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1.
Pathogens ; 11(5)2022 May 04.
Article in English | MEDLINE | ID: covidwho-1875723

ABSTRACT

STUDY AIM: Effective Tuberculosis (TB) control measures in Oman have reduced the annual incidence of tuberculosis cases by 92% between 1981 and 2016. However, the current incidence remains above the program control target of <1 TB case per 100,000 population. This has been partly attributed to a high influx of migrants from countries with high TB burdens. The present study aimed to elucidate Mycobacterium tuberculosis infection dynamics among nationals and foreigners over a period of 10 years. Methods. The study examined TB cases reported between 2009 and 2018 and examined the spatial heterogeneity of TB cases and the distribution of M. tuberculosis genotypes defined by spoligotypes and MIRU-VNTR among Omanis and foreigners. Results. A total of 484 spoligoprofiles were detected among the examined isolates (n = 1295). These include 943 (72.8%) clustered and 352 (27.2%) unique isolates. Diverse M. tuberculosis lineages exist in all provinces in Oman, with most lineages shared between Omanis and foreigners. The most frequent spoligotypes were found to belong to EAI (318, 30.9%), CAS (310, 30.1%), T (154, 14.9%), and Beijing (88, 8.5%) lineages. However, the frequencies of these lineages differed between Omanis and foreigners. Of the clustered strains, 192 MTB isolates were further analysed via MIRU-VNTR. Each isolate exhibited a unique MIRU-VNTR profile, indicative of absence of ongoing transmission. Conclusions. TB incidence exhibits spatial heterogeneity across Oman, with high levels of diversity of M. tuberculosis lineages among Omanis and foreigners and sub-lineages shared between the two groups. However, MIRU-VNTR analysis ruled out ongoing transmission.

2.
Int J Infect Dis ; 112: 269-277, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1654549

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.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , Cross-Sectional Studies , Female , Humans , Male , Oman/epidemiology , Seroepidemiologic Studies , Surveys and Questionnaires
3.
Front Public Health ; 9: 770946, 2021.
Article in English | MEDLINE | ID: covidwho-1591003

ABSTRACT

Despite the apparent challenges inflicted by COVID-19 globally, the pandemic provided an opportunity to utilize and expand existing public health capacities for a more adaptive and resilient system during and after each wave of the disease. This paper provides a narrative review of Oman's public health response to the COVID-19 pandemic from January 2020 to July 2021, and the challenges it faced for a more rapid and efficient response. The review demonstrates that the three main pillars influencing the direction of the pandemic and aiding the control are Oman's unified governmental leadership, the move to expand the capacity of the health care system at all levels, and community partnership in all stages of the response including the COVID-19 vaccination campaign. The opportunities identified during response stages in the harmonization of the multisectoral response, streamlining communication channels, addressing vulnerable communities (dormitories, residences at border regions), and providing professional technical leadership provide an excellent precursor for expediting the transformation of Oman's health care system to one with a multisectoral holistic approach. Some of the major challenges faced are the shortage of the public health cadre, lack of a fully integrated digital platform for surveillance, and the scarcity of experts in risk communication and community engagement. A future health system where the center for diseases surveillance and control acts as a nucleus for multisectoral expertise and leadership, which includes community representatives, is crucial to attain optimum health. The destruction inflicted by this prolong COVID-19 pandemic at all levels of human life had valued the importance of investing on preventive and preparedness strategies.


Subject(s)
COVID-19 , Pandemics , COVID-19 Vaccines , Health Services , Humans , Oman/epidemiology , Pandemics/prevention & control , SARS-CoV-2
4.
Oman Med J ; 36(5): e297, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1526934

ABSTRACT

OBJECTIVES: Considering the increasing, significant burden that coronavirus disease 2019 (COVID-19) imposes on the healthcare system, the need for simple, rapid, and affordable diagnostic tests to support the existing costly and demanding polymerase chain reaction (PCR) assay becomes required. This prospective diagnostic test accuracy study aims to evaluate the performance of four different COVID-19 rapid antigen tests compared to real-time reverse transcription PCR (rRT-PCR) between June and July 2020 to determine the feasibility of integrating these tests into the diagnostic algorithm in clinical settings. METHODS: Swabs were collected from 306 patients and analyzed using rRT-PCR and antigen tests from four different providers. RESULTS: The antigen tests' sensitivities were 65.8%, 69.8%, 64.0%, and 64.3% for the STANDARD™ Q COVID-19 Ag test, PCL COVID-19 Ag Rapid fluorescent immunoassay (FIA) test, BIOCREDIT COVID-19 Ag test, and Sofia SARS-CoV-2 antigen FIA test, respectively. Specificity was 94.1% for PCL COVID-19 Ag Rapid test and 100% for the other three assays. All assays showed a significant negative correlation between the reference rRT-PCR Ct values and Ag test results. Besides, sensitivities of the STANDARD™ Q COVID-19 Ag test, PCL COVID-19 Ag Rapid FIA test, and BIOCREDIT COVID-19 Ag test improved to ≥ 85% after exclusion of samples with PCR Ct values > 30. CONCLUSIONS: The high specificity of the rapid antigen tests and other parameters like simplicity, rapidity, and affordability suggest that antigen tests are likely to be helpful if integrated and interpreted appropriately in stepwise diagnostic algorithms. Given the low sensitivity of 64.0-69.8% of the antigen tests, we recommend that clinically relevant negative results undergo further testing Ag to confirm or exclude a COVID-19 diagnosis.

5.
Int J Environ Res Public Health ; 18(19)2021 10 08.
Article in English | MEDLINE | ID: covidwho-1463672

ABSTRACT

BACKGROUND: Non-pharmaceutical interventions (NPIs), particularly mobility restrictions, are mainstay measures for the COVID-19 pandemic worldwide. We evaluated the effects of Oman's mobility restriction strategies to highlight their efficacy in controlling the pandemic. METHODS: Accessible national data of daily admissions and deaths were collected from 1 April 2020 to 22 May 2021. Google Community Mobility Report (CMR) data were downloaded for the same period. Among six CMR categories, three were used and reduced to one index-the community mobility index (CMI). We used a generalised linear model with a negative binomial distribution combined with a non-linear distributed lag model to investigate the short-term effects of CMI on the number of admitted PCR-confirmed COVID-19 cases and deaths, controlling for public holidays, day of the week, and Eid/Ramadan days. RESULTS: We demonstrated the feasibility of using CMRs in the evaluation and monitoring of different NPIs, particularly those related to movement restriction. The best movement restriction strategy was a curfew from 7 p.m. to 5 a.m. (level 3 of CMI = 8), which had a total reduction of 35% (95% confidence interval (CI); 25-44%) in new COVID-19 admissions in the following two weeks, and a fatality reduction in the following four weeks by 52% (95% CI; 11-75%). CONCLUSION: Evening lockdown significantly affected the course of the pandemic in Oman which lines up with similar studies throughout the world.


Subject(s)
COVID-19 , Pandemics , Communicable Disease Control , Hospitalization , Humans , Pandemics/prevention & control , SARS-CoV-2
6.
J Infect Public Health ; 14(11): 1590-1594, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1461378

ABSTRACT

BACKGROUND: In Oman, many extended families tend to live in one household. Some families can include 20-30 individuals with the majority of them being children. This study investigates the role of children in spreading SARS-CoV-2 causing COVID-19 within family clusters in Oman. METHODS: This retrospective study includes data of 1026 SARS-CoV-2 positive children (≤18 years) collected from the national surveillance database for COVID-19 between 1 February 2020 and 30 May 2020. RESULTS: We included 1026 patients. Most, 842 were Omani (82%), 52% male, and 28.5% asymptomatic. Close to the half of symptomatic 419 (40%), patients presented with fever associated with other respiratory symptoms. Fifty pediatric patients were index cases who transmitted the virus to 107 patients in total (86 adults and 21 children) with a mode of 1. There is no statistical significance of all studied risk factors in the transmission of the SARS-CoV-2 virus including age, gender, and cycle threshold (CT) value. CONCLUSIONS: According to this study, children are not to be considered a significant driver of transmission of SARS-CoV-2 in Oman.


Subject(s)
COVID-19 , SARS-CoV-2 , Adolescent , Adult , Child , Female , Humans , Male , Oman/epidemiology , Retrospective Studies , Risk Factors
7.
Pan Afr Med J ; 40: 2, 2021.
Article in English | MEDLINE | ID: covidwho-1449273

ABSTRACT

In response to the current COVID-19 pandemic, numerous commercial assays have been developed for the detection of SARS-CoV-2 for use in the clinical diagnostic laboratories. To date, there is limited comparison of testing methods performed in different hospital laboratory sites. The aims of the study were to evaluate the analytical performance of Cepheid Xpert Xpress SARS-CoV-2 when compared to RT-PCR. This is a cross-sectional study. A total of 155 nasopharyngeal swabs were taken in duplicate from patients presenting with suspected COVID-19 to 8 hospitals in Oman. One swab was tested by the hospital laboratory and the duplicate swab was sent to the national Central Public Health Laboratory (CPHL) for testing. We compared the analytical performance of the commercially available point of care Cepheid Xpert Xpress SARS-CoV-2 assay which was used in the 8 different hospitals with assays including Liferiver, Sansure, TIB MOL BIOL, Kingfisher and COBAS 6800 by Roche which were performed at the CPHL. Testing of the duplicate swabs revealed excellent agreement of results with the viral loads of Ct values ranging from 16-43 for the E gene, 18-44 for the N gene and 17-44 for the ORF gene using the Liferiver assay. The overall sample sensitivity and specificity of the Cepheid Xpert Xpress SARS-CoV-2 assay were both 100% and there was 100% agreement across specimens. We conclude that the rapid GeneXpert and RT-PCR kits assessed in this study may be used for routine diagnostic testing of COVID-19 patients by experienced clinical microbiology diagnostic laboratories. Our results highlight the importance of rapid molecular testing at different sites within a country in a public health emergency.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Clinical Laboratory Techniques , SARS-CoV-2/isolation & purification , Cross-Sectional Studies , Humans , Laboratories, Hospital , Molecular Diagnostic Techniques/methods , Oman , Point-of-Care Testing , RNA, Viral/genetics , Sensitivity and Specificity , Specimen Handling , Viral Load
8.
Int J Infect Dis ; 107: 257-263, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1300801

ABSTRACT

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.


Subject(s)
COVID-19/transmission , Health Personnel , SARS-CoV-2 , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Seroepidemiologic Studies
9.
Sultan Qaboos Univ Med J ; 21(2): e195-e202, 2021 May.
Article in English | MEDLINE | ID: covidwho-1296285

ABSTRACT

OBJECTIVES: The aim of the current study was to describe COVID-19's epidemiological characteristics in Oman during the initial stages of the outbreak and compare findings with other countries' reports. METHODS: Data were drawn from a descriptive, records-based review of reported cases of COVID-19 collected through the national COVID-19 Surveillance System from February to April 2020. RESULTS: A total of 2,443 confirmed cases were reported during the study period. The overall first-time testing rate for this period was 851.7 per 100,000, the positivity rate was 53.1 (confidence intervals [CI]: 51.0-55.2) and the death rate was 0.32 (CI: 0.20-0.54) per 100,000 population, respectively. The overall national positive ratio was 5.7% and ranged from 2.2-7.1% across various governorates. Muscat Governorate had the highest positive ratio (12.5%). People in the 51-60 year old age group (RR = 1.97), males (RR = 1.24), non-Omanis (RR = 2.33) and those living in Muscat (RR = 2.14) emerged as categories with significant demographic risk for COVID-19 cases when compared to the national average. The mean age was 35.6 ± 13.4. Asymptomatic cases accounted for nearly 16%. CONCLUSION: The overall rate of COVID-19 cases and deaths were low in Oman compared to the rest of the world during the study period.


Subject(s)
COVID-19/epidemiology , Pandemics , Adolescent , Adult , Aged , Aged, 80 and over , Child , Child, Preschool , Cough/epidemiology , Female , Fever/epidemiology , Fever/etiology , Humans , Infant , Male , Middle Aged , Oman/epidemiology , SARS-CoV-2 , Young Adult
10.
Int J Infect Dis ; 104: 139-149, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-997022

ABSTRACT

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.


Subject(s)
COVID-19/epidemiology , Genome, Viral/genetics , Pandemics , SARS-CoV-2/genetics , Adolescent , Adult , COVID-19/transmission , COVID-19/virology , Child , Child, Preschool , Epidemiological Monitoring , Female , Humans , Infant , Male , Middle Aged , Molecular Epidemiology , Mutation , Oman/epidemiology , Phylogeny , SARS-CoV-2/isolation & purification , Whole Genome Sequencing , Young Adult
11.
Int J Infect Dis ; 104: 102-107, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-988040

ABSTRACT

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.


Subject(s)
COVID-19/mortality , Pandemics , SARS-CoV-2/physiology , Adult , Aged , COVID-19/complications , COVID-19/epidemiology , COVID-19/virology , Cross-Sectional Studies , Epidemiological Monitoring , Female , Humans , Male , Middle Aged , Mortality , Oman/epidemiology , Retrospective Studies
13.
Int J Infect Dis ; 99: 466-472, 2020 Oct.
Article in English | MEDLINE | ID: covidwho-722005

ABSTRACT

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.


Subject(s)
Coronavirus Infections/epidemiology , Epidemiological Monitoring , Pneumonia, Viral/epidemiology , Transients and Migrants , Betacoronavirus , COVID-19 , Coronavirus Infections/therapy , Humans , Oman , Pandemics , Pneumonia, Viral/therapy , Public Health , SARS-CoV-2
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