Viral Load Analysis of the SARS-CoV-2 Virus in Nose Versus Mouth Sites

Study Overview
=================
Brief Summary
-----------------
It is a single-center, non-profit experimental study, intended to evaluate the viral load of SARS COV 2 in nasal and oral samples of positive subjects to evaluate any variation and understand which is the most suitable site for carrying out the swab.

Detailed Description
-----------------
Experimental study on de-identified, biological samples (nasal and buccal swab). The study will be performed on patients admitted to IRCCS Sacro Cuore Don Calabria Hospital or health care workers or their family members, who tested positive for SARS-CoV-2 by either a molecular or antigen test, performed on nasopharyngeal swab, according to current diagnostics. Among the family members, also children >4 years old will be included. The reason for including children and young subjects is based on data indicating that they seems to be highly sensitive to Omicron infection and that their vaccination status could influence viral load. The nose and mouth swab are poor invasive and they could be well tolerated also by children. Whinin 7 days from diagnosis, the subjects will be requested to sample another two specimens i.e. nasal swab and mouth swab, that will be tested for the presence of SARS-CoV-2 RNA. Results, expressed as cycle threshold will be then compared to analyze viral loads from the two different sites. Moreover, an aliquot will be retro-transcribed into cDNA and sequenced by Next Generation Sequencing (NGS) to obtain the virus entire genome sequence or evaluated by RT-PCR for variant determination.

Official Title
-----------------
Viral Load Analysis of the SARS-CoV-2 Virus in Nose Versus Mouth Sites

Conditions
-----------------
Sars-CoV-2 Infection

Intervention / Treatment
-----------------
* Diagnostic Test: Nasal and mouth swab


Participation Criteria
=================
Eligibility Criteria
-----------------
Inclusion Criteria: Patients admitted to IRCCS Sacro Cuore Don Calabria Hospital or health care workers or their family members. Among the family members, also children >4 years old will be included. Subjects verified as positive to SARS-CoV-2 according to either a molecular or antigen test, performed on nasopharyngeal swab, according to current diagnostics. Subjects who will accept to participate to the study and will sign the informed consent. Exclusion Criteria: lack of any needed data or inform consent

Ages Eligible for Study
-----------------
Minimum Age: 4 Years

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

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

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

Design Details

Primary Purpose: Diagnostic
Intervention Model: Single Group Assignment
Masking: None (Open Label)


Arms and Interventions

| Intervention/Treatment |
| --- |
|Diagnostic Test: Nasal and mouth swab|Whinin 7 days from diagnosis, the subjects will be requested to sample another two specimens i.e. nasal swab and mouth swab, that will be tested for the presence of SARS-CoV-2 RNA. Results, expressed as cycle threshold will be then compared to analyze viral loads from the two different sites. Moreover, an aliquot will be retro-transcribed into cDNA and sequenced by Next Generation Sequencing (NGS) to obtain the virus entire genome sequence or evaluated by RT-PCR for variantdetermination.|

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

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| SARS-CoV-2 real time RT-PCR analysis results of the nose and mouth swabs. | SARS-CoV-2 real time RT-PCR analysis results of the nose and mouth swabs. | 2 months | 
| - Droplet digital PCR (ddPCR) results for SARS-CoV-2 | - Droplet digital PCR (ddPCR) results for SARS-CoV-2 | 2 months | 
| - NGS or RT-PCR results for genomic lineages or variant identification. | - NGS or RT-PCR results for genomic lineages or variant identification. | 2 months | 
| - RT-PCR analysis results for subgenomics | - RT-PCR analysis results for subgenomics | 2 months | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| SARS-CoV-2 real time RT-PCR analysis results of the nose and mouth swabs in relationship to the sampling site, to the viral characterization and to the time from diagnosis. | SARS-CoV-2 real time RT-PCR analysis results of the nose and mouth swabs in relationship to the sampling site, to the viral characterization and to the time from diagnosis. | 2 months |