bioRxiv, 2 October 2020 (preprint) - Transmission of SARS-COV-2 from China to Europe and West Africa: a detailed phylogenetic analysis

Title:

Transmission of SARS-COV-2 from China to Europe and West Africa: a detailed phylogenetic analysis

 

Authors:

Wasco Wruck & James Adjaye

 

Published:

bioRxiv, 2 October 2020

[Keep in mind that this article is a preprint and not yet peer reviewed]

https://www.biorxiv.org/content/10.1101/2020.10.02.323519v1

 

From the abstract:

Background: SARS-CoV-2, the virus causing the Covid-19 pandemic emerged in December 2019 in China and raised fears that it could overwhelm healthcare systems worldwide. In June 2020, all African countries registered human infections with SARS-CoV-2. The virus is mutating steadily and this is monitored by a well curated database of viral nucleotide sequences from samples taken from infected individual thus enabling phylogenetic analysis and phenotypic associations. 

 

Methods: We downloaded from the GISAID database, SARS-CoV-2 sequences established from four West African countries Ghana, Gambia, Senegal and Nigeria and then performed phylogenetic analysis employing the nextstrain pipeline. Based on mutations found within the sequences we calculated and visualized statistics characterizing clades according to the GISAID nomenclature.

medRxiv, 19 May 2020 - The infection fatality rate of COVID-19 inferred from seroprevalence data [& blog posts relating to this article] - fascinating

Title:
The infection fatality rate of COVID-19 inferred from seroprevalence data

Author:
John Ioannidis, Stanford University

Published:
medRxiv, 19 May 2020
[Keep in mind that this study has not been peer-reviewed.]
https://www.medrxiv.org/content/10.1101/2020.05.13.20101253v1

From the abstract:
1) Objective: 
To estimate the infection fatality rate of coronavirus disease 2019 (COVID-19) from data of seroprevalence studies. 

2) Methods:
Population studies with sample size of at least 500 and published as peer-reviewed papers or preprints as of May 12, 2020 were retrieved from PubMed, preprint servers, and communications with experts. Studies on blood donors were included, but studies on healthcare workers were excluded. The studies were assessed for design features and seroprevalence estimates. Infection fatality rate was estimated from each study dividing the number of COVID-19 deaths at a relevant time point by the number of estimated people infected in each relevant region. Correction was also attempted accounting for the types of antibodies assessed.

3) Results:
Twelve studies were identified with usable data to enter into calculations. Seroprevalence estimates ranged from 0.113% to 25.9% and adjusted seroprevalence estimates ranged from 0.309% to 33%. Infection fatality rates ranged from 0.03% to 0.50% and corrected values ranged from 0.02% to 0.40%.

4) Conclusions:
The infection fatality rate of COVID-19 can vary substantially across different locations and this may reflect differences in population age structure and case-mix of infected and deceased patients as well as multiple other factors. Estimates of infection fatality rates inferred from seroprevalence studies tend to be much lower than original speculations made in the early days of the pandemic. 


Blog posts linking to this article:

Did Gov Destroy Economy for NOTHING? COVID May Be Less Deadly Than Flu, Study Finds
By Selwyn Duke
Published: New American, 21 May 2020

You’re Telling the Truth, but Your Visualization Isn’t
By Josh Lauer
Published: towards data science, 21 May 2020

Pandemic Blog 23: Why One Published research Finding is Misleading
By: John D. MacArthur, Professor of Mathematics, University of Wisconsin, Madison (owner of the blog)
Published: Quomodocumque, 19 May 2020


Also take note of this article:

COVID-19 Prevalence: John Ioannidis Responds to His Critics
By Michael Schulson
Published: Medscape, 16 May 2020

SOUTH AFRICA - Data lockdown: Tension simmers as questions are raised about access to Covid-19 information

Title:
Data lockdown: Tension simmers as questions are raised about access to Covid-19 information

Author:
Kyle Cowan

Published:
News24, 18 May 2020
https://www.news24.com/SouthAfrica/News/data-lockdown-tension-simmers-as-questions-are-raised-about-access-to-covid-19-information-20200517

From the article:
"Frustration is building among scientists over the government's apparent lack of willingness to make key, detailed Covid-19 data accessible ahead of a meeting of the Covid-19 ministerial advisory committee (MAC) on Monday.  

News24 understands that questions have arisen over the apparent stranglehold by the Department of Health on access to spatial data (geo-located confirmed coronavirus cases), data around testing, screening, contact tracing and hospitalisation data – which includes availability levels of medical supplies and high care beds."