scholarly journals Mutational networks of escape from transmitted HIV-1 infection

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243391
Author(s):  
Elma H. Akand ◽  
Stephen J. Maher ◽  
John M. Murray
Keyword(s):  
Immune Response ◽  
Effective Vaccine ◽  
Subtype C ◽  
Hub And Spoke ◽  
Binding Domains ◽  
Immune Pressure ◽  
Subtype B ◽  
Combined Operations ◽  
Founder Virus ◽  
Coreceptor Binding

Human immunodeficiency virus (HIV) is subject to immune selective pressure soon after it establishes infection at the founder stage. As an individual progresses from the founder to chronic stage of infection, immune pressure forces a history of mutations that are embedded in envelope sequences. Determining this pathway of coevolving mutations can assist in understanding what is different with the founder virus and the essential pathways it takes to maintain infection. We have combined operations research and bioinformatics methods to extract key networks of mutations that differentiate founder and chronic stages for 156 subtype B and 107 subtype C envelope (gp160) sequences. The chronic networks for both subtypes revealed strikingly different hub-and-spoke topologies compared to the less structured transmission networks. This suggests that the hub nodes are impacted by the immune response and the resulting loss of fitness is compensated by mutations at the spoke positions. The major hubs in the chronic C network occur at positions 12, 137 (within the N136 glycan), and 822, and at position 306 for subtype B. While both founder networks had a more heterogeneous connected network structure, interestingly founder B subnetworks around positions 640 and 837 preferentially contained CD4 and coreceptor binding domains. Finally, we observed a differential effect of glycosylation between founder and chronic subtype B where the latter had mutational pathways significantly driven by N-glycosylation. Our study provides insights into the mutational pathways HIV takes to evade the immune response, and presents features more likely to establish founder infection, valuable for effective vaccine design.

scholarly journals Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted Variants

2009 ◽  
Vol 83 (8) ◽  
pp. 3556-3567 ◽  
Author(s):  
M.-R. Abrahams ◽  
J. A. Anderson ◽  
E. E. Giorgi ◽  
C. Seoighe ◽  
K. Mlisana ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Poisson Distribution ◽  
Cytotoxic T Lymphocyte ◽  
Virus Transmission ◽  
Effective Vaccine ◽  
Subtype C ◽  
Genetic Characteristics ◽  
Subtype B ◽  
Independent Events ◽  
Immunodeficiency Virus

ABSTRACT Identifying the specific genetic characteristics of successfully transmitted variants may prove central to the development of effective vaccine and microbicide interventions. Although human immunodeficiency virus transmission is associated with a population bottleneck, the extent to which different factors influence the diversity of transmitted viruses is unclear. We estimate here the number of transmitted variants in 69 heterosexual men and women with primary subtype C infections. From 1,505 env sequences obtained using a single genome amplification approach we show that 78% of infections involved single variant transmission and 22% involved multiple variant transmissions (median of 3). We found evidence for mutations selected for cytotoxic-T-lymphocyte or antibody escape and a high prevalence of recombination in individuals infected with multiple variants representing another potential escape pathway in these individuals. In a combined analysis of 171 subtype B and C transmission events, we found that infection with more than one variant does not follow a Poisson distribution, indicating that transmission of individual virions cannot be seen as independent events, each occurring with low probability. While most transmissions resulted from a single infectious unit, multiple variant transmissions represent a significant fraction of transmission events, suggesting that there may be important mechanistic differences between these groups that are not yet understood.

scholarly journals Nationwide Study of Drug Resistance Mutations in HIV-1 Infected Individuals under Antiretroviral Therapy in Brazil

2021 ◽  
Vol 22 (10) ◽  
pp. 5304
Author(s):  
Ana Santos-Pereira ◽  
Vera Triunfante ◽  
Pedro M. M. Araújo ◽  
Joana Martins ◽  
Helena Soares ◽  
...  
Keyword(s):  
Drug Resistance ◽  
People Living With Hiv ◽  
Resistance Mutations ◽  
Subtype C ◽  
Viral Loads ◽  
Drug Resistance Mutations ◽  
Subtype B ◽  
Low Prevalence ◽  
Living With Hiv ◽  
Hiv 1

The success of antiretroviral treatment (ART) is threatened by the emergence of drug resistance mutations (DRM). Since Brazil presents the largest number of people living with HIV (PLWH) in South America we aimed at understanding the dynamics of DRM in this country. We analyzed a total of 20,226 HIV-1 sequences collected from PLWH undergoing ART between 2008–2017. Results show a mild decline of DRM over the years but an increase of the K65R reverse transcriptase mutation from 2.23% to 12.11%. This increase gradually occurred following alterations in the ART regimens replacing zidovudine (AZT) with tenofovir (TDF). PLWH harboring the K65R had significantly higher viral loads than those without this mutation (p < 0.001). Among the two most prevalent HIV-1 subtypes (B and C) there was a significant (p < 0.001) association of K65R with subtype C (11.26%) when compared with subtype B (9.27%). Nonetheless, evidence for K65R transmission in Brazil was found both for C and B subtypes. Additionally, artificial neural network-based immunoinformatic predictions suggest that K65R could enhance viral recognition by HLA-B27 that has relatively low prevalence in the Brazilian population. Overall, the results suggest that tenofovir-based regimens need to be carefully monitored particularly in settings with subtype C and specific HLA profiles.

scholarly journals Genetic diversity and primary resistance among HIV-1-positive patients from Maringá, Paraná, Brazil

2012 ◽  
Vol 54 (4) ◽  
pp. 207-213 ◽  
Author(s):  
Karine Vieira Gaspareto ◽  
Flávia Myrian Martins de Almeida Mello ◽  
José Ricardo Colleti Dias ◽  
Vera Alice Fernandes Meneguetti ◽  
Marta Evelyn Giansante Storti ◽  
...  
Keyword(s):  
Specific Antigen ◽  
Resistance Mutation ◽  
Drug Resistance Mutation ◽  
Subtype C ◽  
Primary Resistance ◽  
Subtype B ◽  
Pcr Products ◽  
Treatment Naïve ◽  
Positive Treatment ◽  
Hiv 1

The objective of this study is to identify subtypes of Human Immunodeficiency Virus type 1 (HIV-1) and to analyze the presence of mutations associated to antiretroviral resistance in the protease (PR) and reverse transcriptase (RT) regions from 48 HIV-1 positive treatment naïve patients from an outpatient clinic in Maringá, Paraná, Brazil. Sequencing was conducted using PR, partial RT and group-specific antigen gene (gag) nested PCR products from retrotranscribed RNA. Transmitted resistance was determined according to the Surveillance Drug Resistance Mutation List (SDRM) algorithm. Phylogenetic and SimPlot analysis of concatenated genetic segments classified sequences as subtype B 19/48 (39.6%), subtype C 12/48 (25%), subtype F 4/48 (8.3%), with 13/48 (27.1%) recombinant forms. Most recombinant forms were B mosaics (B/F 12.5%, B/C 10.4%), with one C/F (2.1%) and one complex B/C/F mosaic (2.1%). Low levels of transmitted resistance were found in this study, 2/48 (2.1% to NRTIs and 2.1% for PI). This preliminary data may subsidize the monitoring of the HIV evolution in the region.

scholarly journals Analysis and Prospects of Using Recombinant Vaccinia Virus MVA Strain as a Vector in the Development of the Vaccines against Human and Simian Immunodeficiency Virus Diseases

2019 ◽  
pp. 37-44
Author(s):  
L. F. Stovba ◽  
V. T. Krotkov ◽  
D. I. Paveli’ev ◽  
S. A. Mel’nikov ◽  
V. N. Lebedev ◽  
...  
Keyword(s):  
Immune Response ◽  
Simian Immunodeficiency Virus ◽  
Structural Changes ◽  
Rhesus Macaques ◽  
Laboratory Animals ◽  
Cell Immune Response ◽  
Effective Vaccine ◽  
Protective Efficiency ◽  
Immunodeficiency Virus ◽  
Immunodominant Antigens

The review presents the results of preclinical use of vector vaccines against human immunodeficiency virus (HIV) disease and simian immunodeficiency virus (SIV) disease. Application of antiretroviral therapy exclusively is insufficient for elimination of HIV from patient’s body. This dictates the need for an effective vaccine which will reduce the number of new cases of the disease and reduce the risk of virus transmission. Current practice of medicinal product development showed the effectiveness of heterologous prime-boost regimens for the induction of expressed immune response in laboratory animals. Various vector constructs were used as priming vaccines: DNA vaccines, Bacille Calmette-Guerin vaccine, chimpanzee adenovirus, vesicular stomatitis virus, alphavirus repli-clone. Booster vaccine was represented by recombinant MVA strain. In all vector vaccines, different genes of immunodominant antigens of HIV and SIV agents were inserted. On rhesus macaques, murine, rabbit models, it was demonstrated that deployed vaccination schemes were safe and induced immune response. Because membrane HIV protein is highly variable, strongly glycoziled and subjected to structural changes during receptor binding, it cannot be viewed as a target for induction of virus neutralized antibodies. Therefore, we mainly studied the cell immune response that was presented by poly-functional CD8+ T-cells. However, some recent researches are aimed at such modification of envelope HIV immunogene that would provide for virus neutralizing antibody induction. The study of protective efficiency of the induced immunity in rhesus macaques, immunized with recombinant vectors expressing SIV’ s immunodominant antigens, in case of subsequent inoculation with virulent SIV strain has revealed that all monkeys developed illness. Assuming that the constructions with SIV’ s immunodominant antigens under protective efficiency testing on rhesus macaques imitate AIDS in humans, it seems that vaccines, developed up-to-date, will not be effective for collective immunity formation against AIDS. Therefore, the search for novel combinations of expressed immunodominant antigens for the inclusion into the composition of priming and booster vaccines remains a priority area at present time.

scholarly journals Efficiencies of Four Versions of the AMPLICOR HIV-1 MONITOR Test for Quantification of Different Subtypes of Human Immunodeficiency Virus Type 1

1999 ◽  
Vol 37 (1) ◽  
pp. 110-116 ◽  
Author(s):  
K. Triques ◽  
J. Coste ◽  
J. L. Perret ◽  
C. Segarra ◽  
E. Mpoudi ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Viral Load ◽  
Pcr Primers ◽  
Load Test ◽  
Subtype C ◽  
Subtype B ◽  
Immunodeficiency Virus ◽  
Subtype A ◽  
Hiv 1

Three versions of a commercial human immunodeficiency virus (HIV) type 1 (HIV-1) load test (the AMPLICOR HIV-1 MONITOR Test versions 1.0, 1.0+, and 1.5; Roche Diagnostics, Branchburg, N.J.) were evaluated for their ability to detect and quantify HIV-1 RNA of different genetic subtypes. Plasma samples from 96 patients infected with various subtypes of HIV-1 (55 patients infected with subtype A, 9 with subtype B, 21 with subtype C, 2 with subtype D, 7 with subtype E, and 2 with subtype G) and cultured virus from 29 HIV-1 reference strains (3 of subtype A, 6 of subtype B, 5 of subtype C, 3 of subtype D, 8 of subtype E, 3 of subtype F, and 1 of subtype G) were tested. Detection of subtypes A and E was significantly improved with versions 1.0+ and 1.5 compared to that with version 1.0, whereas detection of subtypes B, C, D, and G was equivalent with the three versions. Versions 1.0, 1.0+, and 1.5 detected 65, 98, and 100% of the subtype A-infected samples from patients, respectively, and 71, 100, and 100% of the subtype E-infected samples from patients, respectively. Version 1.5 yielded a significant increase in viral load for samples infected with subtypes A and E (greater than 1 log10 HIV RNA copies/ml). For samples infected with subtype B, C, and D and tested with version 1.5, only a slight increase in viral load was observed (<0.5 log10). We also evaluated a prototype automated version of the test that uses the same PCR primers as version 1.5. The results with the prototype automated test were highly correlated with those of the version 1.5 test for all subtypes, but were lower overall. The AMPLICOR HIV-1 MONITOR Test, version 1.5, yielded accurate measurement of the HIV load for all HIV-1 subtypes tested, which should allow the test to be used to assess disease prognosis and response to antiretroviral treatment in patients infected with a group M HIV-1 subtype.

scholarly journals Viremia in Equine Herpes Virus-1 infection and a possible link to Transient Protective Immunity

2021 ◽  
Vol 9 (1) ◽  
pp. 11-16
Author(s):  
AR Awan ◽  
OL Tulp ◽  
HJ Field
Keyword(s):  
Immune Response ◽  
Immune Responses ◽  
Murine Model ◽  
Herpes Virus ◽  
Natural Infection ◽  
Fluorescent Antibody ◽  
Buffy Coat ◽  
Effective Vaccine ◽  
Infection Model ◽  
Herpès Virus

Equine herpes virus (EHV-1) causes respiratory infections in equine, and results in abortion, paresis, neonatal death, and retinopathy and the virus may become latent following initial infection. Virus entry is via the respiratory route, and the virus replicates in the host in ciliated and non-ciliated epithelial cells of the respiratory tract and in Type 1 and Type 2 pneumocytes in the lung parenchyma. After viral replication in the respiratory system, the virus can become disseminated to other parts of body via viraemic cells. The virus also can cross the placenta which leads to abortion of live or dead fetuses without premonitory signs. Infected horses show transient immunity after natural or experimental infection and immune responses to EHV-1, but the immunoprotective status begins to decline after a few months of active infection. Due to the transient immune response, recovered horses are not immunoprotected and thus are prone to subsequent re-infection. Immunity is not long lived after experimental or natural infection, and as a result the development of an effective vaccine has remained a challenge. In this study viraemic cells were studied in a murine EHV-1 infection model. Mice were infected intranasally and viraemic cells were studied on days three and five which occurs during the peak of the infection. The results of this study may help to identify the nature of viraemic cells and their role in the transient immune response to infection. Buffy coat cells and lungs were removed and stained with a fluorescent antibody test for EHV-1 antigen, and lung specimens were subjected to transmission electron microscopy. Both techniques confirmed the presence of viraemic cells in lung tissues. These viraemic cells were further stained for EHV-1 antigen, and for CD4 or CD8 biomarkers and results are discussed re: pathogenesis of EHV-1 infection, identification of viraemic cells in a murine model and possible link of viraemia to transient immune responses in EHV-1 infection, which demonstrate the validity of this murine model for the investigation of the cytopathologic mechanism and sequelae of EHV manifestation in this model.

scholarly journals Assembly, Biochemical Characterization, Immunogenicity, Adjuvanticity, and Efficacy ofShigellaArtificial Invaplex

mSphere ◽  
2018 ◽  
Vol 3 (2) ◽  
pp. e00583-17 ◽  
Author(s):  
K. Ross Turbyfill ◽  
Kristen A. Clarkson ◽  
Anthony R. Vortherms ◽  
Edwin V. Oaks ◽  
Robert W. Kaminski
Keyword(s):  
Immune Response ◽  
Guinea Pigs ◽  
Biochemical Characterization ◽  
Diarrheal Disease ◽  
Protective Efficacy ◽  
Water Extract ◽  
Effective Vaccine ◽  
Oral Fluids ◽  
Specific Antigens ◽  
New Generation

ABSTRACTThe native Invaplex (InvaplexNAT) vaccine and adjuvant is an ion exchange-purified product derived from the water extract of virulentShigellaspecies. The key component of InvaplexNATis a high-molecular-mass complex (HMMC) consisting of theShigellalipopolysaccharide (LPS) and the invasin proteins IpaB and IpaC. To improve product purity and immunogenicity, artificial Invaplex (InvaplexAR) was developed using recombinant IpaB and IpaC proteins and purifiedShigellaLPS to assemble an HMMC consisting of all three components. Characterization of InvaplexARby various methods demonstrated similar characteristics as the previously reported HMMC in InvaplexNAT. The well-defined InvaplexARvaccine consistently contained greater quantities of IpaB, IpaC, and LPS than InvaplexNAT. InvaplexARand InvaplexNATimmunogenicities were compared in mouse and guinea pig dose escalation studies. In both models, immunization induced antibody responses specific for InvaplexNATand LPS while InvaplexARinduced markedly higher anti-IpaB and -IpaC serum IgG and IgA endpoint titers. In the murine model, homologous protection was achieved with 10-fold less InvaplexARthan InvaplexNATand mice receiving InvaplexARlost significantly less weight than mice receiving the same amount of InvaplexNAT. Moreover, mice immunized with InvaplexARwere protected from challenge with both homologous and heterologousShigellaserotypes. Guinea pigs receiving approximately 5-fold less InvaplexARcompared to cohorts immunized with InvaplexNATwere protected from ocular challenge. Furthermore, adjuvanticity previously attributed to InvaplexNATwas retained with InvaplexAR. The second-generationShigellaInvaplex vaccine, InvaplexAR, offers significant advantages over InvaplexNATin reproducibility, flexible yet defined composition, immunogenicity, and protective efficacy.IMPORTANCEShigellaspecies are bacteria that cause severe diarrheal disease worldwide, primarily in young children. Treatment of shigellosis includes oral fluids and antibiotics, but the high burden of disease, increasing prevalence of antibiotic resistance, and long-term health consequences clearly warrant the development of an effective vaccine. OneShigellavaccine under development is termed the invasin complex or Invaplex and is designed to drive an immune response to specific antigens of the bacteria in an effort to protect an individual from infection. The work presented here describes the production and evaluation of a new generation of Invaplex. The improved vaccine stimulates the production of antibodies in immunized mice and guinea pigs and protects these animals fromShigellainfection. The next step in the product’s development will be to test the safety and immune response induced in humans immunized with Invaplex.

scholarly journals Triggering through CD16 or phorbol esters enhances adhesion of NK cells to laminin via very late antigen 6.

1992 ◽  
Vol 176 (5) ◽  
pp. 1251-1257 ◽  
Author(s):  
A Gismondi ◽  
F Mainiero ◽  
S Morrone ◽  
G Palmieri ◽  
M Piccoli ◽  
...  
Keyword(s):  
Immune Response ◽  
Cell Migration ◽  
Nk Cells ◽  
Biochemical Analysis ◽  
Phorbol Esters ◽  
Nk Cell ◽  
Receptor Expression ◽  
Binding Assays ◽  
Binding Domains ◽  
Late Antigen

Very late antigens VLA-1, VLA-2, VLA-3, and VLA-6, belonging to the beta 1 subfamily of integrins, have been identified as receptors for different binding domains of laminin (LM). We have detected VLA-6, but not VLA-1 and VLA-2 on a subset (50-70%) of fresh peripheral blood CD3-, CD16+, CD56+ human natural killer (NK) cells by immunofluorimetric and biochemical analysis. Binding assays performed on LM-coated plates showed that 10-15% of NK cells spontaneously adhere to LM, and this adhesion is mediated by VLA-6. Activation of NK cells through CD16 triggering or by phorbol ester results in a rapid increase of adhesion to LM, which is still mediated by VLA-6. The enhanced adhesiveness is not associated with changes in beta 1 LM receptor expression, while it correlates with changes in the phosphorylation status of alpha 6 subunit. The expression of VLA-6 on NK cells and the modulation of its avidity by activating stimuli may be relevant for NK cell migration and tissue location during inflammation or immune response.

scholarly journals Long-term and herd immunity against SARS-CoV-2: implications from current and past knowledge

2020 ◽  
Vol 78 (3) ◽  
Author(s):  
Eleni Papachristodoulou ◽  
Loukas Kakoullis ◽  
Konstantinos Parperis ◽  
George Panos
Keyword(s):  
Immune Response ◽  
Herd Immunity ◽  
Effective Vaccine ◽  
Natural Immunity ◽  
Infection Rates ◽  
Mutant Strains ◽  
Current Infection ◽  
The Stability ◽  
Urgent Necessity

ABSTRACT Effective herd immunity against SARS-CoV-2 will be determined on many factors: the percentage of the immune population, the length and effectiveness of the immune response and the stability of the viral epitopes. The required percentage of immune individuals has been estimated to be 50–66% of the population which, given the current infection rates, will take long to be achieved. Furthermore, data from SARS-CoV suggest that the duration of immunity may not be sufficiently significant, while the immunity response against SARS-CoV-2 may not be efficiently effective in all patients, as relapses have already been reported. In addition, the development of mutant strains, which has already been documented, can cause the reemergence of the epidemic. In conclusion, the development of an effective vaccine is an urgent necessity, as long-term natural immunity to SARS-CoV-2 may not be sufficient for the control of the current and future outbreaks.

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