Risk Assessment and Travelers Characteristics: 6-Month Travel Clinic Experience From Qatar

Introduction: The number of international travelers is increasing, yet currently, there is no data on risk assessment and travelers’ characteristics from Qatar. To identify and minimize the risks associated with travel, a detailed knowledge of travelers’ characteristics is needed. Methods: This retrospective descriptive study was conducted in a travel clinic in the Communicable Disease Center, Qatar. All patients seen in the clinic from February 2017 to August 2017 were included. Data was analyzed using SPSS version 22 software. Results: A total of 279 travelers were included in this study. The top 2 most visited countries were Tanzania and Kenya. Tourism (57.3%) was the number one purpose for travel, while travelers visiting friends and relatives (VFRs) accounted for 10.7% of travel. Among the study population, 21% of participants had pre-existing medical conditions with hypertension and diabetes as the most common comorbidities. Mean travel duration was 46.5 days (range = 3 to 90 days). Vaccinations were required by 97% of the study population with the most commonly prescribed vaccines being the typhoid (69%), Tdap (62%), hepatitis A (55%), flu (49.3%), and yellow fever (39%) vaccines. Conclusion: Travelers from Qatar tend to visit high-risk destinations; the lack of proper travel medicine services and awareness among travelers may increase the risk of illness, especially in Qatar where a large number of expatriates reside and travel frequently to and from their home countries (VFRs)

Influenza Prevalence and Vaccine Efficacy in Diabetic Patients in Qatar

Introduction: Diabetes (DM) is often recognized as ?an independent risk factor for developing severe respiratory tract infections. Influenza infections are associated with higher hospitalization, morbidity and mortality in DM patients. Vaccination against Influenza virus would reduce the burden of flu infection in DM patients. Aim: To assess the prevalence and burden of influenza infection in DM patients in Qatar and to evaluate the efficacy of influenza vaccination in DM patients Methods: The study included 26,989 patients between 2016- 2018. Virology test results (20 pathogens) as well as the levels of HbA1c were collected for all participant. Data was filtered and analysed to explore the influenza prevalence and vaccine efficiacy among diabetis patients in comparision to non-diabetic. Findings: This study shows that DM patients are at higher-risk for influenza infection. In general, Influenza infections covers around 50 % of total respiratory infections in patients with flu like symptoms in Qatar. However, in vaccinated DM patients, influenza test positivity was low. This study reports the efficacy of routine flu vaccination to reduce the burden of influenza infection in DM patients

Promoting cross-regional collaboration in antimicrobial stewardship: Findings of an infectious diseases working group survey in Arab countries of the Middle East.

Abstract Background Antimicrobial resistance is a significant global issue that presents an increasing threat to patients' wellbeing. Although a global concern, the emergence of multi-drug resistant organisms is of particular significance in the Middle East. In recent years, this region has seen an alarming increase in antimicrobial resistance presenting a major challenge to physicians managing various infectious diseases. Methods A Working Group comprising experts in infectious diseases from Arab countries of Middle East assembled to review similarities and differences in antimicrobial practices and management of multi-drug resistant organisms across the region and assess the barriers to achieving cross-regional collaboration. The Working Group conducted an anonymous online survey to evaluate current practice and understanding of management of multi-drug resistant organisms across the region. Results A total of 122 physicians from Arab countries of the Middle East responded to the survey. Their responses demonstrated heterogeneity between countries in awareness of local epidemiology, management of multi-drug resistant organisms and antimicrobial stewardship practices. The Working Group recognized similarities and differences in the management of multi-drug resistant organisms across the region, and these were validated by the data collected in the survey. Overall, the similarities across the region reflect several key issues that can have an impact on the management of multi-drug resistant organisms and the prevention of antimicrobial resistance. Conclusions This paper highlights the urgency of addressing antimicrobial resistance in Arab countries of the Middle East. The Working Group identified key barriers to effective management which may guide the development of future coherent strategies to promote effective antimicrobial stewardship in the region. Here, we outline a call to action for the region, with a need to focus on training and education, capacity building, infrastructure, regional research, and regional surveillance

Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes

The diversity of RNA viruses dictates their evolution in a particular host, community or environment. Here, we reported within- and between-host pH1N1virus diversity at consensus and sub-consensus levels over a three-year period (2015–2017) and its implications on disease severity. A total of 90 nasal samples positive for the pH1N1 virus were deep-sequenced and analyzed to detect low-frequency variants (LFVs) and haplotypes. Parallel evolution of LFVs was seen in the hemagglutinin (HA) gene across three scales: among patients (33%), across years (22%), and at global scale. Remarkably, investigating the emergence of LFVs at the consensus level demonstrated that within-host virus evolution recapitulates evolutionary dynamics seen at the global scale. Analysis of virus diversity at the HA haplotype level revealed the clustering of low-frequency haplotypes from early 2015 with dominant strains of 2016, indicating rapid haplotype evolution. Haplotype sharing was also noticed in all years, strongly suggesting haplotype transmission among patients infected during a specific influenza season. Finally, more than half of patients with severe symptoms harbored a larger number of haplotypes, mostly in patients under the age of five. Therefore, patient age, haplotype diversity, and the presence of certain LFVs should be considered when interpreting illness severity. In addition to its importance in understanding virus evolution, sub-consensus virus diversity together with whole genome sequencing is essential to explain variabilities in clinical outcomes that cannot be explained by either analysis alone

Within-Host Diversity of SARS-CoV-2 in COVID-19 Patients With Variable Disease Severities.

The ongoing pandemic of SARS-COV-2 has already infected more than eight million people worldwide. The majority of COVID-19 patients either are asymptomatic or have mild symptoms. Yet, about 15% of the cases experience severe complications and require intensive care. Factors determining disease severity are not yet fully characterized. Here, we investigated the within-host virus diversity in COVID-19 patients with different clinical manifestations. We compared SARS-COV-2 genetic diversity in 19 mild and 27 severe cases. Viral RNA was extracted from nasopharyngeal samples and sequenced using the Illumina MiSeq platform. This was followed by deep-sequencing analyses of SARS-CoV-2 genomes at both consensus and sub-consensus sequence levels. Consensus sequences of all viruses were very similar, showing more than 99.8% sequence identity regardless of the disease severity. However, the sub-consensus analysis revealed significant differences in within-host diversity between mild and severe cases. Patients with severe symptoms exhibited a significantly (-value 0.001) higher number of variants in coding and non-coding regions compared to mild cases. Analysis also revealed higher prevalence of some variants among severe cases. Most importantly, severe cases exhibited significantly higher within-host diversity (mean = 13) compared to mild cases (mean = 6). Further, higher within-host diversity was observed in patients above the age of 60 compared to the younger age group. These observations provided evidence that within-host diversity might play a role in the development of severe disease outcomes in COVID-19 patients; however, further investigations are required to elucidate this association.This work was supported by Qatar University under internal grant (QUCG-BRC-20/21-1) and Qatar National Research Fund grant under grant (RRC-2-039)

Epidemiology of respiratory infections among adults in Qatar (2012-2017).

Limited data is available about the etiology of influenza like illnesses (ILIs) in Qatar. This study aimed at providing preliminary estimates of influenza and other respiratory infections circulating among adults in Qatar. We retrospectively collected data of about 44,000 patients who visited Hamad General Hospital clinics, sentinel sites, and all primary healthcare centers in Qatar between 2012 and 2017. All samples were tested for influenza viruses, whereas about 38,000 samples were tested for influenza and a panel of respiratory viruses using Fast Track Diagnostics (FTD) RT-PCR kit. Among all ILIs cases, 20,278 (46.5%) tested positive for at least one respiratory pathogen. Influenza virus was predominating (22.6%), followed by human rhinoviruses (HRVs) (9.5%), and human coronaviruses (HCoVs) (5%). A detection rate of 2-3% was recorded for mycoplasma pneumonia, adenoviruses, human parainfluenza viruses (HPIVs), respiratory syncytial virus (RSV), and human metapneumovirus (HMPV). ILIs cases were reported throughout the year, however, influenza, RSV, and HMPV exhibited strong seasonal peaks in the winter, while HRVs circulated more during fall and spring. Elderly (>50 years) had the lowest rates of influenza A (13.9%) and B (4.2%), while presenting the highest rates of RSV (3.4%) and HMPV (3.3%). While males had higher rates of HRVs (11.9%), enteroviruses (1.1%) and MERS CoV (0.2%), females had higher proportions of influenza (26.3%), HPIVs (3.2%) and RSV (3.6%) infections. This report provides a comprehensive insight about the epidemiology of ILIs among adults in the Qatar, as a representative of Gulf States. These results would help in improvement and optimization of diagnostic procedures, as well as control and prevention of the respiratory infections.This study was supported by funds from Hamad Medical Corporation (grant # 16335/16) and Qatar University (grant # QUCG-BRC-2018/2019-1)

Burden and disease pathogenesis of influenza and other respiratory viruses in diabetic patients

Over the past two decades, diabetes mellitus (DM) has been receiving increasing attention among autoimmune diseases. The prevalence of type 1 and type 2 diabetes has increased rapidly and has become one of the leading causes of death worldwide. Therefore, a better understanding of the genetic and environmental risk factors that trigger the onset of DM would help develop more efficient therapeutics and preventive measures. The role and mechanism of respiratory viruses in inducing autoimmunity have been frequently reported. On the other hand, the association of DM with respiratory infections might result in severe complications or even death. Since influenza is the most common respiratory infection, DM patients experience disease severity and increased hospitalization during influenza season. Vaccinating diabetic patients against influenza would significantly reduce hospitalization due to disease severity. However, recent studies also report the role of viral vaccines in inducing autoimmunity, specifically diabetes. This review reports causes of diabetes, including genetic and viral factors, with a special focus on respiratory viruses. We further brief the burden of influenza-associated complications and the effectiveness of the influenza vaccine in DM patients

Profiling of intestinal microbiota in patients infected with respiratory influenza a and b viruses

Little is known about the association between respiratory viral infections and their impact on intestinal microbiota. Here, we compared the effect of influenza types, A and B, and influenza shedding in patients’ stools on the gut microbiota diversity and composition. Deep sequencing analysis was performed for the V4 region of the 16S rRNA gene. Fecal samples were collected from 38 adults with active respiratory influenza infection and 11 age-matched healthy controls. Influenza infection resulted in variations in intestinal bacterial community composition rather than in overall diversity. Overall, infected patients experienced an increased abundance of Bacteroidetes and a corresponding decrease in Firmicutes. Differential abundance testing illustrated that differences in gut microbiota composition were influenza type-dependent, identifying ten differentially abun-dant operational taxonomic units (OTUs) between influenza A-and influenza B-infected patients. Notably, virus shedding in fecal samples of some patients had significantly reduced gut bacterial diversity (p = 0.023). Further taxonomic analysis revealed that the abundance of Bacteroides fragilis was significantly higher among shedders compared to non-shedders (p = 0.037). These results pro-vide fundamental evidence of the direct effect of influenza infection on gut microbiota diversity, as reported in patients shedding the virus

Darunavir-Cobicistat versus Lopinavir-Ritonavir for COVID-19 Pneumonia: Qatar's Experience

Background: Coronavirus Disease 2019 (COVID-19) was first discovered in China and resulted in a pandemic crisis. 1,2 Many agents were investigated with inconclusive outcomes. 3 This study was conducted to compare the efficacy and safety outcomes of darunavir-cobicistat versus lopinavir-ritonavir in the treatment of patients with COVID-19. Methods: This retrospective, multicenter, observational study was conducted on adult patients hospitalized in COVID-19 facilities in Qatar. Patients were included if they had pneumonia and received darunavir-cobicistat or lopinavir-ritonavir for at least three days as part of their COVID-19 treatment. Data were collected from patients' electronic medical records. The primary outcome was a composite endpoint of time to clinical improvement and/or virological clearance. Data were analyzed descriptively and inferential statistics were applied at alpha level of 0.05. Results: A total of 400 patients' medical records were analyzed, of whom 100 received darunavir-cobicistat and 300 received lopinavir-ritonavir. The majority of patients were male (92.5%), with a mean (SD) time from symptoms onset to start of therapy of 7.57 days (SD 4.89). Patients who received lopinavir-ritonavir had a significantly faster time to the primary composite endpoint of clinical improvement and/or virological clearance than patients who received darunavir-cobicistat (4 days [IQR 3-7] vs. 6.5 days [IQR 4-12]; HR 1.345 [95%CI: 1.070-1.691], p = 0.011) [Figure 1]. Patients who received lopinavir-ritonavir had a significantly faster time to clinical improvement (5 days [IQR 3-8] vs. 8 days [IQR 4-13]; HR 1.520 (95%CI: 1.2-1.925), p = 0.000), and slower time to virological clearance than those who received darunavir-cobicistat (25 days [IQR 15-33] vs. 21 days [IQR 12.8-30]; HR 0.772 (95%CI: 0.607-0.982), p = 0.035) [Figure 2]. No significant difference in adverse events incidence or severity was observed. Conclusion: In patients with COVID-19, early treatment with lopinavir-ritonavir was associated with faster time to reach the primary composite endpoint of clinical improvement and/or virological clearance than treatment with darunavir-cobicistat. Future trials are warranted to confirm these findings.qscienc