scholarly journals A Combination of M50I and V151I Polymorphic Mutations in HIV-1 Subtype B Integrase Results in Defects in Autoprocessing

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2331
Author(s):  
Jun Yang ◽  
Ming Hao ◽  
Muhammad A. Khan ◽  
Muhammad T. Rehman ◽  
Helene C. Highbarger ◽  
...  
Keyword(s):  
Population Analysis ◽  
Hiv Replication ◽  
Rna Sequences ◽  
Plasma Virus ◽  
Subtype B ◽  
Virus Rna ◽  
Viral Particles ◽  
Back Mutation ◽  
Defective Virus ◽  
Western Blotting Assay

We have recently reported that a recombinant HIV-1NL4.3 containing Met-to-Ile change at codon 50 of integrase (IN) (IN:M50I) exhibits suppression of the virus release below 0.5% of WT HIV, and the released viral particles are replication-incompetent due to defects in Gag/GagPol processing by inhibition of the initiation of autoprocessing of GagPol polyproteins in the virions and leads to replication-incompetent viruses. The coexisting Ser-to-Asn change at codon 17 of IN or Asn-to-Ser mutation at codon 79 of RNaseH (RH) compensated the defective IN:M50I phenotype, suggesting that both IN and RH regulate an HIV infectability. In the current study, to elucidate a distribution of the three mutations during anti-retroviral therapy among patients, we performed a population analysis using 529 plasma virus RNA sequences obtained through the MiSeq. The result demonstrated that 14 plasma HIVs contained IN:M50I without the compensatory mutations. Comparing the sequences of the 14 viruses with that of the defective virus illustrated that only Val-to-Ile change at codon 151 of IN (IN:V151I) existed in the recombinant virus. This IN:V151I is known as a polymorphic mutation and was derived from HIVNL4.3 backbone. A back-mutation at 151 from Ile-to-Val in the defective virus recovered HIV replication capability, and Western Blotting assay displayed that the back-mutation restored Gag/GagPol processing in viral particles. These results demonstrate that a combination of IN:M50I and IN:V151I mutations, but not IN:M50I alone, produces a defective virus.

scholarly journals Ongoing HIV Replication During ART Reconsidered

2017 ◽  
Vol 4 (3) ◽  
Author(s):  
Mary F Kearney ◽  
Ann Wiegand ◽  
Wei Shao ◽  
William R McManus ◽  
Michael J Bale ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Mononuclear Cells ◽  
Chain Reaction ◽  
Hiv Replication ◽  
Rna Sequences ◽  
Peripheral Blood Mononuclear ◽  
Plasma Virus ◽  
Hiv Rna ◽  
Blood Mononuclear Cells ◽  
Polymerase Chain

Abstract Lorenzo-Redondo et al. recently analyzed HIV RNA sequences in plasma virus and proviral DNA sequences in lymph nodes (LN) and peripheral blood mononuclear cells (PBMC) from samples collected over a 6-month period from 3 individuals following initiation of antiretroviral therapy (ART) and concluded that ongoing HIV replication occurred in LN despite ART and that this replication maintained the HIV reservoir. We analyzed the same sequences and found that the dataset was very limited (median of 5 unique RNA or DNA sequences per sample) after accounting for polymerase chain reaction resampling and hypermutation and that the few remaining DNA sequences after 3 and 6 months on ART were not more diverse or divergent from those in pre-ART in any of the individuals studied. These findings, and others, lead us to conclude that the claims of ongoing replication on ART made by Lorenzo-Redondo et al. are not justified from the dataset analyzed in their publication.

scholarly journals Reverse Transcription-PCR Analysis of Bottled and Natural Mineral Waters for the Presence of Noroviruses

2003 ◽  
Vol 69 (11) ◽  
pp. 6541-6549 ◽  
Author(s):  
Gilbert Thierry Lamothe ◽  
Thierry Putallaz ◽  
Han Joosten ◽  
Joey D. Marugg
Keyword(s):  
Reverse Transcription ◽  
Membrane Filtration ◽  
Limit Of Detection ◽  
Mineral Waters ◽  
Pcr Analysis ◽  
Rna Sequences ◽  
Natural Mineral ◽  
Reverse Transcription Pcr ◽  
Viral Particles ◽  
Nonspecific Amplification

ABSTRACT A seminested reverse transcription-PCR method coupled to membrane filtration was optimized to investigate the presence of norovirus (NV) RNA sequences in bottled and natural mineral waters. The recovery of viral particles by filtration varied between 28 and 45%, while the limit of detection of the overall method ranged from 6 to 95 viral particles. The assay was broadly reactive, as shown by the successful detection of 27 different viral strains representing 12 common genotypes of NVs. A total of 718 bottled and natural mineral water samples were investigated, including 640 samples of finished, spring, and line products (mostly 1 to 1.5 liters), collected from 36 different water brands of various types and from diverse geographic origins over a 2-year period. In addition, 78 samples of larger volume (10 and 400 to 500 liters) and environmental swabs were investigated. From the 1,436 analyses that were performed for the detection of NVs belonging to genogroups I and II, 34 samples (2.44%) were presumptively positive by seminested RT-PCR. However, confirmation by DNA sequence analysis revealed that all presumptive positive results were either due to nonspecific amplification or to cross-contamination. In conclusion, these results do not provide any evidence for the presence of NV genome sequences in bottled waters.

Synchronous sensing of three conserved sequences of Zika virus using a DNAs@MOF hybrid: experimental and molecular simulation studies

2019 ◽  
Vol 6 (1) ◽  
pp. 148-152 ◽  
Author(s):  
Bao-Ping Xie ◽  
Gui-Hua Qiu ◽  
Bin Sun ◽  
Zi-Feng Yang ◽  
Wen-Hua Zhang ◽  
...  
Keyword(s):  
Molecular Simulation ◽  
Dna Sequences ◽  
Hybrid Material ◽  
Zika Virus ◽  
Metal Organic Framework ◽  
Simulation Studies ◽  
Synchronous Detection ◽  
Rna Sequences ◽  
Virus Rna ◽  
Metal Organic

A metal–organic framework of Cu(ii) has been prepared and impregnated with three dye-labeled DNA sequences. The hybrid material formed is capable of synchronous detection of three conserved Zika virus RNA sequences.

scholarly journals Efficient Interaction between Arenavirus Nucleoprotein (NP) and RNA-Dependent RNA Polymerase (L) Is Mediated by the Virus Nucleocapsid (NP-RNA) Template

2015 ◽  
Vol 89 (10) ◽  
pp. 5734-5738 ◽  
Author(s):  
Masaharu Iwasaki ◽  
Nhi Ngo ◽  
Beatrice Cubitt ◽  
Juan C. de la Torre
Keyword(s):  
Rna Polymerase ◽  
Gene Transcription ◽  
Viral Genome ◽  
Rna Replication ◽  
Rna Dependent Rna Polymerase ◽  
Rna Sequences ◽  
L Protein ◽  
Virus Rna

In this study, we document that efficient interaction between arenavirus nucleoprotein (NP) and RNA-dependent RNA polymerase (L protein), the twotrans-acting viral factors required for both virus RNA replication and gene transcription, requires the presence of virus-specific RNA sequences located within the untranslated 5′ and 3′ termini of the viral genome.

scholarly journals Viruses Associated with Rusty Mottle and Twisted Leaf Diseases of Sweet Cherry Are Distinct Species

2013 ◽  
Vol 103 (12) ◽  
pp. 1287-1295 ◽  
Author(s):  
D. E. V. Villamor ◽  
K. C. Eastwell
Keyword(s):  
Distinct Species ◽  
Mottle Virus ◽  
Distribution Data ◽  
Virus Species ◽  
Rna Sequences ◽  
Sequence Comparisons ◽  
Protein Coding ◽  
Green Ring ◽  
Virus Rna ◽  
The Family

Virus RNA sequences related to those of the family Betaflexiviridae were amplified from trees affected with the following diseases: cherry twisted leaf, apricot ring pox, cherry necrotic rusty mottle, cherry rusty mottle, and cherry green ring mottle. Phylogenetic analysis of virus sequences obtained from these diseased trees from western North America, along with published sequences of Cherry green ring mottle virus (CGRMV) and Cherry necrotic rusty mottle virus (CNRMV), revealed four major clades. Segregation into these four populations correlated with distinct symptom expression on woody indicators, suggesting that each clade represents a distinct virus species within the family Betaflexiviridae. The viruses occupying each clade were designated clade I: Cherry twisted leaf associated virus, clade II: CNRMV, clade III: Cherry rusty mottle associated virus, and clade IV: CGRMV. Potential recombination events were predicted to occur within and between these viruses, the latter being strongly supported by incongruent phylogenies. Examination of frequency distribution data derived from pairwise sequence comparisons of coat protein coding sequences resulted in a proposal for alternative guidelines for species demarcation for this family of viruses.

Mechanism of Action of the Anti-Influenza Virus Active Kampo (Traditional Japanese Herbal) Medicine, Hochuekkito

Pharmacology ◽  
2017 ◽  
Vol 101 (3-4) ◽  
pp. 148-155 ◽  
Author(s):  
Katsuaki Dan ◽  
Keita Takanashi ◽  
Hiroko Akiyoshi ◽  
Kaori Munakata ◽  
Hideki Hasegawa ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Mechanism Of Action ◽  
Plaque Assay ◽  
Virus Titer ◽  
Acid Synthesis ◽  
Infection Process ◽  
Assay Method ◽  
Virus Adsorption ◽  
Virus Rna ◽  
Viral Particles

When the Kampo medicine, Hochuekkito (Hochu), was administered to normal mice for 2 weeks, influenza virus titer was reduced. The mechanism of action of Hochu was examined using the plaque assay method. It was suggested that Hochu may either obstruct the first stage of the infection process (adsorption and entry) or may directly target viral particles. Using the plaque assay method, these 2 modes of action could not be differentiated. Virus RNA in the infected cell was verified by quantitative real-time polymerase chain reaction. An equal inhibition effect was obtained when Hochu was preprocessed for normal cells and when they were made to act simultaneously with virus adsorption. The viral load at the cell surface following UV irradiation was higher in the Hochu-administered group as compared with that of the control. Moreover, the affinity of Hochu for the influenza virus was hundred times higher than its affinity for the host cell. The effect of entry obstruction by Hochu was observed via image analysis, where the amount of virus nucleocapsid protein (NP) invading the cell was visualized with FITC-labeled NP antibody. Hochu does not seem to have an effect on nucleic acid synthesis, viral release from infected cells, and on the subsequent second round of infection. In conclusion, Hochu binds to viral particles and forms complexes that can obstruct the entry of influenza virus into cells.

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