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Journal articles on the topic 'Viral quasi-species'

Author: Grafiati

Published: 7 June 2025

Last updated: 2 August 2025

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1

Lim, Seng Gee, Yan Cheng, Stephane Guindon, et al. "Viral Quasi-Species Evolution During Hepatitis Be Antigen Seroconversion." Gastroenterology 133, no. 3 (2007): 951–58. http://dx.doi.org/10.1053/j.gastro.2007.06.011.

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2

Moussaoui, Ali, and Vitaly Volpert. "The impact of immune cell interactions on virus quasi-species formation." Mathematical Biosciences and Engineering 21, no. 11 (2024): 7530–53. http://dx.doi.org/10.3934/mbe.2024331.

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<p>The process of viral infection spreading in tissues was influenced by various factors, including virus replication within host cells, transportation, and the immune response. Reaction-diffusion systems provided a suitable framework for examining this process. In this work, we studied a nonlocal reaction-diffusion system of equations that modeled the distribution of viruses based on their genotypes and their interaction with the immune response. It was shown that the infection may persist at a certain level alongside a chronic immune response, exhibiting spatially uniform or oscillator

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3

R., Jaisankar, and Deepa S. "On Estimating the Time from HIV Infection to AIDS - A Stochastic Modeling Approach." Indian Journal of Science and Technology 18, no. 15 (2025): 1170–76. https://doi.org/10.17485/IJST/v18i15.63.

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Abstract <strong>Objectives:</strong> To construct a statistical model through which one can estimate the mean time to get AIDS condition in a HIV infected individual. <strong>Methods:</strong> The methodology adopted for the construction of the statistical model for estimating the time to get AIDS condition considers the antigenic diversity threshold and the antigenic diversity induced by the virus entered through every individual infected sexual contact and the antigenic diversity induced by their corresponding quasi – species. A comparison has been made with the existin

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4

Nieto-Rabiela, F., G. Suzán, A. Wiratsudakul, and O. Rico-Chávez. "Viral metacommunities associated to bats and rodents at different spatial scales." Community Ecology 19, no. 2 (2018): 168–75. https://doi.org/10.5281/zenodo.13531157.

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(Uploaded by Plazi for the Bat Literature Project) One of the main goals of community ecology is to measure the relative importance of environmental filters to understand patterns of species distribution at different temporal and spatial scales. Likewise, the identification of factors that shape symbiont metacommunity structures is important in disease ecology because resulting structures drive disease transmission. We tested the hypothesis that distributions of virus species and viral families from rodents and bats are defined by shared responses to host phylogeny and host functional characte

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5

Nieto-Rabiela, F., G. Suzán, A. Wiratsudakul, and O. Rico-Chávez. "Viral metacommunities associated to bats and rodents at different spatial scales." Community Ecology 19, no. 2 (2018): 168–75. https://doi.org/10.5281/zenodo.13531157.

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(Uploaded by Plazi for the Bat Literature Project) One of the main goals of community ecology is to measure the relative importance of environmental filters to understand patterns of species distribution at different temporal and spatial scales. Likewise, the identification of factors that shape symbiont metacommunity structures is important in disease ecology because resulting structures drive disease transmission. We tested the hypothesis that distributions of virus species and viral families from rodents and bats are defined by shared responses to host phylogeny and host functional characte

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6

Fahim, Qanita, Irfan Ali Mirza, Ayesha Khalid, Anum Imtiaz, and Asad Ahmad. "THE HEPATITIS C UNTYPE-ABLE GENOTYPES, AN EMERGENCE OF QUASI-SPECIES IN HCV INFECTED PATIENTS." PAFMJ 71, Suppl-1 (2021): S106–12. http://dx.doi.org/10.51253/pafmj.v71isuppl-1.2603.

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Objective: To determine the frequency of Type-able and untype-able genotypes in hepatitis C infected patients,and to observe their association with gender, age, Alanine Aminotranferease and viral load. Study Design: Cross-sectional analytical study. Place and Duration of Study: Department of Microbiology, Combined Military Hospital, and Lahore, Pakistanfrom Sep 2017 to Mar 2018. Methodology: Six hundred forty seven anti HCV antibodies positive serum samples by Enzyme Linked ImmunoSorbant Assay were received from a total of 6791 serum samples. The positive sera were subjected

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7

Alonso, Julia, and Hugo Fort. "Error catastrophe for viruses infecting cells: analysis of the phase transition in terms of error classes." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 368, no. 1933 (2010): 5569–82. http://dx.doi.org/10.1098/rsta.2010.0274.

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RNA viruses offer a very exciting arena in which to study evolution in ‘real time’ owing to both their high replication rate—many generations per day are possible—and their high mutation rate, leading to a large phenotypic variety. They can be regarded as a swarm of genetically related mutants around a dominant or master genetic sequence. This system is called a ‘viral quasi-species’. Thus, a common framework to describe RNA viral dynamics is by means of the quasi-species equation (QSE). The QSE is in fact a system of a very large number of nonlinear coupled equations. Here, we consider a simp

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8

Lee, Guinevere Q. "Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness." Viruses 13, no. 9 (2021): 1874. http://dx.doi.org/10.3390/v13091874.

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HIV persists via integration of the viral DNA into the human genome. The HIV DNA pool within an infected individual is a complex population that comprises both intact and defective viral genomes, each with a distinct integration site, in addition to a unique repertoire of viral quasi-species. Obtaining an accurate profile of the viral DNA pool is critical to understanding viral persistence and resolving interhost differences. Recent advances in next-generation deep sequencing (NGS) technologies have enabled the development of two sequencing assays to capture viral near-full- genome sequences a

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9

Wu, Shuang, Fumio Imazeki, Fuat Kurbanov, et al. "Evolution of hepatitis B genotype C viral quasi-species during hepatitis B e antigen seroconversion." Journal of Hepatology 54, no. 1 (2011): 19–25. http://dx.doi.org/10.1016/j.jhep.2010.06.018.

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10

Mandary, Madiiha Bibi, Malihe Masomian, Seng-Kai Ong, and Chit Laa Poh. "Characterization of Plaque Variants and the Involvement of Quasi-Species in a Population of EV-A71." Viruses 12, no. 6 (2020): 651. http://dx.doi.org/10.3390/v12060651.

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Viral plaque morphologies in human cell lines are markers for growth capability and they have been used to assess the viral fitness and selection of attenuated mutants for live-attenuated vaccine development. In this study, we investigate whether the naturally occurring plaque size variation reflects the virulence of the variants of EV-A71. Variants of two different plaque sizes (big and small) from EV-A71 sub-genotype B4 strain 41 were characterized. The plaque variants displayed different in vitro growth kinetics compared to the parental wild type. The plaque variants showed specific mutatio

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11

Jaisankar, R., and S. Deepa. "On Estimating the Time from HIV Infection to AIDS - A Stochastic Modeling Approach." Indian Journal Of Science And Technology 18, no. 15 (2025): 1170–76. https://doi.org/10.17485/ijst/v18i15.63.

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Objectives: To construct a statistical model through which one can estimate the mean time to get AIDS condition in a HIV infected individual. Methods: The methodology adopted for the construction of the statistical model for estimating the time to get AIDS condition considers the antigenic diversity threshold and the antigenic diversity induced by the virus entered through every individual infected sexual contact and the antigenic diversity induced by their corresponding quasi – species. A comparison has been made with the existing model in the literature which considers the antigenic diversit

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12

Caldararo, Niccolo. "Coevolution and Adaptation of Viral Infections, Susceptible Populations, Evolution of Disease and Variant Creation Related to SARS-CoV-2." Anthropology and Ethnology Open Access Journal 6, no. 1 (2023): 1–6. http://dx.doi.org/10.23880/aeoaj-16000201.

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Covid-19 has created a major health challenge as a pandemic and demonstrates the threats that human populations face with increased population numbers and density of living situations. Pathogen adaptations to the human immune system are a treat to social complexity and evolution. Present theory argues that human social complexity has advanced in population density due to epidemiologic transition. Globalization and increase human needs for resources with increased density may be reaching limits of the potential for further transitions. The spread of the disease has resulted from mutations makin

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13

Sardanyés, Josep, Andreu Arderiu, Santiago F. Elena, and Tomás Alarcón. "Noise-induced bistability in the quasi-neutral coexistence of viral RNAs under different replication modes." Journal of The Royal Society Interface 15, no. 142 (2018): 20180129. http://dx.doi.org/10.1098/rsif.2018.0129.

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Evolutionary and dynamical investigations into real viral populations indicate that RNA replication can range between the two extremes represented by so-called ‘stamping machine replication’ (SMR) and ‘geometric replication’ (GR). The impact of asymmetries in replication for single-stranded (+) sense RNA viruses has been mainly studied with deterministic models. However, viral replication should be better described by including stochasticity, as the cell infection process is typically initiated with a very small number of RNA macromolecules, and thus largely influenced by intrinsic noise. Unde

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14

Imamichi, Hiromi, Keith A. Crandall, Ven Natarajan, et al. "Human Immunodeficiency Virus Type 1 Quasi Species That Rebound after Discontinuation of Highly Active Antiretroviral Therapy Are Similar to the Viral Quasi Species Present before Initiation of Therapy." Journal of Infectious Diseases 183, no. 1 (2001): 36–50. http://dx.doi.org/10.1086/317641.

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15

Bessonov, Nikolai, Gennady Bocharov, Andreas Meyerhans, Vladimir Popov, and Vitaly Volpert. "Nonlocal Reaction–Diffusion Model of Viral Evolution: Emergence of Virus Strains." Mathematics 8, no. 1 (2020): 117. http://dx.doi.org/10.3390/math8010117.

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This work is devoted to the investigation of virus quasi-species evolution and diversification due to mutations, competition for host cells, and cross-reactive immune responses. The model consists of a nonlocal reaction–diffusion equation for the virus density depending on the genotype considered to be a continuous variable and on time. This equation contains two integral terms corresponding to the nonlocal effects of virus interaction with host cells and with immune cells. In the model, a virus strain is represented by a localized solution concentrated around some given genotype. Emergence of

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16

Cuesta, José A. "Huge progeny production during the transient of a quasi-species model of viral infection, reproduction and mutation." Mathematical and Computer Modelling 54, no. 7-8 (2011): 1676–81. http://dx.doi.org/10.1016/j.mcm.2010.11.055.

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17

Erhouma, Esadk, François Guiguen, Dominique Gauthier, and Yahia Chebloune. "The genetic properties accompanied of "quasi-species" crossing of Small Ruminant LentiViruses (SRLVs)." Journal of Pure & Applied Sciences 20, no. 4 (2021): 206–9. http://dx.doi.org/10.51984/jopas.v20i4.1993.

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The env gene of Small Ruminant LentiViruses (SRLV) encodes a polypeptide precursor which after glycosylation is cleaved to give the two glycoproteins of the viral envelope: the transmembrane protein (TM) and the surface protein (SU). The passage and adaptation of SRLVs in new hosts is always accompanied by genetic mutations in the SU region of the env gene that determines the tropism of the virus by recognition of the cellular receptor. We studied the genetic properties of SRLVs accompanied of the "quasi-species" in Capra ibex. 16 Blood samples of Capra ibex were tested for presence of specifi

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18

Wu, J. C., S. Y. Wang, Y. H. Huang, I. J. Sheen, and T. Y. Chiang. "449 Changes of viral quasi-species in chronic hepatitis D: Immune epitopes and functional domains associated with selection." Journal of Hepatology 40 (January 2004): 133. http://dx.doi.org/10.1016/s0168-8278(04)90449-7.

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19

Attoui, Houssam, Fauziah Mohd Jaafar, Mourad Belhouchet, et al. "Liao ning virus, a new Chinese seadornavirus that replicates in transformed and embryonic mammalian cells." Journal of General Virology 87, no. 1 (2006): 199–208. http://dx.doi.org/10.1099/vir.0.81294-0.

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Seadornaviruses are emerging arboviral pathogens from the south-east of Asia. The genus Seadornavirus contains two distinct species, Banna virus (BAV) isolated from humans with encephalitis and Kadipiro virus. BAV replicates within insect cells and mice but not in cultured mammalian cells. Here, the discovery of Liao ning virus (LNV), a new seadornavirus from the Aedes dorsalis mosquito, which was completely sequenced and was found to be related to BAV and Kadipiro virus, is reported. Two serotypes of LNV could be distinguished by a serum neutralization assay. According to amino acid identity

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20

Han, Sang-Hoon, Byung-Joo Park, Hee-Seop Ahn, et al. "Cross-Species Transmission of Swine Hepatitis E Virus Genotype 3 to Rabbits." Viruses 12, no. 1 (2020): 53. http://dx.doi.org/10.3390/v12010053.

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Hepatitis E virus (HEV) is a quasi-enveloped, positive-sense single stranded RNA virus. HEV continually expands the host ranges across animal species. In this study, the possibility of cross-species infection with swine HEV-3 was investigated using rabbits. A total of fourteen 8-week old, specific pathogen-free rabbits were divided into three experimental groups. Four rabbits were used as negative controls, four rabbits were infected with rabbit HEV as positive controls, and six rabbits were inoculated with swine HEV-3. HEV RNA were detected from serum and fecal samples after viral challenge.

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21

Brenner, Bluma G., Ruxandra-Ilinca Ibanescu, Maureen Oliveira, et al. "HIV-1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture compared with viral isolates from singleton/small clusters." Journal of Antimicrobial Chemotherapy 72, no. 8 (2017): 2171–83. http://dx.doi.org/10.1093/jac/dkx118.

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Abstract Objectives: Viral phylogenetics revealed two patterns of HIV-1 spread among MSM in Quebec. While most HIV-1 strains (n = 2011) were associated with singleton/small clusters (cluster size 1–4), 30 viral lineages formed large networks (cluster size 20–140), contributing to 42% of diagnoses between 2011 and 2015. Herein, tissue culture selections ascertained if large cluster lineages possessed higher replicative fitness than singleton/small cluster isolates, allowing for viral escape from integrase inhibitors. Methods: Primary HIV-1 isolates from large 20+ cluster (n = 11) or singleton/s

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22

Gupta, Phalguni, Caroline Leroux, Bruce K. Patterson, et al. "Human Immunodeficiency Virus Type 1 Shedding Pattern in Semen Correlates with the Compartmentalization of Viral Quasi Species between Blood and Semen." Journal of Infectious Diseases 182, no. 1 (2000): 79–87. http://dx.doi.org/10.1086/315644.

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23

Morris-Love, Jenna, and Walter J. Atwood. "Complexities of JC Polyomavirus Receptor-Dependent and -Independent Mechanisms of Infection." Viruses 14, no. 6 (2022): 1130. http://dx.doi.org/10.3390/v14061130.

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JC polyomavirus (JCPyV) is a small non-enveloped virus that establishes lifelong, persistent infection in most of the adult population. Immune-competent patients are generally asymptomatic, but immune-compromised and immune-suppressed patients are at risk for the neurodegenerative disease progressive multifocal leukoencephalopathy (PML). Studies with purified JCPyV found it undergoes receptor-dependent infectious entry requiring both lactoseries tetrasaccharide C (LSTc) attachment and 5-hydroxytryptamine type 2 entry receptors. Subsequent work discovered the major targets of JCPyV infection in

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24

Laubscher, Florian, Samuel Cordey, Alex Friedlaender, et al. "SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort." Microorganisms 9, no. 10 (2021): 2145. http://dx.doi.org/10.3390/microorganisms9102145.

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Background: Oncological patients have a higher risk of prolonged SARS-CoV-2 shedding, which, in turn, can lead to evolutionary mutations and emergence of novel viral variants. The aim of this study was to analyze biological samples of a cohort of oncological patients by deep sequencing to detect any significant viral mutations. Methods: High-throughput sequencing was performed on selected samples from a SARS-CoV-2-positive oncological patient cohort. Analysis of variants and minority variants was performed using a validated bioinformatics pipeline. Results: Among 54 oncological patients, we an

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25

NADIN-DAVIS, S. A., F. MULDOON, and A. I. WANDELER. "A molecular epidemiological analysis of the incursion of the raccoon strain of rabies virus into Canada." Epidemiology and Infection 134, no. 3 (2005): 534–47. http://dx.doi.org/10.1017/s0950268805005108.

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Three physically separate incursions of the raccoon strain of rabies have entered Canada, two into eastern Ontario in 1999 and one into New Brunswick in 2000. The course of these epizootics is described. Phylogenetic analysis of the index cases from these two provinces with raccoon rabies viruses representative of this strain in the United States supported the independence of these incursions into Canada via cross-border transmission from the United States. Genetic characterization of 190 isolates from these two Canadian provinces over a 550-bp region of the variable central portion of the vir

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Signorini, Lucia, Maria Dolci, Evaldo Favi, et al. "Viral Genomic Characterization and Replication Pattern of Human Polyomaviruses in Kidney Transplant Recipients." Viruses 12, no. 11 (2020): 1280. http://dx.doi.org/10.3390/v12111280.

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Human Polyomavirus (HPyV) infections are common, ranging from 60% to 100%. In kidney transplant (KTx) recipients, HPyVs have been associated with allograft nephropathy, progressive multifocal leukoencephalopathy, and skin cancer. Whether such complications are caused by viral reactivation or primary infection transmitted by the donor remains debated. This study aimed to investigate the replication pattern and genomic characterization of BK Polyomavirus (BKPyV), JC Polyomavirus (JCPyV), and Merkel Cell Polyomavirus (MCPyV) infections in KTx. Urine samples from 57 KTx donor/recipient pairs were

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27

Dickey, Aaron M., Timothy P. L. Smith, Michael L. Clawson, Michael P. Heaton, and Aspen M. Workman. "Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns." F1000Research 9 (July 26, 2021): 1449. http://dx.doi.org/10.12688/f1000research.27898.2.

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Background: Small ruminant lentiviruses (SRLVs) cause a multisystemic chronic wasting disease in sheep across much of the world. SRLV subtype A2 is prevalent in North America and further classified into multiple subgroups based on variation in the group antigens gene (gag) and envelope (env) genes. In sheep, the ovine transmembrane protein 154 (TMEM154) gene is associated with SRLV susceptibility. Ewes with at least one copy of TMEM154 encoding a full-length protein with glutamate at position 35 (E35; haplotypes 2 and 3), are highly susceptible to SRLV infection while ewes with any combination

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28

Dickey, Aaron M., Timothy P. L. Smith, Michael L. Clawson, Michael P. Heaton, and Aspen M. Workman. "Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns." F1000Research 9 (December 11, 2020): 1449. http://dx.doi.org/10.12688/f1000research.27898.1.

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Background: Small ruminant lentiviruses (SRLVs) cause a multisystemic chronic wasting disease in sheep across much of the world. SRLV subtype A2 is prevalent in North America and further classified into multiple subgroups based on variation in the group antigens gene (gag) and envelope (env) genes. In sheep, the ovine transmembrane protein 154 (TMEM154) gene is associated with SRLV susceptibility. Ewes with at least one copy of TMEM154 encoding a full-length protein with glutamate at position 35 (E35; haplotypes 2 and 3), are highly susceptible to SRLV infection while ewes with any combination

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29

Letarov, Andrey V., and Maria A. Letarova. "The Burden of Survivors: How Can Phage Infection Impact Non-Infected Bacteria?" International Journal of Molecular Sciences 24, no. 3 (2023): 2733. http://dx.doi.org/10.3390/ijms24032733.

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The contemporary understanding of complex interactions in natural microbial communities and the numerous mechanisms of bacterial communication challenge the classical concept of bacteria as unicellular organisms. Microbial populations, especially those in densely populated habitats, appear to behave cooperatively, coordinating their reactions in response to different stimuli and behaving as a quasi-tissue. The reaction of such systems to viral infection is likely to go beyond each cell or species tackling the phage attack independently. Bacteriophage infection of a fraction of the microbial co

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Hance, Allan J., Virginie Lemiale, Jacques Izopet, et al. "Changes in Human Immunodeficiency Virus Type 1 Populations after Treatment Interruption in Patients Failing Antiretroviral Therapy." Journal of Virology 75, no. 14 (2001): 6410–17. http://dx.doi.org/10.1128/jvi.75.14.6410-6417.2001.

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ABSTRACT Mutations in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase and protease that confer resistance to antiretroviral agents are usually accompanied by a reduction in the viral replicative capacity under drug-free conditions. Consequently, when antiretroviral treatment is interrupted in HIV-1-infected patients harboring drug-resistant virus, resistant quasi-species appear to be most often replaced within several weeks by wild-type virus. Using a real-time PCR-based technique for the selective quantification of resistant viral sequences in plasma, we have studied the kin

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Fantini, Jacques, Henri Chahinian, and Nouara Yahi. "Convergent Evolution Dynamics of SARS-CoV-2 and HIV Surface Envelope Glycoproteins Driven by Host Cell Surface Receptors and Lipid Rafts: Lessons for the Future." International Journal of Molecular Sciences 24, no. 3 (2023): 1923. http://dx.doi.org/10.3390/ijms24031923.

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Although very different, in terms of their genomic organization, their enzymatic proteins, and their structural proteins, HIV and SARS-CoV-2 have an extraordinary evolutionary potential in common. Faced with various selection pressures that may be generated by treatments or immune responses, these RNA viruses demonstrate very high adaptive capacities, which result in the continuous emergence of variants and quasi-species. In this retrospective analysis of viral proteins, ensuring the adhesion of these viruses to the plasma membrane of host cells, we highlight many common points that suggest th

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32

Gianluigi, Zangari del Balzo. "Methodological notes on pandemic virus SARS-CoV-2 research." Theory in Biosciences 1, no. 1 (2021): 1–16. https://doi.org/10.13140/RG.2.2.25718.01606.

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In the fight against the COVID-19 pandemic, many brilliant results have been achieved, but the thermodynamics of the novel SARS-CoV-2 coronavirus has been completely neglected. This is a serious systematic error, which can compromise the results of the entire pandemic virus SARS-CoV-2 research. In the present work, we therefore study the thermodynamics of SARS-CoV-2 in its environment, from air to endosome and endosome-independent cell entry pathways. In the study of the thermodynamics of the new coronavirus SARS-CoV-2 in air, the presence of pollen, bacteria, other viruses, spores, dust, but

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Shirasaki, Takayoshi, Hui Feng, Helen M. E. Duyvesteyn, et al. "Nonlytic cellular release of hepatitis A virus requires dual capsid recruitment of the ESCRT-associated Bro1 domain proteins HD-PTP and ALIX." PLOS Pathogens 18, no. 8 (2022): e1010543. http://dx.doi.org/10.1371/journal.ppat.1010543.

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Although picornaviruses are conventionally considered ‘nonenveloped’, members of multiple picornaviral genera are released nonlytically from infected cells in extracellular vesicles. The mechanisms underlying this process are poorly understood. Here, we describe interactions of the hepatitis A virus (HAV) capsid with components of host endosomal sorting complexes required for transport (ESCRT) that play an essential role in release. We show release of quasi-enveloped virus (eHAV) in exosome-like vesicles requires a conserved export signal located within the 8 kDa C-terminal VP1 pX extension th

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Pulkkinen, Lauri I. A., Sarah V. Barrass, Aušra Domanska, Anna K. Överby, Maria Anastasina, and Sarah J. Butcher. "Molecular Organisation of Tick-Borne Encephalitis Virus." Viruses 14, no. 4 (2022): 792. http://dx.doi.org/10.3390/v14040792.

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Tick-borne encephalitis virus (TBEV) is a pathogenic, enveloped, positive-stranded RNA virus in the family Flaviviridae. Structural studies of flavivirus virions have primarily focused on mosquito-borne species, with only one cryo-electron microscopy (cryo-EM) structure of a tick-borne species published. Here, we present a 3.3 Å cryo-EM structure of the TBEV virion of the Kuutsalo-14 isolate, confirming the overall organisation of the virus. We observe conformational switching of the peripheral and transmembrane helices of M protein, which can explain the quasi-equivalent packing of the viral

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35

Labrosse, Béatrice, Laurence Morand-Joubert, Armelle Goubard, et al. "Role of the Envelope Genetic Context in the Development of Enfuvirtide Resistance in Human Immunodeficiency Virus Type 1-Infected Patients." Journal of Virology 80, no. 17 (2006): 8807–19. http://dx.doi.org/10.1128/jvi.02706-05.

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ABSTRACT Acquired human immunodeficiency virus type 1(HIV-1) resistance to the fusion inhibitor enfuvirtide (ENF) is primarily associated with mutations within the highly conserved first heptad repeat (HR1) region of gp41. Viral env sequences, however, are remarkably variable, and the envelope genetic background could have an important impact on optimal expression of HR1 mutations. We have examined the genetic evolution of env sequences, ENF susceptibility, and Env replicative capacity in patients failing ENF treatment. Sequential plasma-derived virus populations, obtained from six patients in

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36

Pagliarini, Silvia, and Andrei Korobeinikov. "A mathematical model of marine bacteriophage evolution." Royal Society Open Science 5, no. 3 (2018): 171661. http://dx.doi.org/10.1098/rsos.171661.

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To explore how particularities of a host cell–virus system, and in particular host cell replication, affect viral evolution, in this paper we formulate a mathematical model of marine bacteriophage evolution. The intrinsic simplicity of real-life phage–bacteria systems, and in particular aquatic systems, for which the assumption of homogeneous mixing is well justified, allows for a reasonably simple model. The model constructed in this paper is based upon the Beretta–Kuang model of bacteria–phage interaction in an aquatic environment (Beretta & Kuang 1998 Math. Biosci. 149 , 57–76. ( doi:10

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Franco, Lina S., Susan A. Holechek, Michael Caplan, and Joseph N. Blattman. "Sequence-specific detection of different strains LCMV in a single sample using tentacle probes." Journal of Immunology 196, no. 1_Supplement (2016): 69.3. http://dx.doi.org/10.4049/jimmunol.196.supp.69.3.

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Abstract Viral infections often result in quasi-species of virus strains that can have dramatic impacts on disease outcomes or experimental results. However, sequencing of viruses to determine strain composition is time consuming and often cost-prohibitive. Rapid, cost-effective methods are needed for accurate measurement of virus diversity in order to design appropriate treatment, and can be useful for many experimental systems. We have developed a novel molecular method for simple and accurate detection of RNA virus genetic variants using Tentacle probes coupled with quantitative PCR. Tentac

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Ferretti, Luca, Chandana Tennakoon, Adrian Silesian, and Graham Freimanis andPaolo Ribeca. "SiNPle: Fast and Sensitive Variant Calling for Deep Sequencing Data." Genes 10, no. 8 (2019): 561. http://dx.doi.org/10.3390/genes10080561.

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Current high-throughput sequencing technologies can generate sequence data and provide information on the genetic composition of samples at very high coverage. Deep sequencing approaches enable the detection of rare variants in heterogeneous samples, such as viral quasi-species, but also have the undesired effect of amplifying sequencing errors and artefacts. Distinguishing real variants from such noise is not straightforward. Variant callers that can handle pooled samples can be in trouble at extremely high read depths, while at lower depths sensitivity is often sacrificed to specificity. In

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Mortara, Lorenzo, Franck Letourneur, Helene Gras-masse, Alain Venet, Jean-Gerard Guillet, and Isabelle Bourgault-Villada. "Selection of Virus Variants and Emergence of Virus Escape Mutants after Immunization with an Epitope Vaccine." Journal of Virology 72, no. 2 (1998): 1403–10. http://dx.doi.org/10.1128/jvi.72.2.1403-1410.1998.

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ABSTRACT In this report, we assessed the evolution of the cytotoxic T-lymphocyte (CTL) response induced by an epitope vaccine. In two macaques immunized with a mixture of lipopeptides derived from simian immunodeficiency virus (SIV) Nef and Gag proteins, CTL responses were directed against the same, single epitope of the Nef protein (amino acids 128 to 137) presenting an alanine at position 136 (Nef 128-137/136A). However, after 5 months of SIV infection, peripheral blood mononuclear cells from both macaques lost their ability to be stimulated by autologous SIV-infected cells while still retai

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Althaus, Christian L., and Rob J. De Boer. "Impaired immune evasion in HIV through intracellular delays and multiple infection of cells." Proceedings of the Royal Society B: Biological Sciences 279, no. 1740 (2012): 3003–10. http://dx.doi.org/10.1098/rspb.2012.0328.

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With its high mutation rate, HIV is capable of escape from recognition, suppression and/or killing by CD8 + cytotoxic T lymphocytes (CTLs). The rate at which escape variants replace each other can give insights into the selective pressure imposed by single CTL clones. We investigate the effects of specific characteristics of the HIV life cycle on the dynamics of immune escape. First, it has been found that cells in HIV-infected patients can carry multiple copies of proviruses. To investigate how this process affects the emergence of immune escape, we develop a mathematical model of HIV dynamic

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Namaganda, Maria Magdalene, Hakim Sendagire, David Patrick Kateete, et al. "Next-generation sequencing (NGS) reveals low-abundance HIV-1 drug resistance mutations among patients experiencing virological failure at the time of therapy switching in Uganda." F1000Research 11 (August 4, 2022): 901. http://dx.doi.org/10.12688/f1000research.121980.1.

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Background: The emergence and spread of antiretroviral drug resistant HIV-1 variants is one of the major factors associated with therapeutic failure in persons living with HIV (PLWH) as it jeopardizes the efforts to reduce the progression to AIDS. Whereas Sanger sequencing is the most appropriate conventional method for HIV drug resistance testing, it has limited capacity to detect low-abundance variants. This study assessed the suitability of next generation sequencing (NGS) to reveal low-abundance HIV-1 drug resistance mutations amongst patients experiencing virological failure at the time o

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Gu, Zhengxian, Hengsheng Fang, Horacio Salomon, Qing Gao, and Mark A. Wainberg. "Identification of Mutations that Encode Drug Resistance in the Polymerase Gene of the Human Immunodeficiency Virus." Canadian Journal of Infectious Diseases 5, suppl e (1994): 29E—33E. http://dx.doi.org/10.1155/1994/826340.

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In vitro selection in MT-4 cells was used to generate human immunodeficiency virus-type 1 (HIV 1) variants that are resistant to 2',3'-dideoxycytidine (ddC), 2',3'-didcoxyinosine (ddI) and the (-) enantiomer of 2' ,3'-dideoxy-3'-thiacytidine (3TC). The complete reverse transcriptase open reading frames of these viruses, and portions of flanking protease and integrase within the pol gene, were cloned and sequenced by polymerase chain reaction (PCR) techniques. Mulalions were observed at each of amino acid sites 65 (Lys → Arg: AAA → AGA) and 184 (Met → Val: ATG → GTG) when ddC was used in this p

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Morand-Joubert, Laurence, Charlotte Charpentier, Gwendoline Poizat, et al. "Low Genetic Barrier to Large Increases in HIV-1 Cross-Resistance to Protease Inhibitors during Salvage Therapy." Antiviral Therapy 11, no. 2 (2006): 143–54. http://dx.doi.org/10.1177/135965350601100211.

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HIV-1 resistance to protease inhibitors (PIs) is characterized by extensive cross-resistance within this drug class. Some PIs, however, appear less affected by cross-resistance and are often prescribed in salvage therapy regimens for patients who have failed previous PI treatment. To examine the capacity of HIV-1 to adapt to these treatment changes, we have followed the evolution of HIV-1 protease genotypes and phenotypes in 21 protease-inhibitor-experienced patients in whom 26 weeks of an aggressive salvage regimen associating lopinavir, amprenavir and ritonavir failed to suppress viral repli

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Sager, Garrett, Samuel Gabaglio, Elizabeth Sztul, and George Belov. "Role of Host Cell Secretory Machinery in Zika Virus Life Cycle." Viruses 10, no. 10 (2018): 559. http://dx.doi.org/10.3390/v10100559.

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The high human cost of Zika virus infections and the rapid establishment of virus circulation in novel areas, including the United States, present an urgent need for countermeasures against this emerging threat. The development of an effective vaccine against Zika virus may be problematic because of the cross reactivity of the antibodies with other flaviviruses leading to antibody-dependent enhancement of infection. Moreover, rapidly replicating positive strand RNA viruses, including Zika virus, generate large spectrum of mutant genomes (quasi species) every replication round, allowing rapid s

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Uchiyama, Asako, та Bentley A. Fane. "Identification of an Interacting Coat-External Scaffolding Protein Domain Required for both the Initiation of φX174 Procapsid Morphogenesis and the Completion of DNA Packaging". Journal of Virology 79, № 11 (2005): 6751–56. http://dx.doi.org/10.1128/jvi.79.11.6751-6756.2005.

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ABSTRACT The φX174 external scaffolding protein D mediates the assembly of coat protein pentamers into procapsids. There are four external scaffolding subunits per coat protein. Organized as pairs of asymmetric dimers, the arrangement is unrelated to quasi-equivalence. The external scaffolding protein contains seven α-helices. The protein's core, α-helices 2 to 6, mediates the vast majority of intra- and interdimer contacts and is strongly conserved in all Microviridae (canonical members are φX174, G4, and α3) external scaffolding proteins. On the other hand, the primary sequences of the first

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Ouyang, Fei, Defu Yuan, Wenjing Zhai, Shanshan Liu, Ying Zhou, and Haitao Yang. "HIV-1 Drug Resistance Detected by Next-Generation Sequencing among ART-Naïve Individuals: A Systematic Review and Meta-Analysis." Viruses 16, no. 2 (2024): 239. http://dx.doi.org/10.3390/v16020239.

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Background: There are an increasing number of articles focused on the prevalence and clinical impact of pretreatment HIV drug resistance (PDR) detected by Sanger sequencing (SGS). PDR may contribute to the increased likelihood of virologic failure and the emergence of new resistance mutations. As SGS is gradually replaced by next-generation sequencing (NGS), it is necessary to assess the levels of PDR using NGS in ART-naïve patients systematically. NGS can detect the viral variants (low-abundance drug-resistant HIV-1 variants (LA-DRVs)) of virus quasi-species at levels below 20% that SGS may f

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Kim, Cheorl-Ho. "SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction." International Journal of Molecular Sciences 21, no. 12 (2020): 4549. http://dx.doi.org/10.3390/ijms21124549.

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The recently emerged SARS-CoV-2 is the cause of the global health crisis of the coronavirus disease 2019 (COVID-19) pandemic. No evidence is yet available for CoV infection into hosts upon zoonotic disease outbreak, although the CoV epidemy resembles influenza viruses, which use sialic acid (SA). Currently, information on SARS-CoV-2 and its receptors is limited. O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. SARS-CoV-2 hemagglutinin-esterase (HE) acts as the classical glycan-binding lectin and

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"Viral quasi-species and recombination." Proceedings of the Royal Society of London. Series B: Biological Sciences 263, no. 1376 (1996): 1577–84. http://dx.doi.org/10.1098/rspb.1996.0231.

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Dudouet, Pierre, Philippe Colson, Sarah Aherfi, et al. "SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding." Scientific Reports 12, no. 1 (2022). http://dx.doi.org/10.1038/s41598-022-22060-z.

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AbstractAt the time of a new and unprecedented viral pandemic, many questions are being asked about the genomic evolution of SARS-CoV-2 and the emergence of different variants, leading to therapeutic and immune evasion and survival of this genetically highly labile RNA virus. The nasopharyngeal persistence of infectious virus beyond 17 days proves its constant interaction with the human immune system and increases the intra-individual mutational possibilities. We performed a prospective high-throughput sequencing study (ARTIC Nanopore) of SARS-CoV-2 from so-called "persistent" patients, compar

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Zeng, Hong-Xiang, Wen-Hong Zu, Hai-Yan Wang, et al. "The Intra-Host Evolution of SARS-CoV-2 After Neutralizing Antibody Therapy, Revealed by Nanopore Sequencing." Zoonoses 4, no. 1 (2024). http://dx.doi.org/10.15212/zoonoses-2023-0032.

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Objective: In the context of two Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreaks involving local transmission and an international flight, we used meta-transcriptome and multi-amplicon sequencing to successfully acquire the complete viral genome sequences from clinical samples with varying viral loads. Methods: To enhance viral transcript presence, we used a primer pool for reverse transcription and sequenced the samples with nanopore sequencing, and successfully acquired the entire genomic sequence of the virus within less than 4 hours. In a substantial sample size of a

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