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ABSTRACT: Objectives: Mycobacterium tuberculosis (MTB) is a global public health issue. Although Oman reduced the burden of tuberculosis (TB) by 85% in under 25 years, the annual incidence rate remains stagnant. Whole genome sequencing (WGS) is used to investigate the transmission dynamics of MTB complex. This study aimed to resolve traditional genotype clusters and exploring the geospatial distribution to understand the epidemiology of TB in Oman. Methods: Confirmed cases with spoligotyping clusters were randomly selected. WGS of 70 isolates were selected for final analysis. Correlation of epidemiological and geospatial data was conducted. Results: A total of 233 cases were registered in 2021; 169 had confirmed growth, with an incidence rate of 5.2/100,000 population for 2021. A total of 70 genomes were analyzed, and five large clusters and three medium clusters were identified. The lineages L1, L2, L3, and L4 and several sublineages belonging to the Indo-Oceanic family and East African Indian family were identified as predominant in Oman. There were no multidrug-resistant cases identified. Conclusion: There is a considerable genetic variation among the strains in Oman. This predominance could be linked with the high percentage of non-national population, which represents different countries and frequent traveling to high TB burden countries. WGS combined with geospatial investigations of MTB are required to better understand the disease transmission in Oman, which will support TB elimination efforts.

ABSTRACT: Objective: To assess the seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Oman and longitudinal changes in antibody levels over time within the first 11 months of the coronavirus disease 2019 (COVID-19) pandemic. Methods: This nationwide cross-sectional study was conducted as a four-cycle serosurvey using a multi-stage stratified sampling method from July to November 2020. A questionnaire was used and included demographics, history of acute respiratory infection and list of symptoms, COVID-19 contact, previous diagnosis or admission, travel history and risk factors. Results: In total, 17,457 participants were surveyed. Thirty percent were female and 66.3% were Omani. There was a significant increase in seroprevalence throughout the study cycles, from 5.5% (4.8–6.2%) in Cycle 1 to 22% (19.6–24.6%) in Cycle 4. There was no difference in seroprevalence between genders, but significant differences were found between age groups. There was a transition of seroprevalence from being higher in non-Omanis than Omanis in Cycle 1 [9.1% (7.6–10.9%) vs 3.2% (2.6–3.9%)] to being higher in Omanis than non-Omanis in Cycle 4 [24.3% (21.0–27.9%) vs 16.8% (14.9–18.9%)]. There was remarkable variation in the seroprevalence of SARS-CoV-2 according to governorate. Close contacts of people with COVID-19 had a 96% higher risk of having the disease [adjusted odds ratio (AOR) 1.96, 95% confidence intervals (CI) 1.64–2.34]. Labourers had 58% higher risk of infection compared with office workers (AOR 1.58, 95% CI 1.04–2.35). Conclusion: This study showed a wide variation in the spread of SARS-CoV-2 across governorates in Oman, with higher estimated seroprevalence in migrants in the first two cycles. Prevalence estimates remain low and are insufficient to provide herd immunity.

Objective: To determine the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare workers (HCWs) based on risk of exposure to COVID-19 patients. Method: This was a SARS-CoV-2 seroprevalence cross-sectional study in risk-stratified HCWs randomly selected from three main district hospitals in Oman. Results: 1078 HCWs were included, with an overall SARS-CoV-2 seroprevalence of 21%. The seropositivity rates in low-, variable-, and high-risk groups were 29%, 18%, and 17%, respectively (p-value < 0.001). The study found higher positivity in males (crude odds ratio [COR] 1.71, 95% confidence interval [CI] 1.28–2.3), and workers residing in high-prevalence areas (COR 2.09, 95% CI 1.42–3.07). Compared with doctors, workers from supporting services, administration staff, and nurses were more likely to test positive for SARS-CoV-2 antibodies (COR 9.81, 95% CI 5.26–18.27; 2.37, 95% CI 1.23–4.58; 2.08 95% CI 1.14–3.81). The overall rate of previously undetected infection was 12%, with higher values in low-risk HCWs. High district prevalence was a driving factor for seropositivity in the low-risk group (adjusted odds ratio [AOR] 2.36, 95% CI 1.0–5.59). Conclusion: Low-risk supporting services workers can drive SARS-CoV-2 transmission in hospitals. More attention and innovation within this area will enhance the safety of health care during epidemics/pandemics.

Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been proven to be lethal to human health, which affects almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficiency of the contact tracing system in Oman. Methods: We combined epidemiological data and whole-genome sequence data from 94 samples of SARS-CoV-2 in Oman to understand the origins, genetic variation, and transmissibility. The whole-genome size of sequence data was obtained through a customized SARS-COV-2 research panel. Amplifier methods ranged from 26 Kbp to 30 Kbp and were submitted to GISAID. Findings: The study found that P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). In addition, the study revealed a good agreement between genetic and epidemiological data. Interpretation: Oman’s robust surveillance system was very efficient in guiding the outbreak investigation processes in the country, the study illustrates the future importance of molecular epidemiology in leading the national response to outbreaks and pandemics.

Background: Mortality surveillance provides a crucial method for monitoring disease activity. Coronavirus disease 2019 (COVID-19) can cause excess mortality both directly and indirectly by increasing deaths from other diseases. The aim of this study was to investigate the effects of COVID-19 on mortality in Oman. Methods: A cross-sectional retrospective analysis of mortality data from 1 January 2015 to 16 August 2020 was undertaken. Baseline mortality estimated using the Farrington flexible model and excess mortality were calculated for the pandemic period (16 March–16 August 2020) according to cause of death, place of death and age group. Results: During the pandemic period, there was a 15% [95% confidence interval (CI) 14–17] increase in all-cause mortality from baseline. When classifying by cause, there was a 9% (95% CI 5–12) increase in deaths due to respiratory diseases, a 2% (95% CI 1–4) increase in deaths due to infectious diseases and a 9% (95% CI 8–11) increase in unclassified deaths. In terms of place of death, 12% (95% CI 11–14) of excess mortality occurred in hospitals and 7% (95% CI 5–8) occurred in homes during the pandemic period. Patients aged >60 years recorded a 15% (95% CI 13–16) increase in all-cause mortality during this period. Conclusion: The COVID-19 pandemic has resulted in a 15% increase in all-cause mortality in Oman, mainly as a result of deaths from COVID-19. However, unclassified deaths, deaths due to respiratory diseases and deaths due to infectious diseases have also increased, enforcing the need for a holistic approach and appropriate coordination of health services during such health crises.

Background: COVID-19’s emergence carries with it many uncertainties and challenges, including strategies to manage the epidemic. Oman has implemented non-pharmaceutical interventions (NPIs) to mitigate the impact of COVID-19. However, responses to NPIs may be different across different populations within a country with a large number of migrants, such as Oman. This study investigated the different responses to NPIs, and assessed the use of the time-varying reproduction number (Rt) to monitor them. Methods: Polymerase chain reaction (PCR) laboratory-confirmed COVID-19 data for Oman, from February 24 to June 3, 2020, were used alongside demographic and epidemiological information. Data were arranged into pairs of infector–infectee, and two main libraries of R software were used to estimate reproductive number (Rt). Rt was calculated for both Omanis and non-Omanis. Findings: A total of 13,538 cases were included, 44.9% of which were Omanis. Among all these cases we identified 2769 infector–infectee pairs for calculating Rt. There was a sharp drop in Rt from 3.7 (95% confidence interval [CI] 2.8–4.6) in mid-March to 1.4 (95% CI 1.2–1.7) in late March in response to NPIs. Rt then decreased further to 1.2 (95% CI 1.1–1.3) in late April after which it rose, corresponding to the easing of NPIs. Comparing the two groups, the response to major public health controls was more evident in Omanis in reducing Rt to 1.09 (95% CI 0.84–1.3) by the end of March. Interpretation: Use of real-time estimation of Rt allowed us to follow the effects of NPIs. The migrant population responded differently than the Omani population.

Objective: To describe the clinical and epidemiological profiles of HIV-infected Omani children before and after the implementation of the prevention of mother-to-child transmission of HIV (PMTCT) programme. Methods: A retrospective review of HIV-infected children seen at a national paediatric HIV unit between 1992 and 2015 was performed. Results: Ninety-one HIV-infected children were identified; 59 (65%) were ≤5 years of age at diagnosis, with 28 (47.5%) of these being

Background: In December 2018, routine surveillance identified an autochthonous outbreak of dengue fever in Muscat Governorate, Oman, a region previously free of dengue fever. Methods: Routine surveillance confirmed locally acquired cases in the second week of December, leading to a rapid public health response including case management guidance and epidemiological investigations. The main activity was the vector survey using systematic sampling to assess extent of previously unreported Aedes aegypti presence followed by a campaign aimed to eliminate breeding sites of A. aegypti”. Results: During a 5-month period, 343 suspected cases were reported from Muscat Governorate with 122 from the outbreak affected area. Out of 207 probable cases eligible for laboratory testing as per guidelines issued, 59 cases were confirmed. The vector elimination campaign started on January 8, 2019 after a media advocacy using television and social media and concluded on January 23. By the end of campaign, the case load had decreased significantly in the affected area with no reports of locally acquired cases from adjoining areas of Muscat Governorate, indicating no further spread. Conclusions: Rapid notification and early community-wide, extensive vector control activities effectively contained the autochthonous dengue fever virus outbreak. Keywords: Dengue fever, Autochthonous outbreak, Oman, Aedes aegypti, Vector-borne illness, Disease surveillance