One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar.

Qatar, a country with a strong health system and a diverse population consisting mainly of expatriate residents, has experienced two large waves of COVID-19 outbreak. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population's genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number of mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. These findings raise the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor the SARS-CoV-2 profile and re-emergence in Qatar.

SARS-CoV-2 infection in mortuary and cemetery workers.

BACKGROUND: Mortuary and cemetery workers may be exposed to the bodies of people with SARS-CoV-2 infection; however, prevalence of infection among these groups is unknown. METHODS: Nasopharyngeal swabs (NPS) for RT-PCR and serologic testing for SARS-CoV-2 were performed on mortuary and cemetery workers in Qatar. Data on specific job duties, living conditions, contact history, and clinical course were gathered. Environmental sampling was carried out to explore any association with infection. Logistic regression analysis was used to determine the factors associated with infection. RESULTS: Forty-seven mortuary workers provided an NPS and seven (14.9%) were PCR positive; 32 provided a blood sample and eight (25%) were antibody positive, six (75%) who were seropositive were also PCR positive. Among the 81 cemetery workers, 76 provided an NPS and five (6.6%) were PCR positive; 64 provided a blood sample and 22 (34.4%) were antibody positive, three (13.6%) who were seropositive were also PCR positive. Three (22.2%) and 20 (83.3%) of the infected mortuary and cemetery workers were asymptomatic, respectively. Age <30 years (OR 4.9, 95% CI 1.7-14.6), community exposure with a known case (OR 4.7, 95% CI 1.7-13.3), and presence of symptoms in the preceding 2 weeks (OR 9.0, 95% CI 1.9-42.0) were independently associated with an increased risk of infection (PCR or antibody positive). Of the 46 environmental and surface samples, all were negative or had a Ct value of >35. CONCLUSION: A substantial proportion of mortuary and cemetery workers had evidence of SARS-CoV-2 infection, which was incidentally detected upon serologic testing. These data are most consistent with community acquisition rather than occupational acquisition.

COVID-19 (SARS-CoV-2) outbreak monitoring using wastewater-based epidemiology in Qatar.

Raw municipal wastewater from five wastewater treatment plants representing the vast majority of the Qatar population was sampled between the third week of June 2020 and the end of August 2020, during the period of declining cases after the peak of the first wave of infection in May 2020. The N1 region of the SARS-CoV-2 genome was used to quantify the viral load in the wastewater using RT-qPCR. The trend in Ct values in the wastewater samples mirrored the number of new daily positive cases officially reported for the country, confirmed by RT-qPCR testing of naso-pharyngeal swabs. SARS-CoV-2 RNA was detected in 100% of the influent wastewater samples (7889 ± 1421 copy/L - 542,056 ± 25,775 copy/L, based on the N1 assay). A mathematical model for wastewater-based epidemiology was developed and used to estimate the number of people in the population infected with COVID-19 from the N1 Ct values in the wastewater samples. The estimated number of infected population on any given day using the wastewater-based epidemiology approach declined from 542,313 ± 51,159 to 31,181 ± 3081 over the course of the sampling period, which was significantly higher than the officially reported numbers. However, seroprevalence data from Qatar indicates that diagnosed infections represented only about 10% of actual cases. The model estimates were lower than the corrected numbers based on application of a static diagnosis ratio of 10% to the RT-qPCR identified cases, which is assumed to be due to the difficulty in quantifying RNA losses as a model term. However, these results indicate that the presented WBE modeling approach allows for a realistic assessment of incidence trend in a given population, with a more reliable estimation of the number of infected people at any given point in time than can be achieved using human biomonitoring alone.

Environmental surface contamination with SARS-CoV-2 in professional football clubs.

Background: We assessed SARS-CoV-2 contamination of random surfaces in football training facilities in an environment with a high prevalence of infections.Methods: In six clubs of the Qatar Stars League, surfaces of random locations (high-touch areas, ventilation systems, toilets, cleaning tools, freezers, pantries) in routinely cleaned training facilities, locker rooms, medical and administrative areas were swabbed for SARS-CoV-2. The swabs were screened for the presence of viral RNA using a SARS-CoV-2 qPCR Probe Assay.Results: None of the 103 swabs reached a cycle threshold (cT) value ≤30 (strong viral presence, suggestive of potential surface transmission). Four samples showed cT values >30 and <35 (low quantity of virus) and 16 swabs returned a cT value ≥35 and <40 (inactive virus remnants). The remaining 83 samples were negative (cT value ≥40). Most samples with viral or viral remnant presence originated from high-touch areas.Conclusion: We did not find evidence for potential surface transmission in football club facilities when routine cleaning procedures are in place despite the presence of infected subjects.