The unique structure of the highly conserved PPLP region in HIV-1 Vif is critical for the formation of APOBEC3 recognition interfaces.

The human cellular cytidine deaminases APOBEC3s (A3s) inhibit virion infectivity factor (Vif)-deficient HIV-1 replication. However, virus-encoded Vifs abolish this defense system by specifically recruiting A3s to an E3 ubiquitin ligase complex to induce their degradation. The highly conserved Vif PPLP motif is critical for the Vif-mediated antagonism of A3s and is believed to be important for Vif multimerization.

Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations.

HIV-1 drug resistance genotypic tests have primarily been performed by Sanger sequencing of gene segments encoding different drug target proteins. Since the number of targets has increased with the addition of a new class of antiretroviral drugs, a simple high-throughput system for assessing nucleotide sequences throughout the HIV-1 genome is required. Here, we developed a new solution using nanopore sequencing of viral pangenomes amplified by PCR.

Virological outcomes of various first-line ART regimens in patients harbouring HIV-1 E157Q integrase polymorphism: a multicentre retrospective study.

Background: Integrase strand transfer inhibitors (INSTIs) are recommended as first-line ART for people living with HIV (PLWH) in most guidelines. The INSTI-resistance-associated mutation E157Q, a highly prevalent (2%-5%) polymorphism of the HIV-1 (human immunodeficiency virus type 1) integrase gene, has limited data on optimal first-line ART regimens. We assessed the virological outcomes of various first-line ART regimens in PLWH with E157Q in real-world settings.

Workplace factors associated with willingness to undergo human immunodeficiency virus testing during workplace health checkups.

Background: To examine workplace factors associated with willingness to undergo human immunodeficiency virus (HIV) testing during workplace health checkups.

Methods: This cross-sectional study used an Internet-based self-administered questionnaire to obtain data from a pool of 24,287 Japanese workers. Binary and multiple logistic regression analyses evaluated the association between workplace factors and HIV testing.

Cellular APOBEC3A deaminase drives mutations in the SARS-CoV-2 genome.

The number of genetic variations in the SARS-CoV-2 genome has been increasing primarily due to continuous viral mutations. Here, we report that the human APOBEC3A (A3A) cytidine deaminase plays a critical role in the induction of C-to-U substitutions in the SARS-CoV-2 genome. Bioinformatic analysis of the chronological genetic changes in a sequence database indicated that the largest UC-to-UU mutation signature, consistent with APOBEC-recognized nucleotide motifs, was predominant in single-stranded RNA regions of the viral genome.

Nanopore Sequencing for Characterization of HIV-1 Recombinant Forms.

High genetic diversity, including the emergence of recombinant forms (RFs), is one of the most prominent features of human immunodeficiency virus type 1 (HIV-1). Conventional detection of HIV-1 RFs requires pretreatments, i.e.

Evaluation of the Geenius HIV 1/2 confirmatory assay for HIV-2 samples isolated in Japan.

Background: Although the number of HIV-2-infected individuals is quite low in Japan, at least three groups of HIV-2 (A, B and CRF01_AB) have been detected thus far. In particular, CRF01_AB HIV-2 cases have been found only in limited areas, Cote d'Ivoire and Japan. Here, we demonstrate that Geenius HIV 1/2 Confirmatory Assay (Geenius, Bio-Rad Laboratories) is able to detect HIV-2 samples, including groups A, B and CRF01_AB, isolated in Japan.

Epidemiology of coinfection with tuberculosis and HIV in Japan, 2012-2020.

This report examines the characteristics and treatment outcomes of patients with tuberculosis (TB) who are coinfected with HIV in Japan. Active TB cases newly notified to the Japan Tuberculosis Surveillance system during 2012-2020 were analysed retrospectively, during which 379 HIV-positive TB cases were reported. The proportion of HIV-positive cases among those with known HIV status increased, from 1.

SARS-CoV-2 accessory protein ORF8 is secreted extracellularly as a glycoprotein homodimer.

ORF8 is an accessory protein encoded by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Consensus regarding the biological functions of ORF8 is lacking, largely because the fundamental characteristics of this protein in cells have not been determined. To clarify these features, we herein established an ORF8 expression system in 293T cells.

Retrospective Analysis of the Efficacy of Early Antiretroviral Therapy in HIV-1-Infected Patients Coinfected with .

The early initiation of antiretroviral therapy (ART) in HIV-infected patients shortly after the initiation of treatment for pneumonia (PCP) has not been fully validated in a clinical setting. We retrospectively extracted all patients diagnosed with HIV-related PCP (HIV-PCP), including those with severe cases, who were treated with first-line ART in our hospital. The HIV-PCP patients were divided into two groups: an early ART group (patients who commenced ART within 21 days after the start of PCP treatment) and a deferred ART group (patients who started ART after 22 days).

Impact of long-term antiretroviral therapy on gut and oral microbiotas in HIV-1-infected patients.

In HIV-1-infected patients, antiretroviral therapy (ART) is a key factor that may impact commensal microbiota and cause the emergence of side effects. However, it is not fully understood how long-term ART regimens have diverse impacts on the microbial compositions over time. Here, we performed 16S ribosomal RNA gene sequencing of the fecal and salivary microbiomes in patients under different long-term ART.

Factors Associated with Attrition: Analysis of an HIV Clinic in Japan.

This study evaluated the impact of a public medical interpreter on the follow-up clinic attendance rate of foreign-born people with HIV who live in Japan. Participants were patients who visited Nagoya Medical Center from 2009 to 2016. Lost to follow-up was defined as an absence from follow-up visits for more than six months without any notification.

Network overlap and knowledge of a partner's HIV status among young men who have sex with men.

For individuals living with HIV, disclosure of HIV status to their partners can be a source of psychological and emotional stress. Minimal information about serostatus disclosure is available for young men who have sex with men (YMSM). This study examined the disclosure of HIV status to social and sexual partners among YMSM using social and sexual network data.

Discovery of 4-oxoquinolines, a new chemical class of anti-HIV-1 compounds.

Antiretroviral therapy (ART) against HIV-1 infection offers the promise of controlling disease progression and prolonging the survival of HIV-1-infected patients. However, even the most potent ART regimens available today cannot cure HIV-1. Because patients will be exposed to ART for many years, physicians and researchers must anticipate the emergence of drug-resistant HIV-1, potential adverse effects of the current drugs, and need for future drug development.

Structural basis of chimpanzee APOBEC3H dimerization stabilized by double-stranded RNA.

APOBEC3H (A3H) is a mammal-specific cytidine deaminase that potently restricts the replication of retroviruses. Primate A3Hs are known to exert key selective pressures against the cross-species transmission of primate immunodeficiency viruses from chimpanzees to humans. Despite recent advances, the molecular structures underlying the functional mechanisms of primate A3Hs have not been fully understood.

The relationship between repolarization parameters and serum electrolyte levels in patients with J wave syndromes.

Background: Intravenous administration of magnesium (Mg(2+)) is effective for polymorphic ventricular tachycardia via homogenization of transmural ventricular repolarization. Mg(2+) likely plays some role in the heterogeneity of repolarization in J wave syndromes.

Objective: To investigate the relationship between the repolarization parameters and serum Mg(2+), potassium (K(+)), and calcium (Ca(2+)) levels in J wave syndromes.

Olfaction-inspired sensing using a sensor system with molecular recognition and optimal classification ability for comprehensive detection of gases.

In this study, we examined the comprehensive detection of numerous volatile molecules based on the olfactory information constructed by using olfaction-inspired sensor technology. The sensor system can simultaneously detect multiple odors by the separation and condensation ability of molecularly imprinted filtering adsorbents (MIFAs), where a MIP filter with a molecular sieve was deposited on a polydimethylsiloxane (PDMS) substrate. The adsorption properties of MIFAs were evaluated using the solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS).

Concentrating materials covered by molecular imprinted nanofiltration layer with reconfigurability prepared by a surface sol-gel process for gas-selective detection.

Sensors that recognize molecules are acquired for the comprehensive detection of great many kinds of gases. Adsorbents with high molecular recognition and condensation ability were developed for selective gas sensing with a molecular imprinting technique. Developed adsorbents have multilayer structures consisted of a chemically modified polymer layer on the surface of a substrate covered by a TiO2 gel monolayer by the surface sol-gel process.