For week two of the project I decided to investigate the possible evolution paths that COVID-19 could take in its future phylogenetic trees. I attempted to do so by examining phylogenetic trees of other single-stranded RNA viruses to see if there are any commonalities that could be anticipated in COVID-19's evolution. The viruses with phylogenetic trees based on their complete genomes I was able to locate include HIV-1, rhinovirus, Hepatitis C, and dengue virus.
This article in the Journal of Virology outlines viral mutation rates among the most common viruses which affect humans. The article notes that RNA viruses typically have higher mutation rates than DNA viruses due to the more error prone replication process. RNA viruses typically have mutation rates between 10^−6 and 10^−4 substitutions per nucleotide site per cell infection (s/n/c) and evolutionary rates between 10^-3 to 10^-2 substitutions per nucleotide per year. The following image shows the mutation rates of HIV-1, rhinovirus, hep C, and other RNA viruses in chart B.
From my research, there is not currently a clear number on what the mutation rate is for COVID-19. However, I was able to locate this article from 2004 which notes that the SARS coronavirus had a evolutionary rate of 0.80 – 2.38 × 10^-3 nucleotide substitution per site per year. Due to COVID-19 being in the same family as this SARS virus, I would say we can use this number as a close estimate of what COVID-19's genuine evolutionary rate is. Since its evolutionary rate falls in line with the viruses, it is fair to say COVID-19 could follow similar evolutionary paths over time.
The above image is a phylogenetic tree of HIV-1 clusters using near complete genomes from this article in Nature. The tree was generated by a team of researchers investigating the timescale, evolutionary history, and population genetics of specific HIV-1 strains. The inner surrounding circle denotes geographical location (A in the legend) and the outer circle denotes associated risk groups (B in the legend).
Here is the phylogenetic tree obtained from this article in Science magazine where researchers analyzed all known rhinovirus sequences in an attempt to reveal information on its evolution.
This phylogenetic tree for Hepatitis C is slightly different than those above as it only considers genomes from infected patients in Portugal rather than worldwide data used for the other trees. Nonetheless, I think even a smaller scale tree can exhibit some patterns that one might anticipate from COVID-19. This tree comes from this article in Nature.
This analysis from PeerJ on the genotype diversity of Dengue Virus yields the above phylogenetic tree which again looks rather similar to the other RNA viruses shown.
Each phylogenetic tree above shows that RNA viruses are rather prone to semi-significant changes throughout their evolutions. As each tree grows outwards, the number of identifiable mutations increases although these mutations are not always significant enough to form a new clade of the virus. However, each tree shows multiple points in the evolutionary history of the viruses where they strayed notably from their ancestors resulting in a new definable strain, such as in Rhinoviruses tree where we can see the separation of HRV-C, HRV-B, and HRV-A.
The common minor divergences and occasional major divergences that increase genetic diversity among RNA viruses are one of the factors that make it so difficult to immunize against and prevent the spread of these pathogens. Assuming COVID-19 follows the above evolutionary paths it could very well become another seasonal virus like Rhinovirus or Influenza as it follows similar tranmission methods and is more contagious. Annual flu shots attempting to vaccinate against specific strains could become commonplace for COVID-19 as well in the future once the initial few waves of the pandemic has ceased.
Today (4/29/2020) GISAID posted a phylogenetic tree for COVID-19 using full genome sequences and as expected it looks rather similar to other RNA virus trees.
Already there are three major clades present with COVID-19, and its phylogenetic tree resembles other RNA viruses after only a few months time. Once again we see infrequent but stark changes closer to the center of the tree and more frequent but less significant changes further away. As time moves forward and more genomes are sequenced, I expect to see more clades appear which again indicates we could be stuck with COVID-19 for awhile despite current vaccination research attempts.