

The issue of women's under-representation in politics continues to be controversial and pressing in countries all over the world. According to the Inter Parliamentary Union, only 14.7 per cent of the world's legislators are women.1 In no country do women achieve parity with men in terms of parliamentary representation. The record of many of the world's most developed countries is particularly poor. Looking at lower houses of the legislature, in the US women's representation is only 14 per cent, in the UK 18 per cent, France 12 per cent and Italy 10 per cent. These countries are considerably out-performed by others such as South Africa and Argentina, both at 30 per cent.2

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