UNITED STATES OF AMERICA - Study suggests possible new COVID-19 timeline in the U.S. [American Red Cross, 1 December 2020]

Title:

Study suggests possible new COVID-19 timeline in the U.S.

 

Article attributed to:

Dr Susan Stramer, vice president of Scientific Affairs at the American Red Cross

Published:

American Red Cross, 1 December 2020

Click here to read

From this article:

The findings of this study indicate that that it is possible the virus that causes COVID-19 may have been present in California, Oregon, and Washington as early as Dec. 13-16, 2019, and in Connecticut, Iowa, Massachusetts, Michigan, Rhode Island, and Wisconsin as early as Dec. 30, 2019 - Jan. 17, 2020.

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 [Scholarly Article - Infection, Genetics and Evolution, 2020]

Title:

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2

 

Authors:

Lucy van Dorp, Mislav Acman, Damien Richard [et al.]

 

Published:

Infection, Genetics and Evolution, Volume 83, 2020

https://www.sciencedirect.com/science/article/abs/pii/S1567134820301829

Abstract:

SARS-CoV-2 is a SARS-like coronavirus of likely zoonotic origin first identified in December 2019 in Wuhan, the capital of China's Hubei province. The virus has since spread globally, resulting in the currently ongoing COVID-19 pandemic. The first whole genome sequence was published on January 5 2020, and thousands of genomes have been sequenced since this date. This resource allows unprecedented insights into the past demography of SARS-CoV-2 but also monitoring of how the virus is adapting to its novel human host, providing information to direct drug and vaccine design. We curated a dataset of 7666 public genome assemblies and analysed the emergence of genomic diversity over time. Our results are in line with previous estimates and point to all sequences sharing a common ancestor towards the end of 2019, supporting this as the period when SARS-CoV-2 jumped into its human host. Due to extensive transmission, the genetic diversity of the virus in several countries recapitulates a large fraction of its worldwide genetic diversity. We identify regions of the SARS-CoV-2 genome that have remained largely invariant to date, and others that have already accumulated diversity. By focusing on mutations which have emerged independently multiple times (homoplasies), we identify 198 filtered recurrent mutations in the SARS-CoV-2 genome. Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2. Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. We additionally provide an interactive user-friendly web-application to query the alignment of the 7666 SARS-CoV-2 genomes.

medRxiv, 31 August 2020 [preprint] - The Role of Air Conditioning in the Diffusion of Sars-CoV-2 in Indoor Environments: a First Computational Fluid Dynamic Model, based on Investigations performed at the Vatican State Childrens Hospital

Title:
The Role of Air Conditioning in the Diffusion of Sars-CoV-2 in Indoor Environments: a First Computational Fluid Dynamic Model, based on Investigations performed at the Vatican State Childrens Hospital

Authors:
Luca Borro, Lorenzo Mazzei, Massimiliano Raponi, Prisco Piscitelli, Alessandro Miani & Aurelio Secinaro

Published:
medRxiv, 31 August 2020
[Keep in mind that this article is a preprint and not yet peer reviewed.]
https://www.medrxiv.org/content/10.1101/2020.08.25.20181420v1

From the abstract:
Background: About 15 million people worldwide were affected by the Sars-Cov-2 infection, which already caused 600,000 deaths. This virus is mainly transmitted through exhalations from the airways of infected persons, so that Heating, Ventilation and Air Conditioning (HVAC) systems might play a role in spreading the infection in indoor environments.

medRxiv, 10 July 2020 (preprint) - SARS-CoV-2 spread across the Colombian-Venezuelan border

Title:
SARS-CoV-2 spread across the Colombian-Venezuelan border

Authors:
Alberto Paniz-Mondolfi, Marina Munoz, Carolina Florez, Sergio Gomez, Angelica Rico, Lisseth Pardo, Esther C Barros, Carolina Hernandez, Lourdes Delgado, Jesus Jaimes, Luis Perez, Anibal Teheran, Hala Alshammary, Ajay Obla, Zenab Khan, Ana Gonzalez-Reiche, Matthew Hernandez, Emilia Sordillo, Viviana Simon, Harm van Bakel & Juan David Ramirez

Published:
medRxiv, 10 July 2020
[Keep in mind that this article is a preprint and not yet peer reviewed.]
https://www.medrxiv.org/content/10.1101/2020.07.09.20149856v1

Abstract:
Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuelan ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region. We sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages Pangolin tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference. We found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. An additional three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome. Conclusions: Genomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.

bioRxiv, 24 June 2020 (preprint) - Development of a fluorescence based, high-throughput SARS-CoV-2 3CLpro reporter assay

Title:
Development of a fluorescence based, high-throughput SARS-CoV-2 3CLpro reporter assay

Authors:
Heather M Froggatt, Brook E Heaton & Nicholas S Heaton

Published:
bioRxiv, 24 June 2020
[Keep in mind that this article is a preprint and not yet peer reviewed.]
https://www.biorxiv.org/content/10.1101/2020.06.24.169565v1

Abstract:
In late 2019 a human coronavirus, now known as SARS-CoV-2, emerged, likely from a zoonotic reservoir. This virus causes COVID-19 disease, has infected millions of people, and has led to hundreds of thousands of deaths across the globe. While the best interventions to control and ultimately stop the pandemic are prophylactic vaccines, antiviral therapeutics are important to limit morbidity and mortality in those already infected. At this time, only one FDA approved anti-SARS-CoV-2 antiviral drug, remdesivir, is available and unfortunately, its efficacy appears to be limited. Thus, the identification of new and efficacious antivirals is of highest importance. In order to facilitate rapid drug discovery, flexible, sensitive, and high-throughput screening methods are required. With respect to drug targets, most attention is focused on either the viral RNA-dependent RNA polymerase or the main viral protease, 3CLpro. 3CLpro is an attractive target for antiviral therapeutics as it is essential for processing newly translated viral proteins, and the viral lifecycle cannot be completed without protease activity. In this work, we present a new assay to identify inhibitors of the SARS-CoV-2 main protease, 3CLpro. Our reporter is based on a GFP-derived protein that only fluoresces after cleavage by 3CLpro. This experimentally optimized reporter assay allows for antiviral drug screening in human cell culture at biosafety level-2 (BSL2) with high-throughput compatible protocols. Using this screening approach in combination with existing drug libraries may lead to the rapid identification of novel antivirals to suppress SARS-CoV-2 replication and spread.

Science, 25 May 2020 - Study tells ‘remarkable story’ about COVID-19’s deadly rampage through a South African hospital

Title:
Study tells ‘remarkable story’ about COVID-19’s deadly rampage through a South African hospital

Author:
Linda Nordling

Published:
Science, 25 May 2020
https://www.sciencemag.org/news/2020/05/study-tells-remarkable-story-about-covid-19-s-deadly-rampage-through-south-african

From the article:
"On 9 March, a patient who had recently traveled to Europe and had symptoms of COVID-19 visited the emergency department of St Augustine’s, a private hospital in Durban, South Africa. Eight weeks later, 39 patients and 80 staff linked to the hospital had been infected, and 15 patients had died—fully half the death toll in KwaZulu-Natal province at that time."

Scholarly Article (May 2020) - COVID-19 immunity passports and vaccination certificates: scientific, equitable, and legal challenges

Title:
COVID-19 immunity passports and vaccination certificates: scientific, equitable, and legal challenges

Author:
Alexandra L. Phelan

Published:
Lancet, Volume 395, Issue 10237, pp. 1595-1598 (May 2020)
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)31034-5/fulltext

From the abstract:
"Many governments are looking for paths out of restrictive physical distancing measures imposed to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With a potential vaccine against coronavirus disease 2019 (COVID-19) many months away,1 one proposal that some governments have suggested, including Chile, Germany, Italy, the UK, and the USA,2 is the use of immunity passports—ie, digital or physical documents that certify an individual has been infected and is purportedly immune to SARS-CoV-2. Individuals in possession of an immunity passport could be exempt from physical restrictions and could return to work, school, and daily life. However, immunity passports pose considerable scientific, practical, equitable, and legal challenges."

DailyMail, 19 May 2020 - Fears of new coronavirus outbreak in Chinese region of 100million people after two cities went into Wuhan-style lockdown

Title:
Fears of new coronavirus outbreak in Chinese region of 100million people after two cities went into Wuhan-style lockdown

Author:
Emilia Jiang

Published:
DailyMail, 19 May 2020
https://www.dailymail.co.uk/news/article-8335235/Mysterious-COVID-19-cluster-ravages-Chinese-region-100-million-people.html

Key points from the article:
* Fears have raised that an outbreak could erupt in Dongbei in China's north-east 
* More than five million residents in two cities in Jilin province are under lockdown