Race for a nonexistent vaccine: Covid19

The number of coronavirus infections continues to grow and the WHO recognizes that the pandemic has reached a point of global uncontrol. However, the race to discover the nonexistent vaccine will drastically reduce the mortality caused by the Covid19 coronavirus.

The virus has caused more than 330 thousand confirmed cases and almost 15 thousand deaths, however in almost all countries the number of infections has not yet reached a peak, which means its increase in the coming days.

According to the following graph, we can see that the expansion of the coronavirus in the world continues on an ascending curve, still exponential.

Discovering the genome of Covid19

The increase in deaths and mutations of the virus have accelerated the search for vaccines. Due to the large number of existing mutations of the virus, there has been an arduous global task of searching and monitoring the genomes of the Covid-19 coronavirus in order to obtain the adequate vaccine and thus stop the pandemic that has already had more than 6,000 killed only in Italy and several more in other parts of the world, the most affected being China, Spain and USA.

The most recent discoveries have shown evolutionary relationships of the HCoV-19 viruses of the new coronavirus pandemic. All samples are still closely related to few mutations in relation to a common ancestor, suggesting a common ancestor was shared sometime around November to December 2019.

This means that the first human infection should have started in the months of November-December 2019, followed by uninterrupted human-to-human transmission thus generating new samples.

Scheme of 172 genomes, obtained from Covid-19 between December 2019 to March 2020. Note the colors of the samples obtained with those on the map. Source: Nextstrain

Definition of the project

The numbering of the site and structure of the genomes of Covid-19 coronavirus, use the name Wuhan-Hu-1/2019 as a reference. The genome has its roots in relation to the first samples from Wuhan.

Temporal resolution assumes a nucleotide substitution rate of 5×10^-4 per site by year. Full details on bioinformatic processing is found in this Github project.

To compare the phylogenetic context of nCoV in SARS-related beta coronaviruses, pandemic with another viral structure, we can compare the genetic sequence. Available metadata is available by their authors, through GISAID, on which this research is based.

You can clone the project with the following git command:

git clone https://github.com/nextstrain/ncov.git