scholarly journals Phylogenetic Characterization of Arboviruses in Patients Suffering from Acute Fever in Rondônia, Brazil

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 889
Author(s):  
Jackson Alves da Silva Queiroz ◽  
Luan Felipo Botelho-Souza ◽  
Felipe Souza Nogueira-Lima ◽  
Rita de Cássia Pontello Rampazzo ◽  
Marco Aurélio Krieger ◽  
...  
Keyword(s):  
Viral Load ◽  
Phylogenetic Analyses ◽  
Metropolitan Region ◽  
Evolutionary Analysis ◽  
Detectable Viral Load ◽  
Conventional Pcr ◽  
Serum Samples ◽  
Phylogenetic Characterization ◽  
Genotype V ◽  
Genotype Ii

The purpose of the study was to classify, through phylogenetic analyses, the main arboviruses that have been isolated in the metropolitan region of Porto Velho, Rondônia, Brazil. Serum samples from patients with symptoms suggesting arboviruses were collected and tested by One Step RT-qPCR for Zika, Dengue (serotypes 1–4), Chikungunya, Mayaro and Oropouche viruses. Positive samples were amplified by conventional PCR and sequenced utilizing the Sanger method. The obtained sequences were aligned, and an evolutionary analysis was carried out using Bayesian inference. A total of 308 samples were tested. Of this total, 20 had a detectable viral load for Dengue, being detected DENV1 (18/20), co-infection DENV1 and DENV2 (1/20) and DENV4 (1/20). For Dengue serotype 3 and for the CHIKV, ZIKV, MAYV and OROV viruses, no individuals with a detectable viral load were found. A total of 9 of these samples were magnified by conventional PCR for sequencing. Of these, 6 were successfully sequenced and, according to the evolutionary profile, 5 corresponded to serotype DENV-1 genotype V, and 1 to serotype DENV-4 genotype II. In the study, we demonstrate co-circulation of the DENV-1 genotype V and the DENV-4 genotype II. Co-circulation of several DENV serotypes in the same city poses a risk to the population and is correlated with the increase of the most severe forms of the disease. Similarly, co-circulation of genetically distinct DENV and the occurrence of simultaneous infections can affect recombination events and lead to the emergence of more virulent isolates.

scholarly journals Linkage to intensive adherence counselling among HIV-positive persons on ART with detectable viral load in Gomba district, rural Uganda

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Rita Nakalega ◽  
Nelson Mukiza ◽  
Henry Debem ◽  
George Kiwanuka ◽  
Ronald Makanga Kakumba ◽  
...  
Keyword(s):  
Viral Load ◽  
Health Center ◽  
Health Facility ◽  
Transmission Risk ◽  
World Health ◽  
Hiv Positive ◽  
Art Adherence ◽  
Detectable Viral Load ◽  
Adherence Support ◽  
Adherence Counselling

Abstract Background Antiretroviral therapy (ART) adherence is a primary determinant of sustained viral suppression, HIV transmission risk, disease progression and death. The World Health Organization recommends that adherence support interventions be provided to people on ART, but implementation is suboptimal. We evaluated linkage to intensive adherence counselling (IAC) for persons on ART with detectable viral load (VL). Methods Between January and December 2017, we conducted a retrospective chart review of HIV-positive persons on ART with detectable VL (> 1000 copies/ml), in Gomba district, rural Uganda. We abstracted records from eight HIV clinics; seven health center III’s (facilities which provide basic preventive and curative care and are headed by clinical officers) and a health center IV (mini-hospital headed by a medical doctor). Linkage to IAC was defined as provision of IAC to ART clients with detectable VL within three months of receipt of results at the health facility. Descriptive statistics and multivariable logistic regression analyses were used to evaluate factors associated with linkage to IAC. Results Of 4,100 HIV-positive persons on ART for at least 6 months, 411 (10%) had detectable VL. The median age was 32 years (interquartile range [IQR] 13–43) and 52% were female. The median duration on ART was 3.2 years (IQR 1.8–4.8). A total of 311 ART clients (81%) were linked to IAC. Receipt of ART at a Health Center level IV was associated with a two-fold higher odds of IAC linkage compared with Health Center level III (adjusted odds ratio [aOR] 1.78; 95% CI 1.00–3.16; p = 0.01). Age, gender, marital status and ART duration were not related to IAC linkage. Conclusions Linkage to IAC was high among persons with detectable VL in rural Uganda, with greater odds of linkage at a higher-level health facility. Strategies to optimize IAC linkage at lower-level health facilities for persons with suboptimal ART adherence are needed.

scholarly journals Utility of the Cobas® Plasma Separation Card as a Sample Collection Device for Serological and Virological Diagnosis of Hepatitis C Virus Infection

Diagnostics ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 473
Author(s):  
Fernando Velásquez-Orozco ◽  
Ariadna Rando-Segura ◽  
Joan Martínez-Camprecios ◽  
Paula Salmeron ◽  
Adrián Najarro-Centeno ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Viral Load ◽  
Hepatitis C ◽  
Virus Infection ◽  
Hepatitis C Virus Infection ◽  
Sample Collection ◽  
Serum Samples ◽  
Plasma Separation ◽  
Virological Diagnosis ◽  
A Prospective Study

Diagnosis and clinical management of people infected with hepatitis C virus (HCV) relies on results from a combination of serological and virological tests. The aim of this study was to compare the performance of dried plasma spots (DPS), prepared using the cobas® Plasma Separation Card (PSC), to plasma and serum from venipuncture, for HCV diagnosis. We carried out a prospective study using DPS and paired plasma or serum samples. Serum and DPS samples were analyzed by immunoassay using Elecsys® Anti-HCV II (Roche). Plasma and DPS samples were analyzed using the cobas® HCV viral load and cobas® HCV genotyping tests (Roche). All DPS samples that had high anti-HCV antibody titers in serum were also antibody-positive, as were five of eight samples with moderate titers. Eight samples with low titers in serum were negative with DPS. Among 80 samples with plasma HCV viral loads between 61.5 and 2.2 × 108 IU/mL, 74 were RNA-positive in DPS. The mean viral load difference between plasma and DPS was 2.65 log10 IU/mL. The performance of DPS for detection of serological and virological markers of hepatitis C virus infection was comparable to that of the conventional specimen types. However, the limits of detection were higher for DPS.

scholarly journals Multicenter Evaluation of the Cepheid Xpert® HBV Viral Load Test

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 297
Author(s):  
Fabbio Marcuccilli ◽  
Stephane Chevaliez ◽  
Thomas Muller ◽  
Luna Colagrossi ◽  
Giulia Abbondanza ◽  
...  
Keyword(s):  
Viral Load ◽  
Standard Deviation ◽  
Hbv Infection ◽  
Load Test ◽  
Serum Samples ◽  
Viral Load Test ◽  
Deming Regression ◽  
B Virus ◽  
Edta Plasma ◽  
Viral Load Assay

Accurate measurement of the hepatitis B virus (HBV) DNA is important for the management of patients with chronic HBV infection. Here, the performance of the Xpert® HBV Viral Load test (Xpert HBV Viral Load) versus the Roche COBAS® Ampliprep/COBAS® TaqMan® system (CAP/CTM HBV) HBV test v2.0 was evaluated. From September 2017 to December 2017, a total of 876 prospectively collected or archived serum or EDTA plasma specimens from subjects chronically infected with HBV were tested using the Xpert HBV Viral Load and the CAP/CTM HBV v2.0 assays. Of the 876 specimens tested, 560 were within the quantitative range of both assays. The agreement between the two methods was 90.0%. No difference in plasma or serum samples was observed. Deming regression analysis showed a good correlation of the Xpert HBV Viral Load assay with the CAP/CTM HBV v2.0 assay. The Bland–Altman analysis showed a good agreement between the results of the Xpert HBV Viral Load assay and the CAP/CTM HBV assay, with a mean difference (±1.96 standard deviation) of 0.0091 ± 0.3852 Log IU/mL. Comparing the two assays, only nineteen specimens (2.1%) had a difference greater than 1.96 times the standard deviation. The Xpert® HBV Viral Load test is suitable for monitoring patients with HBV infection and is useful in diagnostic settings.

scholarly journals Evolutionary Analysis of Cystatins of Early-Emerging Metazoans Reveals a Novel Subtype in Parasitic Cnidarians

Biology ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 110
Author(s):  
Pavla Bartošová-Sojková ◽  
Jiří Kyslík ◽  
Gema Alama-Bermejo ◽  
Ashlie Hartigan ◽  
Stephen D. Atkinson ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Organization ◽  
Gene Repertoire ◽  
Evolutionary Analysis ◽  
Ancestral Gene ◽  
Protein Architecture ◽  
Basal Metazoan ◽  
Cystatin Gene ◽  
Evolutionary Aspects

The evolutionary aspects of cystatins are greatly underexplored in early-emerging metazoans. Thus, we surveyed the gene organization, protein architecture, and phylogeny of cystatin homologues mined from 110 genomes and the transcriptomes of 58 basal metazoan species, encompassing free-living and parasite taxa of Porifera, Placozoa, Cnidaria (including Myxozoa), and Ctenophora. We found that the cystatin gene repertoire significantly differs among phyla, with stefins present in most of the investigated lineages but with type 2 cystatins missing in several basal metazoan groups. Similar to liver and intestinal flukes, myxozoan parasites possess atypical stefins with chimeric structure that combine motifs of classical stefins and type 2 cystatins. Other early metazoan taxa regardless of lifestyle have only the classical representation of cystatins and lack multi-domain ones. Our comprehensive phylogenetic analyses revealed that stefins and type 2 cystatins clustered into taxonomically defined clades with multiple independent paralogous groups, which probably arose due to gene duplications. The stefin clade split between the subclades of classical stefins and the atypical stefins of myxozoans and flukes. Atypical stefins represent key evolutionary innovations of the two parasite groups for which their origin might have been linked with ancestral gene chimerization, obligate parasitism, life cycle complexity, genome reduction, and host immunity.

scholarly journals Molecular detection of vector borne pathogens in anemic and thrombocytopenic dogs in southern Brazil

2018 ◽  
Vol 27 (4) ◽  
pp. 505-513 ◽  
Author(s):  
Anna Cláudia Baumel Mongruel ◽  
Priscila Ikeda ◽  
Keyla Carstens Marques de Sousa ◽  
Jyan Lucas Benevenute ◽  
Margarete Kimie Falbo ◽  
...  
Keyword(s):  
18S Rrna ◽  
Molecular Detection ◽  
Phylogenetic Analyses ◽  
Southern Brazil ◽  
Conventional Pcr ◽  
Pathogenic Potential ◽  
Vector Borne ◽  
Pcr Assays ◽  
Etiological Agents ◽  
Positive Results

Abstract Arthropod-borne pathogens are medically important because of their ability to cause diseases in their hosts. The purpose of this study was to detect the occurrence of Ehrlichia spp., piroplasmids and Hepatozoon spp. in dogs with anemia and thrombocytopenia in southern Brazil. EDTA-whole blood was collected from 75 domestic dogs presenting anemia or/and thrombocytopenia from Guarapuava, state of Paraná, Brazil. DNA samples were subjected to conventional PCR assays for Ehrlichia spp. (dsb), piroplasmids (18S rRNA) and Hepatozoon spp. (18S rRNA), followed by sequencing and phylogenetic analyses. Among the 75 dogs, one (1.33%) was positive for Hepatozoon sp. and six (8%) were positive for piroplasmids in 18S rRNA cPCR assays. None of the dogs showed positive results in Ehrlichia spp.-cPCR targeting dsb gene. The phylogenetic analyses revealed that three piroplasm sequences were clustered with Rangellia vitalii, while one sequence was grouped with B. vogeli. The only sequence obtained from Hepatozoon spp.-PCR protocol was pooled with H. canis. Therefore, there is urgent need for differential molecular diagnosis of the two piroplasm species cited as etiological agents in clinical cases of canine hemoparasitic diseases, given the higher pathogenic potential of R. vitalii than of B. vogeli.

scholarly journals Clinical, virological and epidemiological characterization of dengue outbreak in Myanmar, 2015

2017 ◽  
Vol 145 (9) ◽  
pp. 1886-1897 ◽  
Author(s):  
A. K. KYAW ◽  
M. M. NGWE TUN ◽  
M. L. MOI ◽  
T. NABESHIMA ◽  
K. T. SOE ◽  
...  
Keyword(s):  
Primary Infection ◽  
Phylogenetic Analyses ◽  
Molecular Techniques ◽  
Severe Dengue ◽  
Envelope Gene ◽  
Mosquito Vector ◽  
Serum Samples ◽  
Denv Serotypes ◽  
Significant Difference ◽  
Study Sites

SUMMARYHospital-based surveillance was conducted at two widely separated regions in Myanmar during the 2015 dengue epidemic. Acute phase serum samples were collected from 332 clinically diagnosed dengue patients during the peak season of dengue cases. Viremia levels were measured by quantitative real-time PCR and plaque assays using FcγRIIA-expressing and non-FcγRIIA-expressing BHK cells to specifically determine the infectious virus particles. By serology and molecular techniques, 280/332 (84·3%) were confirmed as dengue patients. All four serotypes of dengue virus (DENV) were isolated from among 104 laboratory-confirmed patients including two cases infected with two DENV serotypes. High percentage of primary infection was noted among the severe dengue patients. Patients with primary infection or DENV IgM negative demonstrated significantly higher viral loads but there was no significant difference among the severity groups. Viremia levels among dengue patients were notably high for a long period which was assumed to support the spread of the virus by the mosquito vector during epidemic. Phylogenetic analyses of the envelope gene of the epidemic strains revealed close similarity with the strains previously isolated in Myanmar and neighboring countries. DENV-1 dominated the epidemic in 2015 and the serotype (except DENV-3) and genotype distributions were similar in both study sites.

scholarly journals Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020

2021 ◽  
Vol 26 (43) ◽  
Author(s):  
Maximilian Muenchhoff ◽  
Alexander Graf ◽  
Stefan Krebs ◽  
Caroline Quartucci ◽  
Sandra Hasmann ◽  
...  
Keyword(s):  
Healthcare Workers ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Local Level ◽  
University Hospital ◽  
Metropolitan Region ◽  
Viral Genomes ◽  
Genomic Epidemiology ◽  
Viral Spread ◽  
Spatio Temporal

Background In the SARS-CoV-2 pandemic, viral genomes are available at unprecedented speed, but spatio-temporal bias in genome sequence sampling precludes phylogeographical inference without additional contextual data. Aim We applied genomic epidemiology to trace SARS-CoV-2 spread on an international, national and local level, to illustrate how transmission chains can be resolved to the level of a single event and single person using integrated sequence data and spatio-temporal metadata. Methods We investigated 289 COVID-19 cases at a university hospital in Munich, Germany, between 29 February and 27 May 2020. Using the ARTIC protocol, we obtained near full-length viral genomes from 174 SARS-CoV-2-positive respiratory samples. Phylogenetic analyses using the Auspice software were employed in combination with anamnestic reporting of travel history, interpersonal interactions and perceived high-risk exposures among patients and healthcare workers to characterise cluster outbreaks and establish likely scenarios and timelines of transmission. Results We identified multiple independent introductions in the Munich Metropolitan Region during the first weeks of the first pandemic wave, mainly by travellers returning from popular skiing areas in the Alps. In these early weeks, the rate of presumable hospital-acquired infections among patients and in particular healthcare workers was high (9.6% and 54%, respectively) and we illustrated how transmission chains can be dissected at high resolution combining virus sequences and spatio-temporal networks of human interactions. Conclusions Early spread of SARS-CoV-2 in Europe was catalysed by superspreading events and regional hotspots during the winter holiday season. Genomic epidemiology can be employed to trace viral spread and inform effective containment strategies.

scholarly journals Gammaproteobacteria as essential primary symbionts in the striped shield bug, Graphosoma Lineatum (Hemiptera: Pentatomidae)

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Naeime Karamipour ◽  
Yaghoub Fathipour ◽  
Mohammad Mehrabadi
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Adult Stage ◽  
Phylogenetic Analyses ◽  
Light And Electron Microscopy ◽  
Pcr Analysis ◽  
Evolutionary Analysis ◽  
Bacterial Cells ◽  
Stink Bug ◽  
Surface Sterilization

Abstract Many members of suborder Heteroptra harbor heritable symbiotic bacteria. Here we characterize the gut symbiotic bacterium in Graphosoma lineatum (Hemiptera: Pentatomidae) by using molecular phylogeny, real-time PCR analysis as well as light and electron microscopy observations. The microscopy observations revealed the presence of a large number of rod-shaped bacterial cells in the crypts. A very high prevalence (98 to 100%) of the symbiont infection was found in the insect populations that strongly supports an intimate association between these two organisms. Real-time PCR analysis also showed that the Gammaproteobacteria dominated the crypts. The sequences of 16sr RNA and groEL genes of symbiont showed high levels of similarity (93 to 95%) to Pantoea agglomeranse and Erwinia herbicola Gammaproteobacteria. Phylogenetic analyses placed G. lineatum symbiont in a well-defined branch, divergent from other stink bug bacterial symbionts. Co-evolutionary analysis showed lack of host-symbiont phylogenetic congruence. Surface sterilization of eggs resulted in increased pre-adult stage in the offspring (aposymbionts) in comparison to the normal. Also, fecundity, longevity, and adult stage were significantly decreased in the aposymbionts. Therefore, it seems that the symbiont might play a vital function in the host biology, in which host optimal development depends on the symbiont.

Thyroid hormone suppression in feeder pigs following polymicrobial or porcine reproductive and respiratory syndrome virus-2 challenge

2021 ◽  
Author(s):  
J Alex Pasternak ◽  
Daniel J MacPhee ◽  
Joan K Lunney ◽  
Raymond R R Rowland ◽  
PigGen Canada ◽  
...  
Keyword(s):  
Viral Load ◽  
Thyroid Hormone ◽  
Thyroid Hormones ◽  
Average Daily Gain ◽  
Respiratory Syndrome Virus ◽  
Post Inoculation ◽  
Serum Samples ◽  
Cross Sectional ◽  
Post Exposure ◽  
Daily Gain

Abstract Thyroid hormones are powerful regulators of growth, development and basal metabolic rate and can be dysregulated under conditions of severe stress or illness. To understand the role of these hormones in porcine disease response, serum samples were obtained from 3 batches of nursery-aged pigs (n=208) exposed to a natural polymicrobial disease challenge with an array of bacterial and viral pathogens. Levels of total thyroxin (T4) and triiodothyronine (T3) assessed in sera by radioimmunoassay (RIA), decreased significantly by 14 days post exposure (DPE). Levels of T3 partially rebounded by 48 DPE, while T4 levels remain depressed. Post-exposure T3 and T4 levels were positively correlated with acute and long-term average daily gain. Cross-sectional sampling of animals maintained at the high health source farms, showed no equivalent change in either hormone when managed under standard industry conditions. To further elucidate the effect of PRRSV-infection on thyroid hormone levels, archived sera over 42 days post inoculation (DPI) from nursery pigs (N=190) challenged with one of two PRRSV2 strains by the PRRS Host Genetics Consortium (PHGC) were similarly assessed, with animals selected in a two-by-two design, to investigate biological extremes in average daily gain (ADG) and viral load. All animals showed a similar decrease in both thyroid hormones reaching a minimum at 7 DPI and returning to near pre challenge levels by 42 DPI. Post challenge T3 and T4 levels were significantly greater in high ADG groups, with no significant association with viral load or strain. The results of this study demonstrate porcine susceptibility to thyroid disruption in response to disease challenge and demonstrate a relationship between this response and growth performance.

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