Full title: Characterisation of SARS-CoV-2 in saliva of healthcare workers in high-risk settings and assessment of the use of the Cepheid Xpert®Xpress SARS CoV-2 cartridge
Funder: OUCRU (Wellcome Funding)
Principal Investigator: Abhilasha Karkey
Location of activity: Nepal
Diagnostic testing to identify persons infected with severe acute respiratory syndrome related coronavirus-2 (SARS-CoV-2) infection is central to control of the global pandemic of COVID-19. In a few countries, the use of diagnostic testing on a massive scale has been a cornerstone of successful containment strategies. In contrast, Nepal has been hampered by limited testing capacity within the country. However, various point of care technologies are emerging and of particular interest for our setting is the GenXpertXpert® Xpress SARS-CoV-2 cartridge. Cepheid has developed an automated molecular test for the qualitative detection of SARS-CoV-2. The test leverages the design principle in which multiple regions of the viral genome are targeted. The test can provide rapid detection of the current pandemic coronavirus in as soon as 30 minutes for positive results. The GenXpert machines have already been rolled out massively nationwide in Nepal since 2018. Therefore, providing evidence that the cartridges are efficient would be a tipping point towards successful containment. As rapid diagnostic tests to date remain to be highly unreliable and PCR capacity in the country is severly lacking, the use of the already existing GenXpert would be a cost effective and efficient way to screen and diagnose. The Xpert® Xpress SARS-CoV-2 cartridges have also already received FDA emergency approval.
- To provide evidence for national recommendation on the use of Cepheid Xpert®Xpress SARS CoV-2 cartridge on the GenXpert.
- To define the frequency and characteristics of asymptomatic carriage of SARS-CoV-2 in HCWs caring for COVID-19 patients.
- To define the frequency of SARS-CoV-2 infection in HCWs caring for COVID-19 patients.
- To define the duration of detectable SARS-CoV-2 in HCWs prior to developing symptoms.
- To determine whether transmission of SARS-CoV-2 occurs from HCW (asymptomatic and prodromal) to community contacts.
- To demonstrate the utility of filter paper collection of saliva as a surveillance tool for SARS-CoV-2 infection.
- To investigate the molecular epidemiology, intrahost diversity and evolution of SARS-CoV-2 in asymptomatic and symptomatic SARS-CoV-2 infections in HCWs.
Providing evidence for the use of the Cepheid SARS CoV-2 cartridge would be a cost effective method of rolling out the test for the current pandemic coronavirus in Nepal. Understanding the risk of carriage and transmission to and by HCWs will enable the design of interventions to reduce this risk.
- Early identification and understanding of the incidence of symptomatic and asymptomatic infection in HCWs
- Sequence & epidemiological analysis of transmission from infected patients (coupling with data collected in Vietnam)
- Assessment of filter paper-based saliva sample collection for the diagnosis and sequence characterisation of SARS-CoV-2
- Assessment of turnover time and efficiency of Xpert®Xpress SARS CoV-2 cartridge for nationwide rollout.
Description of the team
The laboratory teams of Patan hospital (PH), the Institute of Medicine: Teaching hospital (IOM) and the CMDN/Intrepid laboratory are involved in this study. All three centers are based in Kathmandu. PH and IOM are public hub hospitals for COVID-19 while CMDN/INPL is a molecular diagnostics center.