LAB-Net was actively involved in RECOVER (Rapid European COVID-19 Emergency Research Response). For SOS-COVID, one of the RECOVER studies, LAB-Net offered laboratory expertise related to strategies for sample collection and management, and analysed the samples for the presence of viral and/or bacterial ethiologies.
About SOS-COVID
SOS-COVID (SARS-CoV-2 Observational Study of community acquired-acute respiratory tract infection during a time of widespread suspected COVID-19 in European primary care), was a prospective, observational study of acute respiratory tract infections in primary care settings across Europe. Participating patients were sampled (a combined throat and nose swab) to determine the aetiology of their illness, SARS-CoV-2 or another viral/bacterial infection. Patients were followed up to determine the following outcomes: duration of illness, non-productive days, impacts on daily life and complications, like pneumonia and hospitalisation.
With a full description of the illness spectrum and outcomes of COVID-19, the study aimed to determine the risk factors of getting COVID-19 and for a complicated course of disease.
Recruitment and sample collection
The study started in March 2020 and enrolled its first patients in the Netherlands on 14 April 2020. Between April 2020 – March 2021, SOS-COVID recruited 876 patients from 9 countries* who contacted their GP with symptoms of an RTI of unknown aetiology. A combined oropharyngeal and nasal swab (both nostrils) was collected from 855 patients using one flocked swab. This swab was stored in universal transport media, frozen between -20 and -80 °C and shipped in batches to the central laboratory in Antwerp. Upon arrival they were stored at -80 °C until analysis.
Findings
The following organisms could be detected in a Quantstudio 7 flex instrument by using a custom-made microarray (ThermoFisher scientific):
- Influenza A, B, A-H1, A-H3,
- human coronaviruses NL63, 229E, OC43, HKU1, MERS, SARS-Co-V 1 and 2,
- parainfluenza viruses 1-4,
- human metapneumovirus,
- rhinovirus,
- RSV A and B,
- adenovirus,
- enterovirus,
- enterovirus D68,
- parechovirus, and
- bocavirus.
A total of 855 SOS-COVID specimens were collected from and investigated by PCR for the detection of SARS-CoV-2 and other respiratory targets. Of these samples, 7% were collected in children and 93% in adults. As to be expected during the COVID pandemic, SARS-CoV-2 viruses were most frequently detected, with an overall positivity rate of 22.8%, followed by rhinoviruses (15.7%), seasonal coronaviruses (3.3%), and human metapneumoviruses (3%). Influenza A and influenza B viruses were not detected at all, neither were RSV A/B viruses. Also none of the specimens were found to be positive for parainfluenza viruses, MERS, SARS, enterovirus D68 or parechovirus.
The SARS-CoV-2 positivity rate ranged from 7.1% in Ireland to 52.0% in Moldova. The other coronaviruses were most prevalent in Moldova and Poland, rhinovirus in Hungary and human metapneuviruses in Poland. E.g. rhinovirus positivity rates ranged between 7.3% in Georgia and 27.0% in Hungary.
More details on the clinical status of the patients can be found in the publication:
Alike W. van der Velden, Milensu Shanyinde, Emily Bongard, Femke Böhmer, Slawomir Chlabicz, Annelies Colliers, Ana García-Sangenís, Lile Malania, Jozsef Pauer, Angela Tomacinschii, Ly-Mee Yu, Katherine Loens, Margareta Ieven, Theo J. Verheij, Herman Goossens, Akke Vellinga & Christopher C. Butler (2023) Clinical diagnosis of SARS-CoV-2 infection: An observational study of respiratory tract infection in primary care in the early phase of the pandemic, European Journal of General Practice, 29:1, DOI: 10.1080/13814788.2023.2270707
About LAB-Net
LAB-Net is the central laboratory and biobank for SOS-COVID, a SARS-CoV-2 Observational Study of community acquired-acute respiratory tract infections during a time of widespread suspected COVID-19 in European primary care. The coordinating lab is located at the Laboratory of Medical Microbiology (LMM) at the University of Antwerp.
For analysis of the respiratory specimens collected in ECRAID-BASE POS-ARI-ER and POS-ARI-PC and in ECRAID-PRIME, LAB-Net will also apply a microarray for simultaneous detection of the etiological agents.
* Belgium (n=6 practices), Germany (n=1 testing hub, which recruited patients from about 40 GPs), Spain (n=5), Georgia (n=5), Hungary (n=3), Ireland (n=5), Moldova (n=5), the Netherlands (n=1 large center where patients with RTI from 6 practices were seen) and Poland (n=5))