Sequencing and Tracking of Phylogeny in COVID-19 Study

The current Covid-19 pandemic has caused significant strain on the health care system, and an
unprecedented Governmental response to stem the spread of the disease through social
distancing and self-isolation. Covid-19 is a pneumonia-like severe acute respiratory syndrome
(SARS) caused by a virus, SARS-CoV-2, with similarity to the SARS virus responsible for a
worldwide outbreak in 2002. Due to the original SARS outbreak, a large body of genomic data
exists for SARS coronaviruses, allowing researchers to understand how the new virus
SARS-CoV-2 has evolved to be so virulent in humans.

Whilst testing kits have been designed to target specific genes in the viral RNA, whole
genome sequencing of the virus offers increased scope to track the epidemiology of the virus.
In addition, through the use of current sequencing technology available from Oxford Nanopore
Technologies (ONT), genome scanning can be performed in real time and allow for
identification of specific viral variants within patient samples. As the pandemic continues
to spread, understanding the evolution of the virus and its spread across the globe will help
researchers to begin to predict the future spread of the virus, estimate the number of
worldwide cases, and aid in the development of epidemiological models for estimating a
potential end point to the pandemic crisis. In addition, the ability to track mutations in
real time allows researchers access to a large body of data to explore in order to identify
potential targets for cures and vaccines. These data will also feed into the design of
RNA-based therapeutic targets and diagnostics using patented array technology.

In this project, the investigators aim to use Nanopore-based sequencing technology to
assemble viral genomes from patients who have presented to Portsmouth Hospital NHS Trust
(PHT) in the Wessex region with symptoms of Covid-19. PHT, has containment level 3 (CL3)
facilities within their Microbiology Department required for inactivation of the virus and
extraction of viral RNA, and has recently begun testing of potential Covid-19 patients. Viral
RNA samples from patients who show positive results will be selected for sequencing using
Nanopore sequencing technology. Whole genome sequences will be compared using phylogenetic
analysis to identify the spread of the virus within the local area, will be analysed in the
context of anonymised patient level data to look for trends in the adaptation of the virus,
and will be compared with a global database of such sequences to help develop global maps of
transmission.

As part of the COVID-19 Genomics UK Consortium (COG-UK), the investigators will contribute
sequencing data to the consortium which will monitor changes in the virus on a national scale
to understand how the virus is mutating and spreading and whether different strains are
emerging