COVID-19 Genomic Sequencing for Nosocomial Outbreak Investigations

Study Overview
=================
Brief Summary
-----------------
This is a tertiary care hospital-based prospective molecular epidemiology study in Montreal, Canada. When nosocomial transmission was suspected by local infection control teams' investigations, SARS-CoV-2 viral genomic sequencing was performed locally for all putative outbreak cases and contemporary controls. Molecular and conventional epidemiology data were confronted in real time to improve understanding of COVID-19 transmission and reinforce or adapt prevention measures.

Detailed Description
-----------------
This study will include infected healthcare workers (HCW) and patients for whom a nosocomial infection in CHUM is suspected. The CHUM laboratory is responsible for COVID-19 diagnostic testing in all eligible HCW and patients. After initial diagnosis on standard PCR testing, samples are maintained at -80. Viral RNA is extracted and next-generation sequencing of the viral genome is performed using Nanopore long read sequencing platform. Preliminary data suggest that SARS-CoV-2 has a molecular clock of 2 single nucleotide polymorphism (SNP) per month. The analysis and between-isolate comparaison of those SNP among epidemiologically related cases will allow to support or refute the hypothesis of person to person nosocomial transmission. All infected patients will be matched 1:1 with contemporary community cases to provide a viral genome back catalog and better contextualize molecular epidemiology analyses. Molecular clusters will be reported to infection prevention and control teams and resulting interventions will be monitored.

Official Title
-----------------
On-Demand Point-of-Care SARS-CoV-2 Genomic Sequencing to Support Nosocomial Outbreak Investigations: A Prospective Molecular Epidemiology Study in Montreal

Conditions
-----------------
COVID-19, Molecular Sequence Variation, Nosocomial Infection

Intervention / Treatment
-----------------
* Diagnostic Test: SARS-CoV-2 genomic sequencing


Participation Criteria
=================
Eligibility Criteria
-----------------
Inclusion Criteria: Hospitalized in the institution during the study period Healthcare workers in the institution during the study period Exclusion Criteria: None

Ages Eligible for Study
-----------------
Minimum Age: 18 Years
Maximum Age: 100 Years

Sexes Eligible for Study
-----------------
All

Accepts Healthy Volunteers
-----------------
Accepts Healthy Volunteers

Study Plan
=================
How is the study designed?
-----------------

Arms and Interventions

| Intervention/Treatment |
| --- |
|Diagnostic Test: SARS-CoV-2 genomic sequencing|SARS-CoV-2 viral genomic sequencing and phylogenetic analyses|

What is the study measuring?
-----------------
Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Outbreak control measures improvement | Collaborative (infection control and molecular epidemiology teams) resolution of putative outbreaks. Transmission is either refuted or further supported by molecular analyses. Additional investigation efforts are discontinued or necessary corrective measures are implemented. | Through study completion, an average of 2 years |