scholarly journals A cross-sectional overview of SARS-CoV-2 genome variations in Turkey

2021 ◽  
Author(s):  
Koray Ergünay ◽  
Mücahit Kaya ◽  
Muhittin Serdar ◽  
Yakut Akyön ◽  
Engin Yılmaz
Keyword(s):  
Immune Response ◽  
Avian Influenza ◽  
Virus Genome ◽  
Cross Sectional ◽  
Disease Epidemiology ◽  
Virus Diversity ◽  
Complete Genomes ◽  
Genome Variations ◽  
Probable Impact ◽  
Global Initiative

Abstract Introduction: Nearly a year following the emergence of COVID-19 in Turkey, we analysed SARS-CoV-2 sequences to identify virus genome variations and their probable impact on epidemiology, immune response and clinical disease.Materials and Methods: Complete genomes and partial Spike (S) region sequences originating from Turkey were accessed from the Global Initiative on Sharing Avian Influenza Data (GISAID) database. The genomes were aligned and analysed for variations and recombinations using appropriate softwares. Results: 410 complete genomes and 206 S region sequences were included. Overall, 1200 distinct nucleotide variations were noted. Mean variation count was noted as 14.2 per genome and increased significantly during the course of the pandemic. The most frequent variations were identified as A23403G (D614G; 92.9,%), C14408T (P323L, 92.2%), C3037T (89.8%), C241T (83.4%) and GGG28881AAC (RG203KR, 62.6%). The A23403G mutation was the most frequent variation in the S region sequences (99%). Majority of the genomes (%98.3) belonged in the SARS-CoV-2 haplogroup A. No evidence for recombination was identified in genomes representing sub-haplogroup branches. The variants of concern B.1.1.7, B.1.351 and P.1 were detected, with a statistically-significant time-associated increase in the variant B.1.1.7 prevalence. Discussion: We described prominant SARS-CoV-2 variantions as well as comparisons with global virus diversity. Continuing a molecular surveillence in agreement with local disease epidemiology appears to be crucial, as vaccination and mitigation efforts are ongoing.

scholarly journals A cross-sectional overview of SARS-CoV-2 genome variations in Turkey

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Koray Ergünay ◽  
Mücahit Kaya ◽  
Muhittin Serdar ◽  
Yakut Akyön ◽  
Engin Yılmaz
Keyword(s):  
Immune Response ◽  
Genome Diversity ◽  
Cross Sectional ◽  
Molecular Surveillance ◽  
Disease Epidemiology ◽  
Virus Diversity ◽  
Complete Genomes ◽  
Genome Variations ◽  
Probable Impact ◽  
Global Initiative

Abstract Objectives We assessed SARS-CoV-2 genome diversity and probable impact on epidemiology, immune response and clinical disease in Turkey. Materials and methods Complete genomes and partial Spike (S) sequences were accessed from the Global Initiative on Sharing Avian Influenza Data (GISAID) database. The genomes were analysed for variations and recombinations using appropriate softwares. Results Four hundred ten complete genomes and 206 S region sequences were included. Overall, 1,200 distinct nucleotide variations were noted. Mean variation count was 14.2 per genome and increased significantly during the course of the pandemic. The most frequent variations were identified as A23403G (D614G; 92.9,%), C14408T (P323L, 92.2%), C3037T (89.8%), C241T (83.4%) and GGG28881AAC (RG203KR, 62.6%). The A23403G mutation was the most frequent variation in the S region sequences (99%). Most genomes (98.3%) belonged in the SARS-CoV-2 haplogroup A. No evidence for recombination was identified in genomes representing sub-haplogroup branches. The variants B.1.1.7, B.1.351 and P.1 were detected, with a statistically-significant time-associated increase in B.1.1.7 prevalence. Conclusions We described prominent SARS-CoV-2 variations as well as comparisons with global virus diversity. Continuing a molecular surveillance in agreement with local disease epidemiology appears to be crucial, as vaccination and mitigation efforts are ongoing.

scholarly journals Single-cell multi-omics analysis of the immune response in COVID-19

2021 ◽  
Author(s):  
Emily Stephenson ◽  
◽  
Gary Reynolds ◽  
Rachel A. Botting ◽  
Fernando J. Calero-Nieto ◽  
...  
Keyword(s):  
Immune Response ◽  
T Cells ◽  
Single Cell ◽  
Mononuclear Cells ◽  
Severe Disease ◽  
Effector Memory ◽  
Peripheral Blood Mononuclear ◽  
Cross Sectional ◽  
Hematopoietic Stem ◽  
Symptomatic Disease

AbstractAnalysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.

scholarly journals Social conditions and immune response in human immunodeficiency virus-seropositive pregnant women: a cross-sectional study in Brazil

2018 ◽  
Vol 51 (1) ◽  
pp. 21-29
Author(s):  
Aletheia Soares Sampaio ◽  
Ana Lucia Ribeiro de Vasconcelos ◽  
Clarice Neuenschwander Lins de Morais ◽  
George Tadeu Nunes Diniz ◽  
Anna Lígia de Castro Figueiredo ◽  
...  
Keyword(s):  
Immune Response ◽  
Human Immunodeficiency Virus ◽  
Pregnant Women ◽  
Cross Sectional Study ◽  
Social Conditions ◽  
Sectional Study ◽  
Cross Sectional ◽  
Immunodeficiency Virus

scholarly journals Comparative safety and efficacy of two bivalent vaccines containing Newcastle disease LaSota and avian influenza H9N2 Sidrap isolate formulated with different oil adjuvants

2020 ◽  
Vol 13 (11) ◽  
pp. 2493-2501
Author(s):  
Jossie Intan Cahyani ◽  
Sitarina Widyarini ◽  
Michael Haryadi Wibowo
Keyword(s):  
Immune Response ◽  
Avian Influenza ◽  
Newcastle Disease ◽  
Hemagglutination Inhibition ◽  
Mineral Oil ◽  
Economic Losses ◽  
Poultry Industry ◽  
Bivalent Vaccine ◽  
Hemagglutination Inhibition Test ◽  
White Mineral

Background and Aim: Newcastle disease (ND) and avian influenza (AI) are two devastating diseases of poultry, which cause great economic losses to the poultry industry and disrupt food security in our country. The use of ND-AI inactive bivalent vaccine is very effective and economical to prevent and control ND and AI disease. Bivalent ND LaSota-AI H9N2 vaccine is not yet available in Indonesia. The inactivated vaccines used in poultry industry often require oil adjuvant to elicit a sufficient immune response. This study aimed to develop the bivalent inactive vaccines containing ND LaSota and AI H9N2 Sidrap isolate which are local isolates as poultry vaccine candidates, and formulated with two different commercial adjuvants, then compared. Materials and Methods: Two vaccines bivalent were prepared by emulsifying inactivated Newcastle disease virus (LaSota strain) and AI H9N2 Sidrap isolate viruses with Marcol white mineral oil and Montanide ISA70 adjuvants. Both of bivalent vaccines were tested for safety (physical and histopathological at the injection site) and efficacy in specific-pathogen-free chickens. Parameters used for the evaluation of the efficacy were immunogenicity by hemagglutination inhibition and protection percentage. Results: Both bivalent vaccines are safe to use. Post-vaccination (PV) immune response was observed using a hemagglutination inhibition test at 2, 3, 4, 5, 6, 7, and 8 weeks of PV. The bivalent vaccine B gives a better immune response to ND at 2, 3, and 4 weeks of PV (p<0.05) compared to the bivalent vaccine A, but in 5, 6, 7, and 8 weeks, the PV does not show differences in the immune response. The immune response to AI H9N2 showed differences at weeks 2 and 3 PV (p<0.05) with the bivalent vaccine B indicated higher immunity. A single immunization with both bivalent vaccines induces 100% protection in chickens that have been vaccinated against the deadly challenge with the virulent ND virus. Conclusion: Both of bivalent vaccines are safe to use and provide good efficacy against virulent ND viruses, but bivalent vaccine B (with Montanide ISA70 adjuvant) shows better immune response than bivalent vaccine A (Marcol white mineral oil adjuvant).

scholarly journals Opinions of healthcare providers on the design of a smartphone application for asthma treatment in the Kingdom of Saudi Arabia

2020 ◽  
Vol 15 ◽  
Author(s):  
Hajed M. Al-Otaibi ◽  
Khalid A. Ansari ◽  
Osama Hamad ◽  
Turki M. Alanzi
Keyword(s):  
Saudi Arabia ◽  
Therapeutic Process ◽  
Healthcare Providers ◽  
Smartphone Application ◽  
Asthma Treatment ◽  
Cross Sectional Survey ◽  
Kingdom Of Saudi Arabia ◽  
Cross Sectional ◽  
Primary Physician ◽  
Global Initiative

Introduction: In several countries of the world, smartphone applications have been designed to contribute to the treatment of asthma. However, none of these applications has been developed in Saudi Arabia. Therefore, the objective of this article is to design a smartphone application for the treatment of asthma based on the opinions of healthcare providers from the Kingdom of Saudi Arabia. Methods: In order to know the opinion of the healthcare providers from Saudi Arabia about the design of an asthmaApp, we used a purposive sampling method and conducted a cross sectional survey employing a questionnaire which was distributed through the QuestionPro.com website to all healthcare providers working in this country. The questionnaire was sent to 376 healthcare providers and the response rate was 25%. Results: The data indicated that the majority of the respondents opined that the following features were important or very important in the design of a smartphone application for asthma treatment in Saudi Arabia: information about. patient diagnosis (98%), primary physician access information(83%), patient satisfaction with the therapeutic process (91%), push notifications about reminder for drugs (95%), push notification for treatment of inhaler and other drugs (92%), push notifications about reminders of clinic visits and therapy sections (81%), push notifications to ask for help sending SMS to primary physician about patients’ attacks (89%), pathophysiology of asthma (82%), asthma triggers (98%), drug guidelines (94%), drug side effects (93%), number of asthma attacks (98%), medication statistics (88%), visual inputs such as peak flow (91%), data to link patients to healthcare providers and to healthcare centers (82%), and Global Initiative for Asthma (GINA) references (72%). Conclusions: According to the opinion of the majority of healthcare providers (92%), the proposed smartphone application designed based on medical guidelines will contribute to improve the treatment of patients with asthma in the Kingdom of Saudi Arabia, and will help to reduce the number of asthma cases that need hospitalization, and the number of asthma cases in the emergency departments of the hospitals of the Kingdom.

scholarly journals P014 Identification of Crohn’s disease immunopathotypes

2020 ◽  
Vol 14 (Supplement_1) ◽  
pp. S137-S137
Author(s):  
H M Baer ◽  
E MacDonald ◽  
A Ferguson ◽  
A M Scott ◽  
M I Khan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Immune Responses ◽  
Mononuclear Cells ◽  
Local Immune Response ◽  
Cross Sectional ◽  
Treatment Responses ◽  
Colonic Biopsies

Abstract Background Crohn’s disease (CD) is a chronic inflammatory gastrointestinal condition, with globally increasing incidence. Patients with CD suffer from a loss of tolerance towards their commensal microbiota causing an aberrant immune response, occurring in a protracted relapse and remission cycle. Although a variety of frontline therapies is currently available, including targeted therapies such as biologic drugs, 30–40% of CD patients still require surgery to manage the disease. At present, the immunobiology of CD is not fully understood. However, differences in immune responses between patients might play an important role in diverse treatment responses. The aim of this study was to identify differences in peripheral and local immune responses of CD to understand differences in disease behaviour and treatment outcome. Methods Peripheral blood mononuclear cells and plasma were isolated from whole blood of a cross-sectional CD patient cohort (nCD = 12) and normal controls (NC, nNC = 28). Flow cytometry analysis and multiplex assays were used to quantify immune cell populations and cytokine levels, respectively. The local immune response was analysed by bulk RNA sequencing of mucosal colonic biopsies either from inflamed CD or normal tissue. Gene signatures were then followed up by validation in publicly deposited gene expression datasets (nCD = 36, nNC = 24), and by measurement of specific proteins using our archived samples. Results Peripheral immunophenotyping of the initial cross-sectional study displayed three different types of CD patients, characterised by either a decrease in leukocyte populations, an increase of cytokines, or a change in both. Analysis of the RNAseq data derived from colonic biopsies revealed four distinct clusters in genes associated with the immune response in CD patients. Further pathway analysis showed one cluster with an enriched B cell signature and another cluster with an elevated macrophage and neutrophil response. We utilised publicly available gene expression datasets to validate these signatures in a larger cohort and identified a selection of patients with an up-regulated pro-inflammatory macrophage response. Using correlation analysis, we suggest an immunopathotype with increased macrophage activation which is potentially associated with a more severe form of the disease. Conclusion We have identified distinct immunopathotypes in both the peripheral and local immune response of CD patients. Further investigation will correlate these distinct immune responses in CD with clinical parameters, to understand associations between diverse treatment responses and disease behaviours.

scholarly journals An analysis of blood pressure screening of 21 112 participants in Armenia: May Measurement Month 2018

2020 ◽  
Vol 22 (Supplement_H) ◽  
pp. H14-H16
Author(s):  
Parounak Zelveian ◽  
Avag Avagyan ◽  
Arsen Minasyan ◽  
Samvel Hayrumyan ◽  
Svetlana Gourgenyan ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Blood Pressure Measurement ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Disability Adjusted Life ◽  
Life Years ◽  
Public Areas ◽  
Temporary Solution ◽  
Global Initiative ◽  
Definition Of

Abstract Elevated blood pressure (BP) is a growing burden worldwide and is the leading cause of mortality and disability-adjusted life years all over the world. May Measurement Month (MMM) is a global initiative aimed to raise awareness of high BP and to act as a temporary solution to the lack of screening programmes worldwide. An opportunistic cross-sectional survey of volunteers aged ≥18 was carried out in May to July 2018. Blood pressure measurement, the definition of hypertension (HTN) and statistical analysis followed the standard MMM protocol. The study was conducted in public areas (17 sites in Yerevan and 22 in regions), both indoor and outdoor, as well as in 78 primary care centres. A total of 21 112 individuals were screened during MMM18, of which 20 732 had three BP measurements available. The mean age of screened individuals was 46.2 ± 17.3 years, 57.8% were female. At the time of screening, 26.1% were on antihypertensive medication. After imputation, the percentage of participants with HTN was 38.7%, and 76.7% of them were aware of their high BP. Of participants receiving treatment, 47.1% had a controlled BP. MMM18 was the largest BP screening campaign undertaken in Armenia. We found that the proportion of HTN is substantial in Armenia, which may be a vital contributor to the growing burden of non-communicable diseases. Our results also suggest that untreated HTN is common and when treated still not adequately controlled in Armenia. The current situation, with an insufficient control rate of HTN, must be changed as soon as possible.

scholarly journals Factors associated with renal dysfunction in hepatitis C-related cirrhosis and its correlation with Child-Pugh score

2019 ◽  
Vol 6 (1) ◽  
pp. e000286 ◽  
Author(s):  
Hamza Waqar Bhatti ◽  
Umama Tahir ◽  
Noman Ahmed Chaudhary ◽  
Sania Bhatti ◽  
Muhammad Hafeez ◽  
...  
Keyword(s):  
Liver Cirrhosis ◽  
Hepatitis C ◽  
Serum Creatinine ◽  
Renal Dysfunction ◽  
Cross Sectional Study ◽  
Military Hospital ◽  
Cross Sectional ◽  
Disease Epidemiology ◽  
Factors Associated ◽  
Level Of Significance

ObjectivesTo assess factors associated with renal dysfunction (RD) in hepatitis C virus (HCV) cirrhosis, correlate renal parameters with Child-Pugh score (CPS) and find a cut-off value of CPS to determine RD.Materials and methodsIt was a cross-sectional study that included 70 cases of liver cirrhosis secondary to HCV from a period of 6 months at Combined Military Hospital, Multan. Diagnosis of HCV was confirmed by serological assay and liver cirrhosis by ultrasonography. CPS was determined and lab reports were taken. Patients were divided into two groups as not having RD (serum creatinine≤1.5 mg/dL) and having RD (serum creatinine≥1.5 mg/dL). Estimated glomerular filtration rate (eGFR) was calculated by chronic kidney disease epidemiology collaboration (CKD-EPI) formula. Data were analyzed using SPSS V.23.0. χ2, Kruskal-Wallis test and Pearson coefficient of correlation were applied. ROC curve was drawn to evaluate cut-off value of CPS for the presence of RD. Level of significance was set at p<0.05.ResultsPatients with CP grade B or C develop RD as compared to patients with CP grade A (p=0.000). Mean age, urea, creatinine and eGFR varies significantly among patients who develop RD and patients who do not (p=0.02, p=0.000, p=0.000 and p=0.000, respectively). eGFR negatively correlates with CPS (r=−0.359, p=0.002). Creatinine, urea and ALBI score positively correlates with CPS (r=+0.417, p=0.000; r=+0.757, p=0.000; r=+0.362, p=0.002, respectively).ConclusionAscites and encephalopathy are associated with RD in HCV cirrhosis.

scholarly journals May Measurement Month 2018: an analysis of blood pressure screening results from Chile

2020 ◽  
Vol 22 (Supplement_H) ◽  
pp. H37-H39
Author(s):  
Fernando Lanas ◽  
Maria Soledad Garcia ◽  
Melanie Paccot ◽  
Jimena Peña ◽  
Pamela Torres ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Antihypertensive Medication ◽  
Blood Pressure Measurement ◽  
National Health Survey ◽  
Uncontrolled Hypertension ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Systematic Screening ◽  
Temporary Solution ◽  
Global Initiative

Abstract Hypertension is highly prevalent in Chile. The National Health Survey 2016–17 reported a 27.6% prevalence, 68.7% awareness, and 33.3% of hypertensives had controlled blood pressure (BP). May Measurement Month (MMM) is a global initiative aimed at raising awareness of high BP and to act as a temporary solution to the lack of screening programmes worldwide. A cross-sectional survey of volunteers aged ≥18 years old was carried out in May 2018. Blood pressure measurement, the definition of hypertension, and statistical analysis followed the MMM protocol. Ninety-four sites participated, most of them from the Public Health System outpatient clinics distributed along the country. In addition, universities, clinical research sites, and private clinics participated. Hypertension was diagnosed as mean systolic BP ≥140 mmHg and/or diastolic BP ≥90 mmHg or receiving antihypertensive medication. Overall 9344 individuals were screened. After multiple imputation, hypertension prevalence was 29.2%, of which 64.0% were aware of their condition. Of those aware of their hypertension diagnosis, 87.7% were receiving antihypertensive medication and 56.1% of the total number of hypertensives were on antihypertensive medication. Moreover, 15.3% of the participants who were not receiving treatment were considered potential hypertensives identified in the MMM18. MMM18 was one of the largest BP screening campaigns performed in Chile. It demonstrated a high prevalence of hypertension with one-third of these individuals having controlled BP. The high percentage of persons untreated or with uncontrolled hypertension while on pharmacologic treatment suggests that systematic screening programmes may be a useful tool to improve hypertension control in Chile.

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