Human immune response transcriptome profile of COVID-19 cases in Alaska


Thomas Kosten

The COVID-19 pandemic has created a major public health crisis, the likes of which have not been seen since the Spanish influenza pandemic of 1918. The loss of life and livelihood by so many and the general lack of preparedness are clear indicators of the threat that pandemic events pose to the health and future of humanity. It is vital to understand the molecular basis of the human immunological response to COVID-19 and other pathogens in order to develop and explore new methods of treatment and prevention[4]. Funding the research that aids humanity’s response to this and future pandemic events is directly aligned with NASA strategic goal 1.1, as it is directly involved in safeguarding and improving life on earth. The efforts to fight the global pandemic in Alaska also present an opportunity to focus on response to pandemic events in areas with limited resources, a situation that is inevitable in the future of human space exploration[10]. An analysis of the genetic mechanisms active during an immune response in a COVID-19 patient will produce the necessary data to gain an accurate portrait of what is taking place at the level of gene expression in the outbreaks that have occurred in Alaska. The Oxford Nanopore MinION sequencer is the perfect candidate to perform this necessary research. The technology is smaller than a cell phone, and full genome sequencing from sample acquisition to real time results can be performed in two days with minimal manpower. Part of NASA’s space technology mission directorate is to explore efficient technology that can be used to further human exploration in space. In principle, this technology has the capability to study the gene expression response to nearly any stimulant on any terrestrial life form which is an invaluable research tool for the current crisis and when novel pathogens emerge.

The spread of the virus has many factors, and Alaska specifically has had a unique experience with the attempts to contain the spread of COVID-19. The state is remote, and the population is widespread and rural, but its economy relies heavily on tourism and a significant amount of outof-state labor. It additionally has very limited medical resources in those rural communities, making an outbreak of COVID-19 a potentially catastrophic event for many of the villages and rural communities. Through previous work using Nanopore sequencing and phylogenetics the University of Alaska Anchorage (U.A.A.) virology lab identified several unique points of outbreak that have occurred for several of the different strains of COVID. By understanding the host immune response through next-generation sequence data it will be possible to quickly identify the necessary preventive measures that must be taken in order to reduce pathogen associated mortality rates. This is an ability of critical value in rural Alaska where preventive measures are sometimes the only healthcare rural communities have access to.


Name: Thomas Kosten, Undergraduate Student

Institution: University of Alaska Anchorage

Major: Natural Sciences

Mentor: Eric Bortz,

Award: Apprenticeship

Funding Period: 2020 to 2021