On the Genetic Similarity During Cross-Species Transmission

During my journey into the world of genetic research, I found viruses to be fascinating, even encouraging in a sense. This is due to the fact that their inner structure is sophisticatedly geared towards generating new mutations as they spread to living creatures (hosts) in a plethora of different pathways: airborne, waterborne, bird migration, feces, and so forth. Inspiringly, the essence of evolution is revealed when mutations in the genetics of viruses provide them with the ability to become sophisticated as they adjust their survival skills over the years. I learned that viruses are not just a bunch of molecules, but actually a unique type of particle named virology, that can only be truly understood within a multidisciplinary context of biology, physics, geography, and even climatology and economics (think of how much power viruses have that they can cause general lockdowns).

Viral transition is the path the virus achieves among different host species. Animal to human viral transmission is called zoonosis. Zoonotic diseases can be transmitted in any context in which there is contact with or consumption of animals, animal products, or animal derivatives. The following modes may give you a clue: food and water, farming, ranching, husbandry, pets, hunting, live animal market, etc. And these are only a small glance at what is actually going on …

Within the framework of this research I focused on four viruses of two families: Coronaviridae (MERS and SARS-CoV-2 viruses) and Orthomyxoviridae (influenza A: H1N1 and H3N2 viruses), and discovered the next topics as the best match to the questions that I dealt with:

  1. Showing the diversity of hosts diagnosed with influenza type A and coronavirus
  2. Examining the genetic similarity between hosts — humans and nonhuman animals, in terms of viral DNA and protein sequences
  3. Exploring the dynamic behavior of viral transmission

Before diving into arithmetics (which is the easy part …), I would like to share my personal concern: I am concerned about us as a nation and our reaction to medical emergency situations caused by worldwide epidemics. Why does the public still suffer from epidemics like the on-going SARS-CoV-2 even though it is not a “brand new” virus (just a mutation of the previous virus in the coronavirus family)? Is it because we have yet to find a way of preventing transmission? Let me remind you of the following previous epidemic events. A prominent epidemic occurred in 1918 when influenza A was endemic in Homo sapiens (the first case was discovered in 1902 in Gallus). Viruses of the coronavirus family are “old” as well, first being collected from avians in 1941, pigs in 1952, and more recently in Homo sapiens in 2003 (in China). This virus is well known as SARS (and is still active). A similar virus structure was collected in 2008 in Saudia Arabia, known as MERS, which involved the presence of the illness in a large number of camels. More details regarding the geographical locations and host species of the viral genetic sequences are demonstrated in the graphs section below.

On the one hand, it seems that humanity in the 21st Century has developed technology in every imaginable field to meet almost every challenge: from metal tools to landing on the moon and artificial intelligence. At times it feels as if human ingenuity has no bounds. Yet, on the other hand, we remain reliant on conservative, even extreme methods such as general closures and enforcing the wearing of stuffy masks (has anyone thought of developing a mask with which one can breathe freely ?…). Bottom line, these “off the shelf” solutions are not adequate and in my opinion ridiculous. It means that we were not prepared, despite all the clear red signals and signs.

In these most difficult times, teams of scientists from varying backgrounds have gathered to “fight back” and “save the world” by developing solutions such as vaccines, medications and large scale data science projects estimating the “track” of the epidemic. However, I am doubtful that these heroes have everyone’s lives in mind. When saying “everyone” I am also referring to nonhuman animals such as: camels, pigs, avians and all the living creatures that we as humans keep, tend to, and breed for our own needs (food, clothing, labor, entertainment, and so on). It is my personal desire that all animals should be free. Until then, we should at least learn how to avoid transmission of viruses between their kind and our kind.

Is the genetic “mechanism” of all living creatures in the aggregate acting as ONE viral system? What are the invariants between hosts in terms of the recreation of the virus structure and the generation of proteins ? All of these questions have led me to explore the genetic similarity between multiple host species.

It turns out that this article is not about a new machine learning technique, but a unique research and perspective. Nevertheless, I assume you have some basic knowledge of neural networks, dimensionality reduction, big data analytics and biology. If the biological part is not clear to you, I recommend reading the literature review section in my blog: Studying the Genetics of COVID-19, and if you are not familiar with neural networks on genetic data, visiting my blog: Bridging the Gap Between Genetics and Neural Networks would be a good start for you.

Data Representation

In order to perform a large scale machine learning experiment, I gathered the publicly available data of viruses consisting of as much diversity of host species as possible in the _National Center for Biotechnology Information _NCBI (if you are not familiar with NCBI, read my blog: Hacking the Genetics of Viruses).

Before performing any calculations on the data, I selected a few informative details about the viruses. I plotted the epidemic scale and proportions without any data manipulation according to the additional sections that are gathered jointly with each genetic sample. The plots present each virus’s geographical location and host species prevalence, normalised and multiplied by 100. As can be seen, Homo sapiens is the first to be diagnosed in all viruses except for the H1N1 virus which was first collected from pigs. Bats are the second to be diagnosed in the coronavirus family. Camels were the most affected species suffered from MERS virus in 2016, while viverrids got first place in 2006, and European minks equalized the amount of Homo sapiens diagnosed with SARS-CoV-2 in 2020. As for the geographical locations, H3N2 was first collected in Asia and second in South Africa while H1N1 was involved in all the examined locations in 2009. The fifth graph is focused on Asia in order to distinguish between the locations in which the viruses were first isolated. Notice that the contribution of avians and pigs to humanity in terms of herd immunity as being suffered from influenza A is well demonstrated for either virus.

#machine-learning #neural-networks #covid19 #vegan #health #deep learning

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 On the Genetic Similarity During Cross-Species Transmission

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