Associated effects of clinical characteristics, risk factors, and comorbidity on disease severity and mortality among patients with COVID-19 in Sulaimani City/ Kurdistan Region of Iraq.

The effects of clinical symptoms, laboratory indicators, and comorbidity status of SARS-CoV-2-infected patients on the severity of disease and the risk of death were investigated. Questionnaires and electronic medical records of 371 hospitalized COVID-19 patients were used for data collection (demographics, clinical manifestation, comorbidities, laboratory data). Association among categorical variables was determined using Kolmogorov-Smirnov test (P-value ≤0.05). Median age of study population (249 males, 122 females) was 65 years. Roc curves analysis found that age ≥64 years and age ≥67 years are significant cut-offs identifying patients with more severe disease and mortality at 30 days. CRP values at cut-off ≥80.7 and ≥95.8 significantly identify patients with more severe disease and mortality. Patients with more severe disease and risk of death were significantly identified with platelet value at the cut-off ≤160,000, hemoglobin value at the cut-off ≤11.7, D-Dimer values ≥1383 and ≥1270, and with values of neutrophil granulocytes (≥8.2 and ≤2) and lymphocytes (≤2 and ≤2.4). Detailed clinical investigation suggests granulocytes together with lymphopenia may be a potential indicator for diagnosis. Older age, several comorbidities (cancer, cardiovascular diseases, hypertension) and more laboratory abnormalities (CRP, D-Dimer, platelets, hemoglobin) were associated with development of more severity and mortality among COVID-19 patients.

Assessment of core and support functions of the communicable disease surveillance system in the Kurdistan Region of Iraq.

Early detection and prompt response are crucial measures to prevent and control outbreaks. Public health agencies, therefore, designed the Communicable Disease Surveillance System (CDSS) to obtain essential data instantaneously to be used for appropriate action. However, a periodic evaluation of CDSS is indispensable to ensure the functionality of the system. For this reason, this study aims to assess the performance of the core and support functions of the CDSS in the Kurdistan Region of Iraq. A descriptive cross-sectional study was used. From a total of 291 health facilities HFs (Primary health care centers and Hospitals) in the Kurdistan region of Iraq that have surveillance activities, 74 HFs were selected using a random stratified sampling approach. The World Health Organization (WHO) generic questionnaire has been used to interview the surveillance staff, together with direct collection of the data. Our analysis shows a lack of surveillance guiding manual in the HFs. Even at the district level, where a surveillance manual existed, case definitions, thresholds, and control measures were still missing. To note, more than 93% of HFs had organized and comprehensive patients registers for the collection of their clinical and secondary data. Also, all HFs had functioning laboratories. The majority of them (almost 93%) were equipped to collect, process, and store blood, stool, and urine specimens. About 72% of these laboratories were also able to transport timely the specimens to more specialized laboratories. At all levels, data reporting to the higher level exceeded the recommended minimum rate of 80%. The reporting system at the district level was based on emails, while in the periphery on hand-delivered in paper-based formats (50%), telephone (22%), and social media (22%). Furthermore, our analysis highlights the lack of data analysis: only 3.8% of Primary Health Care Centers conduct simple data analysis regularly, while hospitals do not do any sort of analysis. Also, only a few HFs investigated an outbreak, though using system routine sources to capture these public health events. Our findings show a lack in epidemic preparedness (3%), in feedback (53%), in standard guidelines, training, supervision, and resource allocations in HFs (0%). Taken together, our data show the importance of strengthening the CDSS in the Kurdistan region of Iraq, by reinforcing the surveillance system with continuous feedback, supervision, well-trained and motivated staff, technical support, and coordination between researchers and physicians.

Investigation of rosemary herbal extracts (Rosmarinus officinalis) and their potential effects on immunity.

The discovery of new curative drugs and the consumption of natural dietary ingredients with the ability to exhibit immunomodulatory activity is urgently needed to decrease the risk of chronic diseases among the population. Rosmarinus officinalis (Lamiaceae) is an aromatic plant that has been traditionally and medicinally used as a carminative, antispasmodic, painkiller, circulatory tonic, to stimulate hair growth and to improve memory dysfunction. This study aimed to assess the potential effects of rosemary solvent extracts on human immune function. Science Direct, Web of Science, Wiley, Elsevier, PubMed, Scopus, and the Google scholar search engines were used to retrieve relevant information included combinations of "rosemary" or "R. officinalis" with "immune function," "immunity," "immune system," "anti-inflammatory," "inflammation," or "health benefit." A number of studies have been found a stimulatory effect of rosemary and its active compounds on the immune system in vitro and animal study, but there is a lack of evidence in humans for supporting this. The results demonstrated the potential of rosemary and its main active components as dietary ingredients with immunomodulatory functionality. Human studies should be performed and a double-blind randomized controlled trial would be ideal.

HIV-1 B-subtype capsid protein: a characterization of amino acid's conservation and its significant association with integrase signatures.

The HIV-1 pre-integration phase and the subsequent integration of viral genome to the host of nuclear chromosomes are not well analyzed so far. Many studies are discussing the question of pre- and post-nuclear viral entry which is to support the assumption that HIV-1 integrase (IN) is maintained in the volume of intact conical structure's capsids through HIV entry. The aim of the current study is to identify the prevalence of capsid's (CA) signatures among drug-naïve and antiretroviral (ARV)-treated patients in a cohort of 827 HIV-1 B-subtype-infected individuals, and subsequently the relationship between IN and CA amino acid's changes was evaluated. These analyses suggest a conceivable co-evolution of IN-CA sequences, especially in relation to steps of nuclear viral entry. The frequency of mutations was calculated, and statistically has been compared between treatment-naïve and ARV-treated patients. The binomial correlation coefficient was used to assess covariation among CA and IN mutations; then, the average linkage hierarchical agglomerative clustering was performed. The results show a detailed conservation of HIV-1 CA protein both in drug-naïve and in ARV-treated patients. Moreover, the specific CA substitutions are significantly associated with different IN signatures at the amino acid level and the topology of the dendrogram has revealed the existence of two strong sub-clusters associated with hypothetical different mutational pathways. The in vitro and in vivo studies are necessary to exclude the hypothetical statistical false positive results and in order to confirm that some CA amino acid signatures are going to establish specific and precise implication in the HIV life cycle.

Phylogenetic and evolutionary analysis of influenza A H7N9 virus.

Recently, human infections with the novel avian-origin influenza A H7N9 virus have been reported from various provinces in China. Human infections with avian influenza A viruses are rare and may cause a wide spectrum of clinical symptoms. This is the first time that human infection with a low pathogenic avian influenza A virus has been associated with a fatal outcome. Here, a phylogenetic and positive selective pressure analysis of haemagglutin (HA), neuraminidase (NA), and matrix protein (MP) genes of the novel reassortant H7N9 virus was carried out. The analysis showed that both structural genes of this reassortant virus likely originated from Euro-Asiatic birds, while NA was more likely to have originated from South Korean birds. The Bayesian phylogenetic tree of the MP showed a main clade and an outside cluster including four sequences from China. The United States and Guatemala classical H7N9-isolates appeared homogeneous and clustered together, although they are distinct from other classical Euro-Asiatic and novel H7N9 viruses. Selective pressure analysis did not reveal any site under statistically significant positive selective pressure in any of the three genes analyzed. Unknown certain intermediate hosts involved might be implicated, so extensive global surveillance and bird-to-person transmission should be closely considered in the future.

Monitoring of KI and WU polyomaviruses in hematopoietic stem cell transplant patients.

Primary infection with KIPyV and WUPyV polyomaviruses occurs early in childhood followed by lifelong persistence in the body. Polyomavirus reactivation can occur in the presence of impaired immunity as in hematological malignancies or during immunosuppresssion induced by medications. In this study, reactivation of KIPyV and WUPyV was monitored by conventional PCR in plasma samples of 26 stem cell transplant patients and in 26 related bone marrow donors. Plasma samples from transplant patients were collected immediately after the end of conditioning regimen and up to 270 days after transplant. All plasma samples from transplant patients were negative for KIPyV and WUPyV DNA. Instead, KIPyV DNA was detected in two bone marrow donors. There was no evidence of KIPyV transmission from the donor to the recipient. The data suggest that detection of KIPyV in plasma is sporadic and that KPIyV and WUPyV do not affect the post-transplant clinical course. However, further studies on a larger sample size and more sensitive PCR methods are needed to confirm these observations.

Molecular analysis of hepatitis B virus in Bulgaria.

Hepatitis B virus infection is a global health problem. Based on the sequence divergence of the entire genome, hepatitis B virus has been classified into eight genotypes which have a characteristic geographic distribution. To date, no data are available on the molecular epidemiology of hepatitis B virus in Bulgaria. The aim of the present study was to reconstruct the epidemiological history of HBV genotypes/subgenotypes circulating in Bulgaria using a phylodynamic approach and a Bayesian statistical inference framework. Sequence analysis of the HBsAg/Reverse Transcriptase overlapping genomic regions revealed that D1 and A2 were the subgenotypes detected most frequently in the patients examined. The tMRCA estimations of the few HBV D1 Bulgarian significant clades dated back to 23-27 years ago, corresponding to the early 1980s. The HBV A2 Bulgarian sequences fell into two closely related supported clusters dated to 2003 and 1996 years, respectively, suggesting a more recent introduction of subgenotype A2 into Bulgaria. The study provides new information about the HBV subgenotypes in Bulgaria.

When phylogenetic analysis complements the epidemiological investigation: a case of HIV-2 infection, Italy.

Human immunodeficiency virus type 2 (HIV-2) infection is geographically restricted, affecting West African countries such as Guinea- Bissau and Cape Verde. We describe a recent case of HIV-2 infection in an Italian patient. Phylogenetic analysis of the V3 region of HIV-2 indicated that the Italian patient was infected by HIV-2 subtype A2. The sequence obtained from the Italian patient clustered significantly with a sequence isolated from Senegal. A phylogenetic doubt may arise from a Guinea Bissau sequence because it was in a major clade with the Italian and Senegal sequences, but was not statistically significant. The discovery of another Italian case over a short time frame stresses the importance of strengthening the surveillance system for HIV-2 because of the increase in migration from endemic areas to Italy.

The lessons of COVID-19 pandemic for communicable diseases surveillance system in Kurdistan Region of Iraq.

Objectives: This study aimed to determine the opportunities of and barriers to communicable diseases surveillance system (CDSS) during the COVID-19 pandemic and the extent to which the disease integrated into the CDSS in the Kurdistan region of Iraq. Study design: A descriptive qualitative approach was applied. Methods: We conducted seven semi-structured interviews and seven interviewee in a focus group discussion (FGD) with purposefully identified Key Informants (KI) from June to December 2020. All interviews were digitally recorded and transcribed verbatim. We adopted a mixed deductive-inductive approach for thematic data analysis, facilitated by using MAXQDA20 software for data management. Results: Although the CDSS was considered appropriate and flexible, the COVID-19 was interpreted not to be integrated into the system due to political influence. The main concerns regarding core and support activities were the lack of epidemic preparedness, timeliness, and partial cessation of training and supervision during the pandemic. The existence of reasonable surveillance infrastructure, i.e., trained staff, was identified as an opportunity for improvement. The main challenges include staff deficiency, absence of motivation and financial support for present staff, scarce logistics, managerial and administrative issues, and lack of cooperation, particularly among stakeholders and surveillance staff. Conclusion: Our findings revealed that the CDSS in the Kurdistan region requires substantial enhancement in epidemic preparedness, strengthening human resources, and logistics. the system can be developed by fostering meaningful intersectoral collaboration. We advocate that the health authorities and policy-makers prioritise the surveillance and effective management of communicable diseases.

Antibiotic susceptibility of vancomyin and nitrofurantoin in Staphylococcus aureus isolated from burnt patients in Sulaimaniyah, Iraqi Kurdistan.

Burns remain a significant public health problem in terms of morbidity and mortality throughout the world, especially in low and middle-income countries. Burning raptures the skin barriers that normally prevent invasion by microorganisms and infection is a major complication in burn patients. Methicillin resistant Staphylococcus aureus (MRSA) is the most important nosocomial pathogen. This retrospective analysis was conducted in the burn unit of the Department of Microbiology in the Sulamaini Plastic Surgery and Burns Hospital. The analysis is based on data collected from the medical records of 2938 burn patients, hospitalized between May 2008 and December 2011. The clinical samples were taken from various body sources for microbiological tests. Patients with a high percentage of total body surface area burnt (P<0.001) and a longer hospital stay (P<0.001) were more likely to have infection compared to other patients. In addition, among all tested antibiotics, vancomycin and nitrofurantion seem to be the most effective antibiotics for MR- SA. Furthermore there was a significant association between age and antibiotic resistance for all antibiotics except for vancomycin and nitrofurantoin. Resistance to antibiotics increased with advancing age. The wide use of antibiotics in the treatment of bacterial infections has probably led to the emergence and spread of resistant strains. Routine microbiological surveillance and careful in vitro testing prior to antibiotic use and strict adherence to hospital antibiotic policy may help in the prevention and treatment of antibiotic resistant pathogens in burn infections.

HIV-2 A-subtype gp125c2-v3-c3 mutations and their association with CCR5 and CXCR4 tropism.

The early events of the HIV replication cycle involve the interaction between viral envelope glycoproteins and their cellular CD4-chemokine (CCR5/CXCR4) receptor complex. In this study, for the first time, the HIV-2 A-subtype gp125(C2-V3-C3) mutations and their tropism association were characterized by analyzing 149 HIV-2 sequences from the Los Alamos database. The analysis has strengthened the importance of C2-V3-C3 region as a determinant factor for co-receptor selection. Moreover, statistically significant correlations were observed between C2-V3-C3 mutations, and several correlated mutations were associated with CXCR4 and CCR5 co-receptor usage. A dendrogram showed two distinct clusters, with numerous associated mutations grouped, thus dividing CCR5- and CXCR4-tropic viruses. Fourteen X4-tropic virus mutations, all in V3 and C3 domains and forming highly significant subclusters, were found. Finally, R5 associations, two strong subclusters were observed, grouping several C2-V3-C3 mutated positions. These data indicate the possible contribution of C2-V3-C3 mutational patterns in regulating HIV-2 tropism.

The novel KI, WU, MC polyomaviruses: possible human pathogens?

Recently, three novel human polyomaviruses KIPyV, WUPyV and MCPyV were uncovered in biological specimens of patients with different underlying clinical conditions. Although it is too early to draw firm conclusions on their role in human pathology, this finding has revitalized the scientific debate on the Polyomaviridae family and their relation to human disease. Seroepidemiological studies showed that, similarly to BKPyV and JCPyV, benign primary exposure to these new viruses occurs early in childhood. The viruses then remain latent in the body, and reactivate in immunosuppressed patients with possible pathological consequences. Furthermore, the discovery of MCPyV in a rare and aggressive skin cancer named Merckel cell carcinoma and its clonal integration within the tumor genome suggests that MCPyV infection may represent an early event in the pathogenesis of this disease. This review describes the general aspects of human polyomavirus infection and pathogenesis. Current topics of investigation and future directions in the field are also discussed.

Genetic variability and circulation pattern of human metapneumovirus isolated in Italy over five epidemic seasons.

Human metapneumovirus (hMPV) is an important aetiological agent of respiratory tract infection (RTI) in infants. Based on genetic differences, hMPVs are separated into two main groups, A and B, and two subgroups 1 and 2. To better understand the genetic diversity of hMPV, we analyzed 435 bp fragments of the F gene from 49 isolates obtained from a paediatric clinical centre in Northern Italy from 2005 to 2009. The phylogenetic analysis showed that our hMPV sequences clustered into five main clades (A1, A2a, A2b, B1, B2) statistically supported. Most of the strains belong to A2 (49%) and to B1 (28.5%) lineages. The intermixing in the phylogenetic tree showed no seasonal distribution between samples collected over a 5 year period. Mean genetic distances showed that clade A2 was more heterogeneous than others. In our F glycoprotein dataset we observed only two positively selected sites with an w value of 1.408 and 1.429, respectively, and 27 negatively selected sites. The two positively selected sites could be considered evolutionary "hot spots" because they were under positive selection and/or relaxed selective constraints. The abundant negatively selected sites reflect a high degree of conservation of F protein, probably necessary for viral infection.

Genetic Variation and Evolution of the 2019 Novel Coronavirus.

INTRODUCTION: SARS-CoV-2 is a new type of coronavirus causing a pandemic severe acute respiratory syndrome (SARS-2). Coronaviruses are very diverting genetically and mutate so often periodically. The natural selection of viral mutations may cause host infection selectivity and infectivity. METHODS: This study was aimed to indicate the diversity between human and animal coronaviruses through finding the rate of mutation in each of the spike, nucleocapsid, envelope, and membrane proteins. RESULTS: The mutation rate is abundant in all 4 structural proteins. The most number of statistically significant amino acid mutations were found in spike receptor-binding domain (RBD) which may be because it is responsible for a corresponding receptor binding in a broad range of hosts and host selectivity to infect. Among 17 previously known amino acids which are important for binding of spike to angiotensin-converting enzyme 2 (ACE2) receptor, all of them are conservative among human coronaviruses, but only 3 of them significantly are mutated in animal coronaviruses. A single amino acid aspartate-454, that causes dissociation of the RBD of the spike and ACE2, and F486 which gives the strength of binding with ACE2 remain intact in all coronaviruses. DISCUSSION/CONCLUSION: Observations of this study provided evidence of the genetic diversity and rapid evolution of SARS-CoV-2 as well as other human and animal coronaviruses.

An Assessment of Timeliness and Quality of Communicable Disease Surveillance System in the Kurdistan Region of Iraq.

BACKGROUND: The quality of the surveillance system can be defined by attributes such as completeness, timeliness, usefulness, simplicity, flexibility, acceptability, and reliability. This study aims to assess these quality features of the communicable disease surveillance system (CDSS) in the Kurdistan Region of Iraq. METHODS: This study was conducted using a retrospective review of records and documents, and the interviews with the surveillance staff (n = 82) of the Kurdistan governorates during 2018, 2019, and 2020. The World Health Organization (WHO) guideline 2006 indicators were used for evaluation and monitoring the quality of the communicable disease surveillance system. The data analyzed and showed as frequencies and percentages using Statistical Package for the Social Sciences (SPSS) version 26 software. RESULTS: The reporting timeliness declined from 98% in 2019 to 69% in 2020. At the same time, there was an improvement in completeness of reporting from 83% in 2018 to 99% in 2020. The total scores of other surveillance quality attributes, simplicity, usefulness, flexibility, acceptability, and reliability, were 75%, 72%, 67%, 72%, and 69%, respectively. CONCLUSION: Current findings demonstrate that the CDSS is still facing significant challenges in timeliness simplicity, usefulness, flexibility, acceptability, and reliability. Further studies to assess the system's quality, particularly the system's timeliness of outbreak response, sensitivity, and specificity, are recommended.

Health related factors contributing to COVID-19 fatality rates in various communities across the world.

INTRODUCTION: Factors such as comorbidity, age and gender distribution are mostly related to hospitalization, numbers requiring intensive care and case fatality rate. In this review, the fatality rate of coronavirus disease 2019 (COVID-19) in different population health background according to comorbidity, age, gender distribution, and laboratory prognosis for COVID-19. METHODOLOGY: The current review was based on the data from copious studies that had homogeneity in relation to the review's objectives. It included the newest studies from December 2019 to September 2020. The epidemiological reasons for the high morbidity and mortality rates among COVID-19 patients were analyzed in different countries. RESULTS: The highest comorbidity prevalence of COVID-19 was recorded in the United States of America (USA) (93.9%) and Italy (68%). Among population health background factors, comorbidity was the most common cause of COVID-19 fatality in the USA. The mean age of the most COVID-19 fatalities was more than 60 years old. Most of the studies show that 60% of COVID-19 patients were male. The fatality rates for the age group of 80-89 years-old in Korea, China, and Italy were 8.7 %, 14.7 %, and 18.8 % respectively. Lymphocytopenia has been observed in 91% of COVID-19 death cases. C - reactive protein had increased in 40-60% of COVID-19 patients. CONCLUSIONS: Many factors contribute to COVID-19 severity and fatality rates. Comorbidity, age, and gender were the main reasons for the Case Fatality Rate. This review recommends to follow preventive measures for overcoming the challenges faced during this emerging pandemic disease.

KI and WU polyomaviruses and CD4+ cell counts in HIV-1-infected patients, Italy.

To investigate an association between KI and WU polyomavirus (KIPyV and WUPyV) infections and CD4+ cell counts, we tested HIV-1-positive patients and blood donors. No association was found between cell counts and virus infections in HIV-1-positive patients. Frequency of KIPyV infection was similar for both groups. WUPyV was more frequent in HIV-1-positive patients.

Identification of Merkel cell polyomavirus in the lower respiratory tract of Italian patients.

Merkel cell polyomavirus (MCPyV) has been found to be integrated monoclonally in a rare skin cancer named Merkel cell carcinoma. More recently, MCPyV has been detected in the upper respiratory tract of pediatric and adult patients. However, the mode of transmission and pathogenic role of MCPyV in the respiratory system has not been determined. In this study, MCPyV was sought in the lower respiratory tract of adult patients admitted to the hospital. MCPyV DNA was detected in 15 (17.24%) out of 87 lower respiratory tract samples. Most of the patients with MCPyV were over 50 years old. Nucleotide sequence of the t-antigen of MCPyV identified in respiratory secretions showed a homology to those found in Merkel cell carcinoma. In addition, phylogenetic analysis undertaken on the t-antigen sequences of Italian isolates and other MCPyVs identified in healthy and cancer tissues showed that all these isolates belonged to the same clade. Selective pressure analysis for the t-antigen revealed the presence of five sites under positive selection (omega = 4.3), with a posterior probabilities above 0.99. The alpha parameter of the gamma distribution was 0.01, showing that this distribution has a characteristic L-shape and suggesting a strong nucleotide substitution rate heterogeneity across sites. This study shows that MCPyV can infect the lower respiratory tract, but further investigations are needed to define its pathogenic role in respiratory diseases. J. Med. Virol. 82:505-509, 2010. (c) 2010 Wiley-Liss, Inc.

Genetic variability of the small t antigen of the novel KI, WU and MC polyomaviruses.

Recently, three novel human polyomaviruses were discovered: KIPyV, WUPyV and MCPyV. To study the genetic variability of these viruses, an evolutionary analysis of the large T antigen, small t antigen, VP1, VP2 and VP3 genes was carried out. Of the genes analyzed, only the small t antigen of KIPyV and MCPyV was found to be under statistically supported selective pressure. In KIPyV, 31 selected sites were found under positive selection (ω(2) = 1.54), with posterior probabilities above 0.75. Of these sites, 17 are located in the J domain and two of these are located in the HPDGG box. Thirteen of these sites were identified as being under positive selection at the 99% confidence level. Moreover, seven codons were under significant purifying selection, particularly in the J domain. In MCPyV, we confirmed the five sites already found to be under positive selection (posterior probabilities 0.99). Selective pressure analysis may provide useful information on viral evolution.

The novel swine-origin H1N1 influenza A virus riddle: is it a domestic bird H1N1-derived virus?

To understand the role of domestic birds in the 2009 H1N1 influenza A outbreak, a phylogenetic analysis of hemagglutinin, neuraminidase and matrix protein genes from human, avian and swine H1N1 viruses was carried out. Analysis of the H1 sequences revealed that the virus evolved most likely from American swine as well as intermixing between Asian swine and American domestic bird H1N1 viruses. Neuroaminidase and matrix protein analysis showed that the H1N1 2009 viruses were more closely related to the H1N1 isolates from Euro-Asiatic domestic birds and swine than wild birds. Domestic birds could act as intermediate hosts of H1N1 reassortants.