scholarly journals Identifying Overlapping Phylogenetic and Geographic Roots of HIV – 1 Evolution through Computational Analyses

2013 ◽  
Vol 7 ◽  
pp. 23-29
Author(s):  
Pankaj Kumar Singh ◽  
Rahul Banik ◽  
Hirak Jyoti Chakraborty ◽  
Sasti Gopal Das ◽  
Sayak Ganguli ◽  
...  
Keyword(s):  
Deficiency Syndrome ◽  
High Rate ◽  
Genome Sequences ◽  
Human Immuno Deficiency Virus ◽  
The Difference ◽  
Phylogenetic Lineages ◽  
Computational Analyses ◽  
High Degree ◽  
Parameter Values ◽  
Hiv 1

HIV-1 or Human Immuno Deficiency Virus-1 is the main causative agent of Acquired Immuno Deficiency Syndrome (AIDS). Human host infected with HIV - 1 extensively harbours many viral variants but very little is known about the difference in pattern[17] of evolution of phylogenetic lineages of HIV-1 non recombinant, normal inter subtype recombinant and main two specific recombinant forms of HIV-1 i.e., Circulating Recombinant Forms (CRFs) and Unique Recombinant Forms (URFs). This study is mainly concerned with study of the difference in evolutionary lineages of non-recombinant and recombinant sequences of HIV-1 genome sequences and identification of geographically rich areas which has reported high degree of HIV-1 occurrence and variety. Total 1550 HIV-1 genome sequences were obtained from HIV Los Alamos Database. The sequences were aligned using MAFFT (Multiple Alignment using Fast Fourier Transform) web server tool. Alignment was carried out using 10 different set of alignment parameter values. After alignment the aligned file was used for constructing N-J phylogenetic tree using Clustal X2 tool. Phylogenetic analysis was performed keeping in mind the category to which the sequence belongs. Upon analysis it was observed that the clade containing the probable ancestor belongs remained constant in all cases of different alignment values. Non recombinant isolates, inter subtype recombinants, CRFs, URFs all followed different patterns of evolution. Non recombinant sequences were found geographically specific and subtype specific to some extent whereas, normal recombinants were subtype specific and less geographically specific. CRFs showed variation among the pattern of their evolution. At some instances the sequences occurred as sister taxa of non-recombinant or normal inter subtype recombinant sequences, while at some instances as sister taxa of other CRFs where they were geographically specific. Three CRFs existed as completely diverged sequences. URFs were four in number; two of them were Indian isolates of while other two were Japanese isolates. URFs were found to be totally geographically specific. Geography wise high rate of variation was observed in India and Japan as these two countries had sequences belonging to all of the above categories. Cameroon and South Africa have very large number isolates and a considerable amount of genetic variation among isolates but they lack URFs.

scholarly journals Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C

2013 ◽  
Vol 94 (9) ◽  
pp. 1995-2004 ◽  
Author(s):  
Rafal Tokarz ◽  
Saddef Haq ◽  
Stephen Sameroff ◽  
Stephen R. C. Howie ◽  
W. Ian Lipkin
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Genomic Analysis ◽  
The Other ◽  
High Rate ◽  
Structural Genes ◽  
Genome Sequences ◽  
Capsid Region ◽  
High Degree ◽  
Degree Of Similarity

Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease.

scholarly journals Genetic Diversity of HIV-1 in Krasnoyarsk Krai: Area with High Levels of HIV-1 Recombination in Russia

2020 ◽  
Vol 2020 ◽  
pp. 1-21
Author(s):  
Lada V. Maksimenko ◽  
Aleksey V. Totmenin ◽  
Mariya P. Gashnikova ◽  
Ekaterina M. Astakhova ◽  
Sergey E. Skudarnov ◽  
...  
Keyword(s):  
Hiv Transmission ◽  
Virus Transmission ◽  
High Rate ◽  
Morbidity Rate ◽  
Krasnoyarsk Krai ◽  
Central Russia ◽  
The Difference ◽  
Epidemic Development ◽  
Subtype A ◽  
Hiv 1

More than a quarter of HIV-infected individuals registered in Russia live in Siberia. Unlike Central Russia where HIV-1 subtype A6 is predominant, in most Siberian regions since 2012, a new HIV-1 CRF63_02A1 genetic variant has spread, with the share of this variant attaining 75–85% among newly identified HIV cases. Krasnoyarsk Krai is considered to be a high-risk territory according to morbidity rate and HIV infection incidence among the population. The current paper aims to study the molecular epidemiologic characteristics of HIV-1 spreading in Krasnoyarsk Krai. Phylogenetic and recombination analyses of pol (PR-RT, IN) and env regions of the virus were used for genotyping 159 HIV-1 isolated in Krasnoyarsk Krai. 57.2% of the isolates belonged to subtype A (A6) specific to Russia, 12.6% to CRF63_02A1, and 0.6% to CRF02_AGСА, and in 29.6% HIV-1 URFs were detected, including URF63/А (23.9%), URFА/В (4.4%), and URF02/А (1.3%). In 6 of 7, HIV-1 URFА/В identical recombination model was detected; the origin of 38 URF63/А was proven to be the result of individual recombination events. Since 2015, a share of the population with newly diagnosed HIV who were infected with HIV-1 URF reached an exceptionally high rate of 38.6%. As distinct from adjacent Siberian regions, the HIV-1 CRF63_02A1 prevalence rate in Krasnoyarsk Krai is within 16%; however, the increased contribution of new HIV-1 into the regional epidemic development was observed due to the recombination of viruses of subtypes А, В, and CRF63_02A1. The difference between the described molecular epidemiologic picture in Krasnoyarsk Krai and in adjacent areas is likely caused by differences in predominant routes of HIV transmission and by more recent HIV-1 CRF63_02A1 transmission in the PWID group, which had a high prevalence of HIV-1 subtype A by the time of the new virus transmission, resulting in increased possibility of coinfection with various HIV-1 genetic variants.

Peritoneal Fluid and Plasma Fibrinolytic Activity in Women with Pelvic Inflammatory Disease

1992 ◽  
Vol 68 (02) ◽  
pp. 102-105 ◽  
Author(s):  
P J Dörr ◽  
E J P Brommer ◽  
G Dooijewaard ◽  
H M Vemer
Keyword(s):  
Pelvic Inflammatory Disease ◽  
Inflammatory Disease ◽  
Peritoneal Fluid ◽  
Fibrinolytic Activity ◽  
Degradation Products ◽  
Adhesion Formation ◽  
High Rate ◽  
Control Group ◽  
The Difference ◽  
Fibrinolytic Parameters

SummaryPrevious studies have shown that the fibrinolytic activity of peritoneum is depressed in local inflammation. We measured fibrinolytic parameters in peritoneal fluid and in plasma of 10 women with pelvic inflammatory disease (PID). Nine women, in whom laparoscopy for sterilisation was performed, served as a control group.In the peritoneal fluid of women with PID, PAI-Ag, t-PA-Ag and u-PA-Ag were many times higher than in the control group. In contrast to the antigens which may be present in inert complexes, the potentially active compounds, measured as t-PA activity and plasmin-activable scu-PA, were not significantly different in the two groups, and in none of the samples was the active enzyme tcu-PA detectable. Nevertheless, the mean peritoneal fluid TDP and FbDP concentrations were about twenty times higher in the PID group than in the control group. In plasma of PID patients, none of the parameters except u-PA-Ag differed from those in the control group. The difference between control and patient plasma u-PA-Ag was statistically significant, but too small to attach any relevance to the observation.Our data suggest that, in contrast to the classical concept of decreased fibrinolytic activity as a cause of adhesion formation, intraperitoneal fibrinolysis is enhanced in peritoneal inflammation through stimulation of the local production of t-PA and u-PA. Despite concomitant production of PAI, fibrinolysis occurs at a high rate, resulting in high levels of fibrin degradation products. Since this activated fibrinolysis does not meet the demand, therapeutic enhancement should be considered to prevent adhesions.

scholarly journals Analysis of Low-Frequency Mutations Associated with Drug Resistance to Raltegravir before Antiretroviral Treatment

2010 ◽  
Vol 55 (3) ◽  
pp. 1114-1119 ◽  
Author(s):  
Jia Liu ◽  
Michael D. Miller ◽  
Robert M. Danovich ◽  
Nathan Vandergrift ◽  
Fangping Cai ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Treatment Failure ◽  
Low Frequency ◽  
Hiv Treatment ◽  
Viral Population ◽  
Virologic Suppression ◽  
Resistance Mutations ◽  
The Difference ◽  
Allele Specific Sequencing ◽  
Hiv 1

ABSTRACTRaltegravir is highly efficacious in the treatment of HIV-1 infection. The prevalence and impact on virologic outcome of low-frequency resistant mutations among HIV-1-infected patients not previously treated with raltegravir have not been fully established. Samples from HIV treatment-experienced patients entering a clinical trial of raltegravir treatment were analyzed using a parallel allele-specific sequencing (PASS) assay that assessed six primary and six secondary integrase mutations. Patients who achieved and sustained virologic suppression (success patients,n= 36) and those who experienced virologic rebound (failure patients,n= 35) were compared. Patients who experienced treatment failure had twice as many raltegravir-associated resistance mutations prior to initiating treatment as those who achieved sustained virologic success, but the difference was not statistically significant. The frequency of nearly all detected resistance mutations was less than 1% of viral population, and the frequencies of mutations between the success and failure groups were similar. Expansion of pre-existing mutations (one primary and five secondary) was observed in 16 treatment failure patients in whom minority resistant mutations were detected at baseline, suggesting that they might play a role in the development of drug resistance. Two or more mutations were found in 13 patients (18.3%), but multiple mutations were not present in any single viral genome by linkage analysis. Our study demonstrates that low-frequency primary RAL-resistant mutations were uncommon, while minority secondary RAL-resistant mutations were more frequently detected in patients naïve to raltegravir. Additional studies in larger populations are warranted to fully understand the clinical implications of these mutations.

scholarly journals Two maize cultivars of contrasting leaf size show different leaf elongation rates with identical patterns of extension dynamics and coordination

AoB Plants ◽  
2021 ◽  
Author(s):  
Tiphaine Vidal ◽  
Hafssa Aissaoui ◽  
Sabrina Rehali ◽  
Bruno Andrieu
Keyword(s):  
Genotypic Variation ◽  
Leaf Size ◽  
High Rate ◽  
Time Interval ◽  
Extension Rate ◽  
Leaf Production ◽  
Maize Cultivars ◽  
Plant Environment ◽  
The Difference ◽  
Leaf Extension

Abstract Simulating leaf development from initiation to maturity opens new possibilities to model plant–environment interactions and the plasticity of plant architecture. This study analyses the dynamics of leaf production and extension along a maize (Zea mays) shoot to assess important modelling choices. Maize plants from two cultivars originating from the same inbred line, yet differing in the length of mature leaves were used in this study. We characterised the dynamics of the blade and sheath lengths of all phytomers by dissecting plants every 2–3 days. We analysed how differences in leaf size were built up and we examined the coordination between the emergence of organs and phases of their extension. Leaf extension rates were higher in the cultivar with longer leaves than in the cultivar with shorter leaves; no differences were found in other aspects. We found that (i) first post-embryonic leaves were initiated at a markedly higher rate than upper leaves; (ii) below ear position, sheaths were initiated at a time intermediate between tip emergence and appearance, while above the ear position, sheaths were initiated at a high rate, such that the time interval between the blade and sheath initiations decreased for these leaves; and (iii) ear position also marked a change in the correlation in size between successive phytomers with little correlation of size between upper and lower leaves. Our results identified leaf extension rate as the reason for the difference in size between the two cultivars. The two cultivars shared the same pattern for the timing of initiation events, which was more complex than previously thought. The differences described here may explain some inaccuracies reported in functional-structural plant models. We speculate that genotypic variation in behaviour for leaf and sheath initiation exists, which has been little documented in former studies.

scholarly journals The Challenge of Diagnosing Constitutional Mismatch Repair Deficiency Syndrome in Brain Malignancies from Young Individuals

2021 ◽  
Vol 22 (9) ◽  
pp. 4629
Author(s):  
Cristina Carrato ◽  
Carolina Sanz ◽  
Ana María Muñoz-Mármol ◽  
Ignacio Blanco ◽  
Marta Pineda ◽  
...  
Keyword(s):  
Brain Tumors ◽  
Mismatch Repair ◽  
Rare Event ◽  
Deficiency Syndrome ◽  
Mismatch Repair Deficiency ◽  
Malignant Brain Tumors ◽  
Repair Deficiency ◽  
Clinical Awareness ◽  
High Degree ◽  
Constitutional Mismatch Repair Deficiency

Biallelic germline mismatch repair (MMR) gene (MLH1, MSH2, MSH6, and PMS2) mutations are an extremely rare event that causes constitutional mismatch repair deficiency (CMMRD) syndrome. CMMRD is underdiagnosed and often debuts with pediatric malignant brain tumors. A high degree of clinical awareness of the CMMRD phenotype is needed to identify new cases. Immunohistochemical (IHC) assessment of MMR protein expression and analysis of microsatellite instability (MSI) are the first tools with which to initiate the study of this syndrome in solid malignancies. MMR IHC shows a hallmark pattern with absence of staining in both neoplastic and non-neoplastic cells for the biallelic mutated gene. However, MSI often fails in brain malignancies. The aim of this report is to draw attention to the peculiar IHC profile that characterizes CMMRD syndrome and to review the difficulties in reaching an accurate diagnosis by describing the case of two siblings with biallelic MSH6 germline mutations and brain tumors. Given the difficulties involved in early diagnosis of CMMRD we propose the use of the IHC of MMR proteins in all malignant brain tumors diagnosed in individuals younger than 25 years-old to facilitate the diagnosis of CMMRD and to select those neoplasms that will benefit from immunotherapy treatment.

scholarly journals The origin of acquired immune deficiency syndrome: Darwinian or Lamarckian?

2001 ◽  
Vol 356 (1410) ◽  
pp. 877-887 ◽  
Author(s):  
Tom Burr ◽  
J. M. Hyman ◽  
Gerald Myers
Keyword(s):  
Immune Deficiency ◽  
Simulated Data ◽  
Immune Deficiency Syndrome ◽  
Acquired Immune Deficiency Syndrome ◽  
Deficiency Syndrome ◽  
Darwinian Evolution ◽  
Immunodeficiency Virus ◽  
Acquired Immune Deficiency ◽  
Hiv 1

The subtypes of human immunodeficiency virus type 1 (HIV–1) group M exhibit a remarkable similarity in their between–subtype distances, which we refer to as high synchrony. The shape of the phylogenetic tree of these subtypes is referred to as a sunburst to distinguish it from a simple star phylogeny. Neither a sunburst pattern nor a comparable degree of symmetry is seen in a natural process such as in feline immunodeficiency virus evolution. We therefore have undertaken forward–process simulation studies employing coalescent theory to investigate whether such highly synchronized subtypes could be readily produced by natural Darwinian evolution. The forward model includes both classical (macro) and molecular (micro) epidemiological components. HIV–1 group M subtype synchrony is quantified using the standard deviation of the between–subtype distances and the average of the within–subtype distances. Highly synchronized subtypes and a sunburst phylogeny are not observed in our simulated data, leading to the conclusion that a quasi–Lamarckian, punctuated event occurred. The natural transfer theory for the origin of human acquired immune deficiency syndrome (AIDS) cannot easily be reconciled with these findings and it is as if a recent non–Darwinian process took place coincident with the rise of AIDS in Africa.

Gebruiksaspecten van het uitroeppartikel wat in het Nederlands en Fries

2020 ◽  
Vol 136 (4) ◽  
pp. 189-209
Author(s):  
Henk Wolf
Keyword(s):  
The Core ◽  
The Difference ◽  
Lexical Phrase ◽  
High Degree ◽  
Lexical Phrases

Abstract Both Dutch and (West) Frisian make use of the exclamative particle wat (‘how’), that adds an element of surprise about a high degree of something to the semantics of the sentence. In this paper I will first show the similarities between the use of the particle in the two languages. I will demonstrate that, in Dutch, its use is largely confined to constructions that are semantically scalable, whereas in Frisian this restriction is far less strict. I will explain the difference by showing that Dutch wat is a syntactic amplifier of lexical phrases, whereas Frisian wat has developed into a pragmatic amplifier of the core predicate. I will try to account for that difference by showing how homophonous words absent in Dutch are likely to have influenced the use of Frisian wat, and how Dutch prosody strengthens the connection between wat and the amplified lexical phrase, whereas Frisian prosody weakens it. Finally, I will show that the system described as ‘Frisian’ is occasionally found in varieties of Dutch too

scholarly journals Nature, Position, and Frequency of Mutations Made in a Single Cycle of HIV-1 Replication

2010 ◽  
Vol 84 (19) ◽  
pp. 9864-9878 ◽  
Author(s):  
Michael E. Abram ◽  
Andrea L. Ferris ◽  
Wei Shao ◽  
W. Gregory Alvord ◽  
Stephen H. Hughes
Keyword(s):  
Viral Replication ◽  
Mutation Rate ◽  
Hot Spots ◽  
High Rate ◽  
Published Data ◽  
Single Cycle ◽  
Efficient System ◽  
Hiv 1

ABSTRACT There is considerable HIV-1 variation in patients. The extent of the variation is due to the high rate of viral replication, the high viral load, and the errors made during viral replication. Mutations can arise from errors made either by host DNA-dependent RNA polymerase II or by HIV-1 reverse transcriptase (RT), but the relative contributions of these two enzymes to the mutation rate are unknown. In addition, mutations in RT can affect its fidelity, but the effect of mutations in RT on the nature of the mutations that arise in vivo is poorly understood. We have developed an efficient system, based on existing technology, to analyze the mutations that arise in an HIV-1 vector in a single cycle of replication. A lacZα reporter gene is used to identify viral DNAs that contain mutations which are analyzed by DNA sequencing. The forward mutation rate in this system is 1.4 × 10−5 mutations/bp/cycle, equivalent to the retroviral average. This rate is about 3-fold lower than previously reported for HIV-1 in vivo and is much lower than what has been reported for purified HIV-1 RT in vitro. Although the mutation rate was not affected by the orientation of lacZα, the sites favored for mutations (hot spots) in lacZα depended on which strand of lacZα was present in the viral RNA. The pattern of hot spots seen in lacZα in vivo did not match any of the published data obtained when purified RT was used to copy lacZα in vitro.

scholarly journals Human immunodeficiency virus 1. Predominance of a group-specific neutralizing epitope that persists despite genetic variation.

1989 ◽  
Vol 170 (5) ◽  
pp. 1681-1695 ◽  
Author(s):  
I Berkower ◽  
G E Smith ◽  
C Giri ◽  
D Murphy
Keyword(s):  
Genetic Diversity ◽  
Human Immunodeficiency Virus ◽  
Neutralizing Antibodies ◽  
Neutralizing Epitope ◽  
Vaccine Strategy ◽  
Disease Pathogenesis ◽  
Immunodeficiency Virus ◽  
High Degree ◽  
Hiv 1 ◽  
Human Immunodeficiency Virus 1

HIV-1 is known to show a high degree of genetic diversity, which may have major implications for disease pathogenesis and prevention. If every divergent isolate represented a distinct serotype, then effective vaccination might be impossible. However, using a sensitive new plaque-forming assay for HIV-1, we have found that most infected patients make neutralizing antibodies, predominantly to a group-specific epitope shared among three highly divergent isolates. This epitope persists among divergent isolates and rarely mutates, despite the rapid overall mutation rate of HIV-1, suggesting that it may participate in an essential viral function. These findings, plus the rarity of reinfections among these patients, suggest that HIV-1 may be more susceptible to a vaccine strategy based on a group-specific neutralizing epitope than was previously suspected.

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