Epidemiology of SARS-CoV2 in Qatar’s primary care population aged 10 years and above

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.

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.

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.

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).

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.

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 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.

Of 18,918 individuals invited for the study, 2044 participated (response rate 10.8%). The recruited sample was 97.2% complete compared to the initially planned study sample (Table 1). Overall, more Qataris were recruited by 6.4%) while expatriates were under recruited by 2.8%. Qatari female 18–49 years (N = − 27; − 25.5%), Qatari females ≥60 years (N = -8; − 34.8%) and expatriate females 18–49 years (N = − 98; − 21.5%) were the most under recruited. Qatari males 10–17 years (N = 24; 44.4%), Qatari females 10–17 years N = 18; 34.6%), and expatriates male ≥60 years (N = 10; 18.9%), were the most over recruited.

Based on the information collected in the questionnaire, it was found that 3.6% (N = 74) study participants had previously tested positive by RT-PCR (Table 2). Of the 2044 participants, 1.6% were found to have an active SARS-CoV2 infection by RT-PCR and 13.3% (N = 272) were found to have had a previous SARS-CoV2 infection by serology. Based on these findings, in Qatar, the overall point prevalence was estimated to be 1.6% (95% CI 1.1–2.2) and period prevalence was estimated to be 14.6% (95% CI 13.1–16.2) (Table 2).

Point prevalence was found to be almost similar across all ages (range 1.4–1.9%) except in ≥60 (0%) (Table 3). Furthermore, point prevalence between females (1.5%; 95% CI 0.8–2.4%) and males (1.6%; 95% CI 1–2.5%) was found to be almost similar. Active SARS-CoV2 infection was found to be highest in North American (3.1%; 95% CI 0.3–13.7%) and Southern Asian nationalities (3%; 95% CI 1.7–4.8%). Point prevalence was lowest in Qatari and Northern African nationalities (0.6 and 0.7% respectively). In terms of geographic region. Al Khor municipality had the highest point prevalence (6.3%; 95% CI 1.8–15.7%) compared to all other municipalities in Qatar.

Period prevalence of SARS-CoV2 infection was not considerably different across age groups (Table 4). It ranged from 14.4–19.8% in participants aged 18 and above. It was lowest in 10–17 age group (9.7%; 95% 6.9–13.1%). SARS-CoV2 infection rate in males was higher than that of females (16. 3 and 12.7% respectively). A significant variation of infection rates was observed by nationality. It ranged from 5.7 to 22.2% with lowest rates in European (5.7%; 95% CI 2.2–12.1%) and Qatari nationalities (7.1%; 5–9.6%). Highest rates were found in Northern African nationalities (19.3%: 95% CI 15.7–23.3%) and Southern Asian (22.2%; 95% CI 18.6–26.2%). By geographic region, Al Shahaniya (35.3%; 95% 16.3–58.9%) and Al Shamal (40%; 9.4–79.1%) municipalities had the highest prevalence rates while Al Daayen municipality had the lowest prevalence rates (6.9%; 95% CI 3.3–12.6%).

Period prevalence of SARS-CoV2 infection did not differ by education levels except in participants with a technical or trade qualification, who were found to have a higher prevalence (20.5%) (Table 5). However, a notable difference in prevalence was seen by employment status. Participants who were retired (6.7%) or students (9.1%) had the lowest prevalence. Similarly, participants with a higher household crowding index had a higher prevalence of SARS-CoV2 infection (≤ 1 = 13.4%; 1.1–2 = 14.5% and > 2 = 20.6%).

Slightly higher prevalence was seen in participants who were either overweight (16.4%) or obese (15.5%) compared to healthy (12.1%) participants. Ex-smokers showed slightly higher prevalence (17.5%) compared to, current (12.3%) and non-smokers (14.8%). In current smokers, those who smoked more had a lower prevalence (8–10.2%) compared to those who smoked least (20.2%). No significant differences were seen related to physical activity or fruit juice consumption. Consuming fruits or vegetable or salads more than once a week found to have lower prevalence rates 8.8% (95% CI 4.9–14.4%) and 5.7 (95% CI 2.4–11.4) respectively.

A history of a BCG or influenza vaccination in previous 12 months did not show a difference in prevalence amongst participants (BCG Yes- 14.4% and No − 14.9; Influenza Yes- 15.8 and No – 14.4). However, a history of 3 or more chronic conditions showed a higher prevalence (24.5%) compared to having two or less chronic conditions (13.7–16.6%). The prevalence was higher in participants who had one or more COVID-19 symptoms since the start of the pandemic (40.7%) compared to those who were asymptomatic (11.6%). Similarly, the prevalence was higher in those who had close contact with an individual suspect or confirmed of COVID-19 (36.9%) compared with those who did not (12.7%).