Sequencing and Tracking of Phylogeny in COVID-19 Study (STOPCOVID19)

The Investigators plan to generate a database of viral RNA sequences for SARS-CoV-2 within the Wessex region. Such whole genome data can be used to monitor mutation rates in real time and, through comparison with global databases of SARS-CoV-2 genome sequences, can be used to map transmission of the virus

Study Overview

• Status: Completed
• Conditions: Coronavirus Infection

Detailed Description

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

• Study Type: Observational
• Enrollment (Actual): 5602

Contacts and Locations

• Study Contact: Name: Samuel Robson; Phone Number: +44 (0) 23 9284 2144; Email: samuel.robson@port.ac.uk

Study Locations

• United Kingdom
  • Hampshire
    • Portsmouth, Hampshire, United Kingdom, PO6 3LY
      • Portsmouth Hospitals NHS Trust, Queen Alexandra Hospital

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 7 years and older (Child, Adult, Older Adult)
• Accepts Healthy Volunteers: N/A
• Genders Eligible for Study: All

• Sampling Method: Non-Probability Sample

Study Population

Focus on those whose tests have provided a positive result so as to maximise the number of SARS-CoV-2 genomes generated.

Description

Inclusion Criteria:

• Have undergone successful testing for Covid-19
• Have sufficient viral RNA remaining for research analysis following testing for Covid-19

Exclusion Criteria:

• Insufficient viral RNA remains following testing for Covid-19

Study Plan

How is the study designed?

Design Details

• Observational Models: Cohort
• Time Perspectives: Retrospective

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Number of whole genome sequences for the SARS-CoV-2 virus from viral RNA samples	Generated using Nanopore-based whole genome sequencing techniques	2 years

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Transmission rates of the SARS-CoV-2 virus	Identify mutations and viral strains prevalent within the Wessex region	2 years

Collaborators and Investigators

• Sponsor: Portsmouth Hospitals NHS Trust
• Collaborators: University of Portsmouth

Study record dates

Study Major Dates

• Study Start (Actual): May 4, 2020
• Primary Completion (Actual): September 30, 2022
• Study Completion (Actual): September 30, 2022

Study Registration Dates

• First Submitted: April 20, 2020
• First Submitted That Met QC Criteria: April 20, 2020
• First Posted (Actual): April 24, 2020

Study Record Updates

• Last Update Posted (Actual): April 3, 2023
• Last Update Submitted That Met QC Criteria: March 30, 2023
• Last Verified: January 1, 2023

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Coronaviridae Infections; Nidovirales Infections; RNA Virus Infections; Virus Diseases; Infections; Coronavirus Infections
• Other Study ID Numbers: PHT/2020/34

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No