Study settings
Qatar is a sovereign and independent state in the Middle East. It has eight municipalities which vary in area and population (Ad Dawhah, Al Rayyan, Al Daayen, Umm Salal, Al Khor, Al Shamal, Al Shahaniya and Al Wakrah). Qatar is known for its extensive development over recent years attracting expatriates from all over the world. It has a modern publicly funded healthcare system. This includes a universal publicly funded health care service delivered by the Primary Health Care Corporation (PHCC – responsible for primary health care) and Hamad Medical Corporation (HMC- responsible for secondary and tertiary care) for its registered population (Qataris and Expatriates). A small number of private clinics and hospitals also operate in the country. PHCC is the largest primary health care provider in Qatar. Majority of the country’s population is registered with PHCC. As of June 2020, a total of 1,461,759 individuals were registered across 27 health centres, all of which are accredited by Accreditation Canada.
Study design and population
The study was designed to include three phases. A 3-month time interval was planned between each phase. Each phase was planned to be conducted within a three-week time duration. Asymptomatic individuals registered with a mobile number on PHCC electronic medical records and ≥ 10 years of age were eligible for inclusion. Individuals below 10 years were excluded for practical reasons. Individuals with difficulties related to mobility and communication, bleeding disorders and mental disabilities were excluded.
A stratified random sampling technique was utilized to identify the study sample. 16 strata were defined using age, gender nationality and their sub-categories. The sample size for each stratum was calculated using the total PHCC registered population within it. The required total sample size for the study was estimated to be 2102. Further details of stratification and sample size calculation are provided in the supplementary file.
Participant recruitment
A full list of eligible participants (N = 1,063,243) was extracted from PHCC’s electronic medical records system with their health record number, name, age, gender, nationality and mobile phone number. Participants were randomly selected to create 5 sets of the required sample in anticipation of a non-response rate of 80%. Participants were sent Short Message Service (SMS) messages on their mobile phones inviting them to participate in the study. Recruitment rates were reviewed at the end of week 1 and week 2 during the 3-week study duration to facilitate targeted invitations by strata in the following week.
Study locations and data collection
Participants were invited to an appointment at one of three PHCC health centres (Qatar University, Al Wakrah and Al Wajbah) identified for the study which operated in two shifts (8 am – 2 pm and 4 pm – 8 pm). In each of the health centres, a separate room with a direct entrance from outside was set up to see patients. The room was divided in 3 stations – Patient registration, patient interview and sample collection station. The rooms were set up as such to facilitate smooth patient flow while adhering to strict social distancing and infection control protocols.
On arrival for their appointment, participants were registered on the electronic medical records system at the registration station. Following registration, at the patient interview station, a member of the research team briefed the participant about the study and obtained written informed consent from adults or assent from minors. Participants were administered an electronic interview based questionnaire that included questions on sociodemographic factors (education level, employment status, number of rooms and individuals in household), lifestyle (physical activity, smoking status, fruit consumption, vegetable or salad consumption, fruit juice consumption), history of chronic conditions (supplementary file), Bacillus Calmette–Guérin (BGC) and influenza vaccine status, previous RT-PCR status, COVID-19 related symptoms and contact with suspected or confirmed cases. Participants' height and weight were also recorded. At the sample collection station, nasal and oropharyngeal swab and blood samples were collected. Prior training was provided to all data collection personnel. They were always supervised by a core research team member to ensure adherence to agreed common protocols.
Laboratory procedures
Both nasal and oropharyngeal swab samples were collected from all participants. The swabs were labelled and transported from the study location to the referral laboratory for the state of Qatar’s at the end of each shift. RNA was extracted and isolated prior to amplification on a number of platforms. These included: ExiPrep 96 Viral DNA/RNA Kit (Bioneer Corporation, South Korea Cat Number K-4614); Chemagic STARS Viral DNA/RNA 300 Kit (Perkin Elmer, US, Cat Number CMG-1774); EZ1 Virus Mini Kit v2.0 (QIAGEN, US Cat Number 955134); Nucleic Acid Extraction Kit (Wuhan MGI Tech Co Ltd., China (Cat Number 1000021043).
Extracted nucleic acid underwent thermal cycling on ABI 7500 Thermal Cyclers (ThermoFischer, US). using a number of thermal mixes. These included: Taqpath Covid 19 RT PCR (ThermoFisher, US, A48102); AccuPower SARS-COV2 RT PCR (Bioneer Corporation, South Korea Cat Number SCV-2122); GeneFinder (OSANG Healthcare Co., Ltd. China, Cat Number IFMR-45. Additionally, 2 fully automated systems combining nucleic acid extraction and thermal cycling were operational. These included: Cobas SARS-CoV2 (Roche, Germany, Cat Number P/N:09175431190); GeneXpert SARS-CoV2 (Cepheid, US Cat Number XPRSARS-COV2–10). A total of 5 different RNA genes in different combinations as dictated by the commercial suppliers were amplified. Each assay was validated for cycle threshold (CT) value interpretation using the manufacturer’s instructions.
Blood samples were labelled and stored at the study location and transported every 24 h to Qatar University’s Biomedical Research Centre laboratory where plasma was separated by centrifugation. 150 μL of plasma was used for detection of anti-SARS-COV2 Immunoglobulin G (IgG) using the CL-900i Chemiluminescence Immunoassay System (Mindray Bio-Medical Electronics Co, Shenzen, China) according to the manufactures instructions. Immunoglobulins were directed against the spike protein (S subunit). The CL-series SARS-COV2 IgG assay is designed to have a precision of ≤10%. Precision was determined according National Committee for Clinical Laboratory Standards (NCCLS) Protocol EP15-A37 (as specified by the manufacturer). The analytical performance of CL-series SARS-CoV2 IgG immunoassay (Cat. No. SARS-CoV2 IgG121) was evaluated using previous RT-PCR test (as a gold standard) results stratified by the symptom category at the time of swab (supplementary file).
Notification of laboratory results
Participants with negative RT-PCR test results were notified by SMS messages. Participants with positive RT-PCR test results were contacted by the Qatar’s Ministry of Public Health for further advice and care provided as required. All blood test results were notified by SMS.
Data analysis
All data was collated at the end of phase one. It was subject to quality assurance. For the purposes of this study, point prevalence was defined as the number of active asymptomatic SARS-CoV2 infections (identified by RT-PCR) over the total sample size while period prevalence was defined as the total number of SARS-CoV2 infections [either identified by RT-PCR or serology (IgM and IgG)] over the total sample size. Initial analysis was undertaken to establish the overall point and period prevalence. Further analysis was undertaken to estimate prevalence by age, gender, nationality (supplementary file) and municipalities. Period prevalence was also estimated by sociodemographic [education level, employment status, household crowding index (HCI)], lifestyle [body mass index (BMI), physical activitysmoking status, fruit consumption, vegetable or salad consumption and fruit juice] and clinical characteristics (BGC and seasonal influenza vaccine status, history of chronic diseases COVID-19 related symptoms and previous contact with suspected or confirmed case).
The 95% confidence intervals (CIs) were calculated for proportions (prevalence rates). Chi-square test of independence was used to assess the statistical significance of associations between nominal or ordinal scale variables. To measure the strength of association between a dichotomous independent variable (a specific group compared to reference group) and a dichotomous outcome variable (having COVID-19) the prevalence ratio (PR) was used. The logarithm method was used in calculation of confidence intervals for the calculated PR. P value less than the 0.05 level of significance was considered statistically significant. All statistical analyses were done using survey commands in IBM SPSS Statistics for Windows (Version 23.0. Armonk, NY: IBM Corp.)..
Ethical considerations
The study was reviewed and approved by Primary Health Care Corporation’s Independent Review Board (Reference number PHCCDCR202005047). Written informed assent was obtained from participants aged 10–18 years and written informed consent was obtained from participants aged 18 or over. Only MAS, ASAN and HAQ had access to the full study data. Overall, the study was conducted with integrity according to generally accepted ethical principles.