Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

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SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2103154118 ◽

2021 ◽

Vol 118 (36) ◽

pp. e2103154118 ◽

Cited By ~ 7

Author(s):

Emanuele Andreano ◽

Giulia Piccini ◽

Danilo Licastro ◽

Lorenzo Casalino ◽

Nicole V. Johnson ◽

...

Keyword(s):

South Africa ◽

Immune Response ◽

Severe Acute Respiratory Syndrome ◽

Receptor Binding ◽

Neutralizing Antibodies ◽

Receptor Binding Domain ◽

The United Kingdom ◽

Effective Immune Response ◽

Recent Emergence ◽

Natural Variants

To investigate the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the immune population, we coincupi bated the authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The plasma fully neutralized the virus for seven passages, but, after 45 d, the deletion of F140 in the spike N-terminal domain (NTD) N3 loop led to partial breakthrough. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed, at day 80, by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. Computational modeling predicts that the deletion and insertion in loops N3 and N5 prevent binding of neutralizing antibodies. The recent emergence in the United Kingdom, South Africa, Brazil, and Japan of natural variants with similar changes suggests that SARS-CoV-2 has the potential to escape an effective immune response and that vaccines and antibodies able to control emerging variants should be developed.

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The vaccination against COVID-19 in Morocco: a success story in progress

10.22514/sv.2021.080 ◽

2021 ◽

Keyword(s):

United States ◽

South Africa ◽

Developing Countries ◽

United Arab Emirates ◽

The United States ◽

Success Story ◽

The United Kingdom ◽

First Case ◽

The World ◽

Novel Coronavirus

Coronavirus disease 2019 is a respiratory sickness that may spread between persons. It is caused by a novel coronavirus that produces an outbreak in Wuhan, China and spread all over the world to become a pandemic. From the appearance of the first case of the new coronavirus in Morocco, Moroccan authorities has spared no effort to promote the health of Moroccans, ahead of that of the country’s economy. On 22 January 2021, 2 million doses, of AstraZeneca COVID-19 vaccine were delivered to Morocco, with a view to vaccinating 1 million Moroccans in a first phase. On 28 January, the campaign started and the King of Morocco was the 1st Moroccan to be vaccinated against the coronavirus. On 27 February 2021, Morocco has received 1 million doses from the Chinese laboratory Sinopharm and 6 million doses of the AstraZeneca vaccine allowing Morocco to vaccinate several audiences and the general public over the age of 60, and the most vulnerable. Thereafter, the COVID-19 vaccine doses administered per 100 people in 31 March 2021 were 115.89 in Israel, 84.01 in the United Arab Emirates, 52.53 in the United Kingdom, 44.93 in the United States, 45.04 in Bahrain, 21.66 in Morocco, 16.44 in Germany, 8.32 in China, 4.72 in India, and 0.44 in South Africa. Also, the population fully vaccinated against COVID-19 in 01 April 2021 were 55.51% in Israel, 22.12% in the United Arab Emirates, 20.08% in Chile, 16.77% in USA, 15.25% in Serbia, 15.14%in Bahrain, 10.21% in Morocco, 8.94% in Hungary, 8.23% in Turkey, 7.29% in UK, 3.07% in Russia, 2.39% in Brazil, 1.70% in Uruguay, 0.70% in India, and 0.45% in South Africa. This allows Morocco to figure in the top 10 countries fully vaccinated against COVID-19 despite the lack of resources and belonging to developing countries. Finally, our study gives an example to other countries to benefit from the Moroccan experience. Nevertheless, vaccination is only one element of a comprehensive COVID-19 strategy, it must be accompanied by measures to reduce circulating infection and keep them low.

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Severe respiratory illness caused by a novel coronavirus, in a patient transferred to the United Kingdom from the Middle East, September 2012

Eurosurveillance ◽

10.2807/ese.17.40.20290-en ◽

2012 ◽

Vol 17 (40) ◽

Author(s):

A Bermingham ◽

M A Chand ◽

C S Brown ◽

E Aarons ◽

C Tong ◽

...

Keyword(s):

United Kingdom ◽

Middle East ◽

Severe Acute Respiratory Syndrome ◽

Human Disease ◽

Respiratory Illness ◽

Gulf Region ◽

The United Kingdom ◽

Coronavirus Infection ◽

Novel Coronavirus ◽

Severe Respiratory Illness

Coronaviruses have the potential to cause severe transmissible human disease, as demonstrated by the severe acute respiratory syndrome (SARS) outbreak of 2003. We describe here the clinical and virological features of a novel coronavirus infection causing severe respiratory illness in a patient transferred to London, United Kingdom, from the Gulf region of the Middle East.

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Neutralizing response against E484K variant after original SARS-CoV-2 infection

10.1101/2021.05.07.21256803 ◽

2021 ◽

Author(s):

Takuma Hayashi ◽

Nobuo Yaegashi ◽

Ikuo Konishi

Keyword(s):

South Africa ◽

United Kingdom ◽

Severe Acute Respiratory Syndrome ◽

The Body ◽

Proliferative Potential ◽

Spike Glycoprotein ◽

Highly Pathogenic ◽

The United Kingdom ◽

The Uk ◽

Neutralization Response

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) variants, which are spreading in the United Kingdom (UK) and elsewhere, have been found in infected individuals in Japan. The virus mutates, to facilitate its life in the host, during the process of repeated proliferation in the body of the host, including humans. In other words, it is natural that a human-compatible mutant strain always predominates in infection and proliferation. As a result, the viral mutants acquire strong proliferative potential in the host and are highly pathogenic. The number of people infected with the mutated SARS-CoV-2 variant E484K, which is different from the SARS-CoV-2 variants that are spreading in the UK, South Africa, and Brazil, is increasing in Tokyo. It has been pointed out that the effects of immunity and vaccines may be reduced against the Tokyo-type SARS-CoV-2 variant E484K. We have investigated the neutralization response to various mutations in the spike glycoprotein using the serum of people already infected with the original SARS-CoV-2. The results showed that SARS-CoV-2 variants with Y543F or N501Y mutations in the spike glycoprotein affect the neutralization reaction. However, single E484K mutations within the spiked glycoprotein of the Tokyo-type SARS-CoV-2 variant are unlikely to have a significant effect on the affinity of the host antibody for the virus.

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

PLoS Biology ◽

10.1371/journal.pbio.3001236 ◽

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.

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Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

10.1101/2021.03.01.433314 ◽

2021 ◽

Author(s):

Nikhil Faulkner ◽

Kevin W. Ng ◽

Mary Wu ◽

Ruth Harvey ◽

Marios Margaritis ◽

...

Keyword(s):

South Africa ◽

United Kingdom ◽

Severe Acute Respiratory Syndrome ◽

Parental Strain ◽

Cross Reactivity ◽

The South ◽

The United Kingdom

We examined the immunogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.7 that arose in the United Kingdom and spread globally. Antibodies elicited by B.1.1.7 infection exhibited significantly reduced recognition and neutralisation of parental strains or of the South Africa B.1.351 variant, than of the infecting variant. The drop in cross-reactivity was more pronounced following B.1.1.7 than parental strain infection, indicating asymmetric heterotypic immunity induced by SARS-CoV-2 variants.

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Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

eLife ◽

10.7554/elife.69317 ◽

2021 ◽

Vol 10 ◽

Author(s):

Nikhil Faulkner ◽

Kevin W Ng ◽

Mary Y Wu ◽

Ruth Harvey ◽

Marios Margaritis ◽

...

Keyword(s):

South Africa ◽

United Kingdom ◽

Severe Acute Respiratory Syndrome ◽

Parental Strain ◽

Cross Reactivity ◽

Major Determinant ◽

Spike Glycoprotein ◽

Neutralising Antibodies ◽

The United Kingdom ◽

Vaccination Campaigns

Background: The degree of heterotypic immunity induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains is a major determinant of the spread of emerging variants and the success of vaccination campaigns, but remains incompletely understood.Methods: We examined the immunogenicity of SARS-CoV-2 variant B.1.1.7 (Alpha) that arose in the United Kingdom and spread globally. We determined titres of spike glycoprotein-binding antibodies and authentic virus neutralising antibodies induced by B.1.1.7 infection to infer homotypic and heterotypic immunity.Results: Antibodies elicited by B.1.1.7 infection exhibited significantly reduced recognition and neutralisation of parental strains or of the South Africa variant B.1.351 (Beta) than of the infecting variant. The drop in cross-reactivity was significantly more pronounced following B.1.1.7 than parental strain infection.Conclusions: The results indicate that heterotypic immunity induced by SARS-CoV-2 variants is asymmetric.

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Faculty Opinions recommendation of Characterization of a novel coronavirus associated with severe acute respiratory syndrome.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1013815.191920 ◽

2003 ◽

Author(s):

Jia-Huai Wang

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Novel Coronavirus

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Novel Coronavirus Disease (COVID-19): A Narrative Review Based on Current Status

Anti-Infective Agents ◽

10.2174/2211352518999201020202540 ◽

2020 ◽

Vol 18 ◽

Author(s):

Rina Das ◽

Dinesh Kumar Mehta ◽

Meenakshi Dhanawat

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Clinical Symptoms ◽

Virus Disease ◽

Relevant Literature ◽

World Health ◽

Current Status ◽

Future Research ◽

Treatment And Prevention ◽

First Case ◽

Novel Coronavirus

Abstract:: A novel virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), appeared and expanded globally by the end of year in 2019 from Wuhan, China, causing severe acute respiratory syndrome. During its initial stage, the disease was called the novel coronavirus (2019-nCoV). It was named COVID-19 by the World Health Organization (WHO) on 11 February 2020. The WHO declared worldwide the SARS-CoV-2 virus a pandemic on March 2020. On 30 January 2020 the first case of Corona Virus Disease 2019 (COVID-19) was reported in India. Now in current situation the virus is floating in almost every part of the province and rest of the globe. -: On the basis of novel published evidences, we efficiently summarized the reported work with reference to COVID-19 epidemiology, pathogen, clinical symptoms, treatment and prevention. Using several worldwide electronic scientific databases such as Pubmed, Medline, Embase, Science direct, Scopus, etc were utilized for extensive investigation of relevant literature. -: This review is written in the hope of encouraging the people successfully with the key learning points from the underway efforts to perceive and manage SARS-CoV-2, suggesting sailent points for expanding future research.

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