Time trend of respiratory viruses before and during the COVID-19 pandemic in severe acute respiratory virus infection in the Sultanate of Oman between 2017 and 2022.

Introduction: Severe acute respiratory illness (SARI) is a potentially lethal condition, necessitating thorough medical care. COVID-19 underscored the SARI threat, but other high-risk pathogens require monitoring alongside SARS-CoV-2. Oman instituted a comprehensive testing system to gauge the prevalence of these pathogens between 2017 and 2021, aiding resource allocation and public health responses to potential respiratory pathogen outbreaks. Methods: Samples from SARI cases admitted to ICU were tested for pathogens using the Fast-Track Diagnostic (FTD) molecular assay, a respiratory virus panel (RVP) that tests for 21 pathogens, including 20 viruses, by qPCR. Results: Between 2017 and 2022, ~30 000 samples were analysed using the RVP panel. Among SARI patients, 8%-42% tested positive for respiratory pathogens, with 4% showing multiple infectious agents, especially in children under 10. A drop in positivity during 2020-2021 can be attributed to SARS-CoV-2 control measures, followed by a rebound in infections in early 2022. Discussion: The COVID-19 pandemic heightened awareness of respiratory pathogens' spread without adequate control measures. Influenza A/B, human rhinoviruses and respiratory syncytial virus constituted over 50% of severe acute respiratory illness cases in Oman over the past 5 years. During the pandemic, the incidence of these infections significantly declined, demonstrating the efficacy of COVID-19 prevention measures in reducing spread of other pathogens.

The Seroprevalence of Hepatitis C Virus (HCV) in Hemodialysis Patients in Oman: A National Cross-Sectional Study.

BACKGROUND: HCV infection in hemodialysis units is a significant cause of morbidity and mortality. The risk of HCV infection among dialysis patients is higher compared to the general population due to high potential blood exposures in hemodialysis settings. This study aims to assess the national HCV seroprevalence in selected dialysis units and to determine the risk factors for acquiring HCV infection. METHODS: This cross-sectional study was conducted from 1 January to 31 March 2021. A total of 734 patients from 11 hemodialysis centers in Oman were included. Samples were tested simultaneously for HCV antibodies and HCV RNA. HCV genotyping was determined in all viremic patients. Demographic and hemodialysis center related data were gathered and their association with the positive HCV serology were explored using univariate and multivariate logistic regression analysis. RESULTS: Out of 800 patients selected from 11 dialysis units for the study, 734 patients (91.8%) were included. The overall seroprevalence of HCV infection among hemodialysis patients was 5.6%. (41/734). HCV RNA was detected in 31.7% (13/41) of seropositive hemodialysis patients. The most common genotype was subtype 1a, followed by subtype 3. Variables associated with high HCV prevalence were family history of HCV and duration of dialysis. CONCLUSION: The prevalence of infection within hemodialysis patients in Oman has significantly decreased but remained higher than the general population. Continuous monitoring and follow-up, including periodic serosurvey and linkage to care and treatment are recommended. Additionally, practice audits are recommended for identifying gaps and ensuring sustainability of best practices and further improvement.

Correlation of Viral Load With the Biochemical and Hematological Profiles of COVID-19 Patients in Al Buraimi Hospital, Sultanate of Oman: A Cross-Sectional Study.

Background Rapid identification of COVID-19 is crucial during the pandemic for the treatment and management of patients. Thus, early diagnosis of the disease using laboratory parameters can help in the rapid management of infected patients. This study aimed to investigate the correlation of viral load with hematological and biochemical parameters. This will ultimately help physicians to better understand the dynamics of this novel virus and aid in the management of patients. Methodology Laboratory confirmation of SARS-CoV-2 was performed by reverse transcription-polymerase chain reaction (RT-PCR) at the Al-Buraimi Hospital Laboratory Department using oropharyngeal and nasopharyngeal swabs. Positive cases were collected from July 2020 to January 2021 to be enrolled in this study. Results In this study, 264 confirmed positive patients were included initially and divided into three groups according to their cycle threshold (Ct) values obtained by PCR. Out of the total 264 patients, 174 (65.9%) were male, while 90 (34.1%) were female. However, the final sample was only 253 patients who met the inclusion criteria. With regard to Ct values, the study population was divided into the following three groups: Group 1 with Ct values of 9-20 (n = 87; 34.4%), group 2 with Ct values of 21-30 (n = 122; 47.8%), and group 3 with Ct values of 31-42 (n = 44; 17.4%). Conclusions We found that the proportion of male patients infected with COVID-19 was higher compared to females. In addition, the highest incidence was among patients in the age group of 51-70 years. The ferritin and alanine transaminase levels were highest in the initial stage of the infection (group 1) and decreased at the recovery stage. However, neutrophil, lymphocyte, alkaline phosphatase, and C-reactive protein showed an increasing trend from high viral load groups to low viral load groups. The values of the rest of the parameters, such as albumin, total bilirubin, lactate dehydrogenase, and D-dimer, were slightly higher in the initial stage of the infection but the decreasing trend was low; therefore, they were not considered helpful in predicting the disease severity reflected by their Ct value in the three different groups.

Prevalence of Hepatitis B Infection Among Pregnant Women in Oman.

OBJECTIVE: The primary objective of our study was to estimate the prevalence of hepatitis B infection among pregnant women in Oman. The secondary objectives were to test for other hepatitis B virus (HBV) serological markers and to determine hepatitis B viral load. METHODS: In this cross-sectional study conducted from June 2019 to December 2020, we randomly selected 2210 Omani women who attended antenatal clinics across the country. Pregnant women were tested for HBV surface antigen (HBsAg) using a commercial enzyme immunoassay; those who tested positive were further analyzed for other HBV serological markers: HBV core total antibody (anti-HBc), HBV core antibody IgM (immunoglobulin M) (anti-HBc IgM), hepatitis B virus e antigen (HBeAg) and hepatitis B virus e antibody (anti-HBe). They were also tested for hepatitis B viral load. RESULTS: This study included 2210 women with a mean age of 39 years. Ninety-five percent of the women who were invited to participate consented and were included in the study. Thirty-three (1.49%) tested positive for HBsAg. All participants tested negative for HBeAg and anti-HBc IgM and positive for anti-HBc and anti-HBe, and 30 (90.9%) women had their hepatitis B viral load measured. Three (10.0%) had undetectable viral loads, 23 (76.7%) had low viral loads of < 2000 (IU/ml), 2 had moderate viral loads between 2000 and 200,000 (IU/ml) and one had a high viral load of 486,000 (IU/ml). CONCLUSION: Our study shows that the HBV prevalence in pregnant women is 1.49%, which is lower than what was reported earlier. Nevertheless, antenatal screening is still warranted, as there are vital interventions for the newborn and the mother.

Evaluation of Four Rapid Antigen Tests for Detection of SARS-CoV-2 virus.

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.

Validation of GeneXpert testing for SARS-CoV-2 RNA in eight hospital laboratories in Oman.

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.

Characteristics and Immunoglobulin G Seropositivity among COVID-19 Positive Healthcare Workers in a Tertiary Care Hospital in Oman.

OBJECTIVES: This study aimed to analyze the characteristics of coronavirus disease 2019 (COVID-19) infected health care workers (HCWs) and to measure their immunoglobulin G (IgG) response. METHODS: This is a retrospective and prospective cohort study where details of COVID-19 infected HCWs were collected in a pre-designed database in Al-Nahdha Hospital between 2 April and 24 July 2020. A single serum sample was collected from participating HCWs to detect the presence of IgG in their sera. RESULTS: Out of 974 HCWs, 103 (10.6%) were infected and tested positive for severe acute respiratory syndrome coronavirus 2 by real-time reverse transcriptase polymerase chain reaction. Nurses and doctors were the most affected groups. The source of infection was the hospital in 50.0% of cases. Nurses were more than four times likely to have a hospital-acquired COVID-19 infection (odds ratio = 4.63, 95% confidence interval: 1.71-12.52, p-value = 0.002). HCWs working in COVID-19 areas were more likely to have hospital-acquired infection than community-acquired infection (p < 0.005). All infected HCWs made a full recovery, with only 3.9% requiring admission. Out of 74 tested HCWs for IgG, 60 (81.1%) were positive. IgG positivity rate was significantly higher among HCWs in COVID-19 areas (p =0.026) and among non-Omanis (p =0.008). Moreover, the median IgG level was significantly higher among non-Omanis (p =0.004). CONCLUSIONS: This study has highlighted the group at higher risk of hospital-acquired COVID-19 infection which was nurses and those working in COVID-19 areas. It highlighted as well the high seropositivity among this infected group. These findings support the national guidelines on priority groups for vaccination among HCWs working in COVID-19 areas with no previous laboratory-confirmed COVID-19.

Seroprevalence of SARS-CoV-2 antibodies in the general population of Oman: results from four successive nationwide sero-epidemiological surveys.

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.

The role of supporting services in driving SARS-CoV-2 transmission within healthcare settings: A multicenter seroprevalence study.

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.

Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country.

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.