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Next Generation Sequencing: Current Technologies and Applications | Book

Next Generation Sequencing: Current Technologies and Applications | Book | Virology and Bioinformatics from Virology.ca | Scoop.it
Explores the most recent advances in NGS instrumentation and data analysis. Includes a comprehensive description of current NGS platforms, their sequencing chemistries, instrument specifications, general workflows and procedures.
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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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It's a group effort - the curators:

It's a group effort - the curators: | Virology and Bioinformatics from Virology.ca | Scoop.it

get in touch if you want to help curate this topic

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Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
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A new ensemble coevolution system for detecting HIV-1 protein coevolution

A new ensemble coevolution system for detecting HIV-1 protein coevolution | Virology and Bioinformatics from Virology.ca | Scoop.it
Background

A key challenge in the field of HIV-1 protein evolution is the identification of coevolving amino acids at the molecular level. In the past decades, many sequence-based methods have been designed to detect position-specific coevolution within and between different proteins. However, an ensemble coevolution system that integrates different methods to improve the detection of HIV-1 protein coevolution has not been developed.

Results

We integrated 27 sequence-based prediction methods published between 2004 and 2013 into an ensemble coevolution system. This system allowed combinations of different sequence-based methods for coevolution predictions. Using HIV-1 protein structures and experimental data, we evaluated the performance of individual and combined sequence-based methods in the prediction of HIV-1 intra- and inter-protein coevolution. We showed that sequence-based methods clustered according to their methodology, and a combination of four methods outperformed any of the 27 individual methods. This four-method combination estimated that HIV-1 intra-protein coevolving positions were mainly located in functional domains and physically contacted with each other in the protein tertiary structures. In the analysis of HIV-1 inter-protein coevolving positions between Gag and protease, protease drug resistance positions near the active site mostly coevolved with Gag cleavage positions (V128, S373-T375, A431, F448-P453) and Gag C-terminal positions (S489-Q500) under selective pressure of protease inhibitors.

Conclusions

This study presents a new ensemble coevolution system which detects position-specific coevolution using combinations of 27 different sequence-based methods. Our findings highlight key coevolving residues within HIV-1 structural proteins and between Gag and protease, shedding light on HIV-1 intra- and inter-protein coevolution.
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The Lancet Zika virus resource centre

The Lancet Zika virus resource centre | Virology and Bioinformatics from Virology.ca | Scoop.it
The Lancet Zika virus resource centre brings together the best evidence from across The Lancet family of journals—offered with free access—to assist researchers, policy makers, and health workers, in understanding the effects of the outbreak and how best to respond. Find out more about Zika virus in thisSpecial Report.
 
 

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Real-time, portable genome sequencing for Ebola surveillance

Real-time, portable genome sequencing for Ebola surveillance | Virology and Bioinformatics from Virology.ca | Scoop.it
The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10−3 and 1.42 × 10−3 mutations per site per year. This is equivalent to 16–27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15–60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.
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Bioecological Drivers of Rabies Virus Circulation in a Neotropical Bat Community

Bioecological Drivers of Rabies Virus Circulation in a Neotropical Bat Community | Virology and Bioinformatics from Virology.ca | Scoop.it
Author Summary The vampire bat is known to be the main reservoir of the rabies virus (RABV) in South America. Nevertheless, other bat species are implicated in the cycle of the virus. Indeed, seven genus-specific rabies lineages have been described in insectivorous bats in Brazil. In French Guiana, we looked for the presence of the virus in a large number of bats, belonging to 30 different species. We found a high rate of seropositive animals, mainly haematophagous bats, and in those living in monospecific colonies and in forest habitats. We also monitored two colonies of vampire bats over a 4-year period and found that some animals became seropositive for the RABV, while others, after being seropositive, were able to become seronegative. These data first of all demonstrate that the virus widely circulates in bat communities with transmission occurring via direct saliva contact with broken skin and mucosa at the intra-specific level in vampire bat species. Exposure of other bat species, including those that do not share the same microhabitat, occurs in all forest strata through modes of transmission that have yet to be determined. Secondly, these animals seem to be exposed regularly, and most of them have a great ability to control and eliminate the virus. Third, these results suggest that pristine forest habitats provide sufficient food resources for the survival of vampire bats and propagation of RABV. In contrast, in disturbed habitats, where resources are decreasing, the vampires might have to shift to alternative resources such as cattle, domestic animals or even human beings. Altogether, the risk of rabies virus transmission may increase on the edge between forest and anthropized areas.
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Yet MORE reasons to fear bats...!

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Seroepidemiological Studies of Crimean-Congo Hemorrhagic Fever Virus in Domestic and Wild Animals

Seroepidemiological Studies of Crimean-Congo Hemorrhagic Fever Virus in Domestic and Wild Animals | Virology and Bioinformatics from Virology.ca | Scoop.it
Crimean-Congo hemorrhagic fever (CCHF) is a widely distributed, tick-borne viral disease. Humans are the only species known to develop illness after CCHF virus (CCHFV) infection, characterized by a nonspecific febrile illness that can progress to severe, often fatal, hemorrhagic disease. A variety of animals may serve as asymptomatic reservoirs of CCHFV in an endemic cycle of transmission. Seroepidemiological studies have been instrumental in elucidating CCHFV reservoirs and in determining endemic foci of viral transmission. Herein, we review over 50 years of CCHFV seroepidemiological studies in domestic and wild animals. This review highlights the role of livestock in the maintenance and transmission of CCHFV, and provides a detailed summary of seroepidemiological studies of wild animal species, reflecting their relative roles in CCHFV ecology.
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One of the ten agents Jon Cohen writing in Science thinks should have a vaccine made for it.

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MicroRNA profiling of the whitefly Bemisia tabaci Middle East-Aisa Minor I following the acquisition of Tomato yellow leaf curl China viru

MicroRNA profiling of the whitefly Bemisia tabaci Middle East-Aisa Minor I following the acquisition of Tomato yellow leaf curl China viru | Virology and Bioinformatics from Virology.ca | Scoop.it
Background

The begomoviruses are the largest and most economically important group of plant viruses exclusively vectored by whitefly (Bemisia tabaci) in a circulative, persistent manner. During this process, begomoviruses and whitefly vectors have developed close relationships and complex interactions. However, the molecular mechanisms underlying these interactions remain largely unknown, and the microRNA profiles for viruliferous and nonviruliferous whiteflies have not been studied.

Methods

Sequences of Argonaute 1(Ago1) and Dicer 1 (Dcr1) genes were cloned from B. tabaci MEAM1 cDNAs. Subsequently, deep sequencing of small RNA libraries from uninfected and Tomato yellow leaf curl China virus (TYLCCNV)-infected whiteflies was performed. The conserved and novel miRNAs were identified using the release of miRBase Version 19.0 and the prediction software miRDeep2, respectively. The sequencing results of selected deregulated and novel miRNAs were further confirmed using quantitative reverse transcription-PCR. Moreover, the previously published B. tabaci MEAM1 transcriptome database and the miRNA target prediction algorithm miRanda 3.1 were utilized to predict potential targets for miRNAs. Gene Ontology (GO) analysis was also used to classify the potential enriched functional groups of their putative targets.

Results

Ago1 and Dcr1orthologs with conserved domains were identified from B. tabaci MEAM1. BLASTn searches and sequence analysis identified 112 and 136 conserved miRNAs from nonviruliferous and viruliferous whitefly libraries respectively, and a comparison of the conserved miRNAs of viruliferous and nonviruliferous whiteflies revealed 15 up- and 9 down-regulated conserved miRNAs. 7 novel miRNA candidates with secondary pre-miRNA hairpin structures were also identified. Potential targets of conserved and novel miRNAs were predicted using GO analysis, for the targets of up- and down-regulated miRNAs, eight and nine GO terms were significantly enriched.

Conclusions

We identified Ago1 and Dcr1 orthologs from whiteflies, which indicated that miRNA-mediated silencing is present in whiteflies. Our comparative analysis of miRNAs from TYLCCNV viruliferous and nonviruliferous whiteflies revealed the relevance of deregulated miRNAs for the post-transcriptional gene regulation in these whiteflies. The potential targets of all expressed miRNAs were also predicted. These results will help to acquire a better understanding of the molecular mechanism underlying the complex interactions between begomoviruses and whiteflies.

 
 
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S African blood not to Zika's taste

S African blood not to Zika's taste | Virology and Bioinformatics from Virology.ca | Scoop.it
Latest news from South Africa, World, Politics, Entertainment and Lifestyle. The home of The Times and Sunday Times newspaper.
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Wrong A aegypti, apparently!

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Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses

Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses | Virology and Bioinformatics from Virology.ca | Scoop.it
Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with other environmental viromes.
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Went with 'em to the pans.  Wonderful places!

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NEAT: a framework for building fully automated NGS pipelines and analyses

In comparison to many publicly available tools including Galaxy, NEAT provides three main advantages: (1) Through the development of double-clickable executables, NEAT is efficient (completes within <24 hours), easy to implement and intuitive; (2) Storage space, maximum number of job submissions, wall time and cluster-specific parameters can be customized as NEAT is run on the institution’s cluster; (3) NEAT allows users to visualize and summarize NGS data rapidly and efficiently using various built-in exploratory data analysis tools including metagenomic and differentially expressed gene analysis.
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A20 Deficiency in Lung Epithelial Cells Protects against Influenza A Virus Infection

A20 Deficiency in Lung Epithelial Cells Protects against Influenza A Virus Infection | Virology and Bioinformatics from Virology.ca | Scoop.it

Author Summary Influenza viruses are a major public health threat. Each year, the typical seasonal flu epidemic affects millions of people with sometimes fatal outcomes, especially in high risk groups such as young children and elderly.

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A Conserved HIV-1-Derived Peptide Presented by HLA-E Renders Infected T-cells Highly Susceptible to Attack by NKG2A/CD94-Bearing Natural Killer Cells

A Conserved HIV-1-Derived Peptide Presented by HLA-E Renders Infected T-cells Highly Susceptible to Attack by NKG2A/CD94-Bearing Natural Killer Cells | Virology and Bioinformatics from Virology.ca | Scoop.it

Author Summary A critical mechanism by which the immune system controls viruses is through destruction of infected cells.

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SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools.

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Chapter Four - Biomarkers in HCV Infection

Liver-related biomarkers have been developed and validated mainly in patients with chronic hepatitis C for the prediction of liver fibrosis or cirrhosis, which is a final pathway of chronic liver injury. They are noninvasive, traceable, and easy-to-use. Biomarkers provide implications related to screening, diagnosis, treatment, and prognosis of chronic hepatitis. For the improvement of performance and coverage, biomarker panels, imaging biomarkers, and even genetic biomarkers have been developed. With the advancement of genomics and proteomics, earlier and more precise prediction is expected in the near future. In this review, multiple biomarker panels for the estimation of the degree of fibrosis in chronic hepatitis C, biomarkers for the screening and diagnosis of hepatitis C, biomarkers for the treatment of hepatitis C, biomarkers for the prediction of complications related to the chronic hepatitis C, and future perspectives will be summarized.
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Continuous Influx of Genetic Material from Host to Virus Populations

Continuous Influx of Genetic Material from Host to Virus Populations | Virology and Bioinformatics from Virology.ca | Scoop.it
Many genes of large double-stranded DNA viruses have a cellular origin, suggesting that host-to-virus horizontal transfer (HT) of DNA is recurrent. Yet, the frequency of these transfers has never been assessed in viral populations. Here we used ultra-deep DNA sequencing of 21 baculovirus populations extracted from two moth species to show that a large diversity of moth DNA sequences (n = 86) can integrate into viral genomes during the course of a viral infection. The majority of the 86 different moth DNA sequences are transposable elements (TEs, n = 69) belonging to 10 superfamilies of DNA transposons and three superfamilies of retrotransposons. The remaining 17 sequences are moth sequences of unknown nature. In addition to bona fide DNA transposition, we uncover microhomology-mediated recombination as a mechanism explaining integration of moth sequences into viral genomes. Many sequences integrated multiple times at multiple positions along the viral genome. We detected a total of 27,504 insertions of moth sequences in the 21 viral populations and we calculate that on average, 4.8% of viruses harbor at least one moth sequence in these populations. Despite this substantial proportion, no insertion of moth DNA was maintained in any viral population after 10 successive infection cycles. Hence, there is a constant turnover of host DNA inserted into viral genomes each time the virus infects a moth. Finally, we found that at least 21 of the moth TEs integrated into viral genomes underwent repeated horizontal transfers between various insect species, including some lepidopterans susceptible to baculoviruses. Our results identify host DNA influx as a potent source of genetic diversity in viral populations. They also support a role for baculoviruses as vectors of DNA HT between insects, and call for an evaluation of possible gene or TE spread when using viruses as biopesticides or gene delivery vectors.
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Concern over Zika virus grips the world - The Lancet

Concern over Zika virus grips the world - The Lancet | Virology and Bioinformatics from Virology.ca | Scoop.it

In the past week, the world has mobilised to tackle the latest threat to global health security—Zika virus, now spreading rapidly in the Americas. Udani Samarasekera and Marcia Triunfol report.

Worldwide concern over Zika virus (panel) and its temporal and geographical association with clusters of birth and neurological conditions escalated this week, with WHO declaring a Public Health Emergency of International Concern.


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Homeopathy: the air guitar of medicine | Gadgette

Homeopathy: the air guitar of medicine | Gadgette | Virology and Bioinformatics from Virology.ca | Scoop.it
Homeopathy is an alternative medicine, which means a few things. It means it’s not medicine, it’s an alternative; it means it’s seen by many as somehow better and healthier than modern medicines; and it means that people are incredibly emotional in their support for it. I’ve received death threats pretty much every time I’ve ever written …
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Long-Lasting Immune Protection after Chikungunya Emergence in a Cambodian Rural Community

Long-Lasting Immune Protection after Chikungunya Emergence in a Cambodian Rural Community | Virology and Bioinformatics from Virology.ca | Scoop.it
Author Summary After first being identified in the 1950s and spreading from Africa in the 1960s, a new pandemic strain of Chikungunya virus emerged in East Africa and the Indian Ocean in 2004–2005, progressing to Asia. Cases have since been described in previously unaffected territories, as well as regions where Chikungunya transmission was never interrupted. Chikungunya circulated in Cambodia in the 1960s and 1970s until the tragic historical events that followed the civil war. After nearly 40 years of absence of the virus, the new pandemic strain was first detected in 2011. We undertook a field investigation of a Chikungunya outbreak in Cambodia in 2012. The usefulness of clinical signs for diagnosis of infection is discussed. Unlike studies from other settings, we show that older age was associated with a lower risk of Chikungunya infection, even after behavioural and occupational factors have been taken into account. This is the first evidence suggesting that infection in the 1960s and 1970s likely provided long-lasting cross-protection against this new strain. These findings, which will be further explored in the laboratory, are important to understand immunity against Chikungunya and to predict future epidemics and public health needs.
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Important lessons for Zika?

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Selection of HIV vaccine candidates for concurrent testing in an efficacy trial

Selection of HIV vaccine candidates for concurrent testing in an efficacy trial | Virology and Bioinformatics from Virology.ca | Scoop.it
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Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009–201

Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009–201 | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract
Background

Human Coronaviruses (HCoV) are a common cause of respiratory illnesses and are responsible for considerable morbidity and hospitalization across all age groups especially in individuals with compromised immunity. There are six known species of HCoV: HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, MERS-CoV and SARS-HCoV. Although studies have shown evidence of global distribution of HCoVs, there is limited information on their presence and distribution in Kenya.

Methods

HCoV strains that circulated in Kenya were retrospectively diagnosed and molecularly characterized. A total of 417 nasopharyngeal specimens obtained between January 2009 and December 2012 from around Kenya were analyzed by a real time RT-PCR using HCoV-specific primers. HCoV-positive specimens were subsequently inoculated onto monolayers of LL-CMK2 cells. The isolated viruses were characterized by RT-PCR amplification and sequencing of the partial polymerase (pol) gene.

Results

The prevalence of HCoV infection was as follows: out of the 417 specimens, 35 (8.4 %) were positive for HCoV, comprising 10 (2.4 %) HCoV-NL63, 12 (2.9 %) HCoV-OC43, 9 (2.1 %) HCoV-HKU1, and 4 (1 %) HCoV-229E. The Kenyan HCoV strains displayed high sequence homology to the prototypes and contemporaneous strains. Evolution analysis showed that the Kenyan HCoV-OC43 and HCoV-NL63 isolates were under purifying selection. Phylogenetic evolutionary analyses confirmed the identities of three HCoV-HKU1, five HCoV-NL63, eight HCoV-OC43 and three HCoV-229E.

Conclusions

There were yearly variations in the prevalence and circulation patterns of individual HCoVs in Kenya. This paper reports on the first molecular characterization of human Coronaviruses in Kenya, which play an important role in causing acute respiratory infections among children.

 
 
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'Zika virus unlikely to reach S Africa'

'Zika virus unlikely to reach S Africa' | Virology and Bioinformatics from Virology.ca | Scoop.it
Institute for Communicable Diseases says people travelling to affected countries need to be extra careful.
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Knew there was more than one good reason to live here...B=-)

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FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases | Abstract

"The accelerated growth of protein databases offers great possibilities for the study of protein function using sequence similarity and conservation. However, the huge number of sequences deposited in these databases requires new ways of analyzing and organizing the data. It is necessary to group the many very similar sequences, creating clusters with automated derived annotations useful to understand their function, evolution, and level of experimental evidence. We developed an algorithm called FastaHerder2, which can cluster any protein database, putting together very similar protein sequences based on near-full-length similarity and/or high threshold of sequence identity. We compressed 50 reference proteomes, along with the SwissProt database, which we could compress by 74.7%. The clustering algorithm was benchmarked using OrthoBench and compared with FASTA HERDER, a previous version of the algorithm, showing that FastaHerder2 can cluster a set of proteins yielding a high compression, with a lower error rate than its predecessor. We illustrate the use of FastaHerder2 to detect biologically relevant functional features in protein families. With our approach we seek to promote a modern view and usage of the protein sequence databases more appropriate to the postgenomic era."

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Digital detection of endonuclease mediated gene disruption in the HIV provirus

Digital detection of endonuclease mediated gene disruption in the HIV provirus | Virology and Bioinformatics from Virology.ca | Scoop.it
Genome editing by designer nucleases is a rapidly evolving technology utilized in a highly diverse set of research fields.
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Differential Toxicity of Antibodies to the Prion Protein

Differential Toxicity of Antibodies to the Prion Protein | Virology and Bioinformatics from Virology.ca | Scoop.it

Author Summary The human prion disease, Creutzfeldt-Jakob disease (CJD), is a progressive neurodegenerative syndrome.

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Loss of Function of Intestinal IL-17 and IL-22 Producing Cells Contributes to Inflammation and Viral Persistence in SIV-Infected Rhesus Macaques

Loss of Function of Intestinal IL-17 and IL-22 Producing Cells Contributes to Inflammation and Viral Persistence in SIV-Infected Rhesus Macaques | Virology and Bioinformatics from Virology.ca | Scoop.it

Author Summary Persistent immune activation and inflammation are key features and strong predictors of morbidity/mortality in HIV infection.

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Guillain-Barré syndrome and Zika viral illnesses | America's North Shore Journal

As mosquitoes continue to spread Zika viral illnesses across Central and South America, Brazil and a number of other countries are noting a perceived surge in

Via Ian M Mackay, PhD
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