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.

METHODS

A multicentre retrospective observational study was conducted on PLWH who underwent integrase genotypic drug-resistance testing before ART initiation between 2008 and 2019 and were found to have E157Q. Viral suppression (<50 copies/mL) rate at 24 and 48 weeks, time to viral suppression and time to viral rebound (≥100 copies/mL) were compared among the first-line ART regimens.

RESULTS

E157Q was detected in 167 (4.1%) of 4043 ART-naïve PLWH. Among them, 144 had available clinical data after ART initiation with a median follow-up of 1888 days. Forty-five started protease inhibitors + 2 NRTIs (PI group), 33 started first-generation INSTI (raltegravir or elvitegravir/cobicistat) + 2 NRTIs (INSTI-1 group), 58 started once-daily second-generation INSTI (dolutegravir or bictegravir) + 2 NRTIs (INSTI-2 group) and eight started other regimens. In the multivariate analysis, the INSTI-2 group showed similar or favourable outcomes compared with the PI group for viral suppression rates, time to viral suppression and time to viral rebound. Two cases in the INSTI-1 group experienced virological failure.

CONCLUSIONS

The general guideline recommendation of second-generation INSTI-based first-line ART for most PLWH is also applicable to PLWH harbouring E157Q.

Association of demographics, HCV co-infection, HIV-1 subtypes and genetic clustering with late HIV diagnosis: a retrospective analysis from the Japanese Drug Resistance HIV-1 Surveillance Network

INTRODUCTION

Late diagnosis of the human immunodeficiency virus (HIV) is a major concern epidemiologically, socially and for national healthcare systems. Although the association of certain demographics with late HIV diagnosis has been reported in several studies, the association of other factors, including clinical and phylogenetic factors, remains unclear. In the present study, we conducted a nationwide analysis to explore the association of demographics, clinical factors, HIV-1 subtypes/circulating recombinant form (CRFs) and genetic clustering with late HIV diagnosis in Japan, where new infections mainly occur among young men who have sex with men (MSM) in urban areas.

METHODS

Anonymized data on demographics, clinical factors and HIV genetic sequences from 39.8% of people newly diagnosed with HIV in Japan were collected by the Japanese Drug Resistance HIV-1 Surveillance Network from 2003 to 2019. Factors associated with late HIV diagnosis (defined as HIV diagnosis with a CD4 count <350 cells/μl) were identified using logistic regression. Clusters were identified by HIV-TRACE with a genetic distance threshold of 1.5%.

RESULTS

Of the 9422 people newly diagnosed with HIV enrolled in the surveillance network between 2003 and 2019, 7752 individuals with available CD4 count at diagnosis were included. Late HIV diagnosis was observed in 5522 (71.2%) participants. The overall median CD4 count at diagnosis was 221 (IQR: 62-373) cells/μl. Variables independently associated with late HIV diagnosis included age (adjusted odds ratio [aOR] 2.21, 95% CI 1.88-2.59, ≥45 vs. ≤29 years), heterosexual transmission (aOR 1.34, 95% CI 1.11-1.62, vs. MSM), living outside of Tokyo (aOR 1.18, 95% CI 1.05-1.32), hepatitis C virus (HCV) co-infection (aOR 1.42, 95% CI 1.01-1.98) and not belonging to a cluster (aOR 1.30, 95% CI 1.12-1.51). CRF07_BC (aOR 0.34, 95% CI 0.18-0.65, vs. subtype B) was negatively associated with late HIV diagnosis.

CONCLUSIONS

In addition to demographic factors, HCV co-infection, HIV-1 subtypes/CRFs and not belonging to a cluster were independently associated with late HIV diagnosis in Japan. These results imply the need for public health programmes aimed at the general population, including but not limited to key populations, to encourage 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. In SARS-CoV-2-infected cells, exogenous expression of A3A but not expression of other APOBEC proteins induced UC-to-UU mutations in viral RNA (vRNA). Additionally, the mutated C bases were often located at the tips in bulge or loop regions in the vRNA secondary structure. Interestingly, A3A mRNA expression was drastically increased by interferons (IFNs) and tumour necrosis factor-α (TNF-α) in epithelial cells derived from the respiratory system, a site of efficient SARS-CoV-2 replication. Moreover, the UC-to-UU mutation rate was increased in SARS-CoV-2 produced from lung epithelial cells treated with IFN-ß and TNF-α, but not from CRISPR/Cas9-based A3A knockout cells. Collectively, these findings demonstrate that A3A is a primary host factor that drives mutations in the SARS-CoV-2 RNA genome via RNA editing.

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. Data were adjusted for sex, age, marital status, education, and history of HIV testing.

RESULTS

We gathered information from 4,143 (17.1%) respondents, of whom 1,129 (27.3%) were willing to be tested for HIV as part of a workplace health checkup. The participants were 20-59 years old. Approximately half of the participants were male (49.9%), half were married (48.9%), and half had completed higher education (47.6%). Workplace hepatitis testing was offered to 15.6% of the respondents, and most participants underwent health checkups without their colleagues (52.1%) at a medical facility (60.2%). Willingness to undergo HIV testing was positively correlated with having an increased risk of occupational blood exposure (vs. not at risk, adjusted odds ratio [OR]: 1.74, 95% confidence interval [CI]: 1.41-2.15) or working in medical and welfare roles (vs. manufacturing, OR: 1.40, 95% CI: 1.07-1.84). The presence of occupational health staff at the workplace (vs. their absence, adjusted OR: 1.35, 95% CI: 1.16-1.59) and hepatitis testing (vs. not testing, adjusted OR: 2.02, 95% CI: 1.66-2.44) increased willingness to undergo HIV testing.

CONCLUSIONS

A pilot HIV-testing program involving individuals at an increased risk of occupational blood exposure and undergoing hepatitis tests in workplaces providing occupational health staff support is recommended.

Practices and attitudes towards tuberculosis and latent tuberculosis infection screening in people living with HIV/AIDS among HIV physicians in Japan

Background

Tuberculosis (TB) continues to be the leading cause of death for people living with HIV/AIDS (PLHIV), and HIV is the strongest known risk factor for progression to active TB disease for persons with latent TB infection (LTBI). Screening for active TB and LTBI, and TB preventive therapy (TPT) is recommended, however, clinical practices regarding LTBI screening for HIV positive population have not been uniform, resulting in low rates of LTBI screening and TPT uptake, in both low and high TB-burden countries. We sought to explore the practices and attitudes towards TB and LTBI screening in PLHIV among HIV physicians in Japan.

Methods

We conducted a cross-sectional survey whereby an on-line questionnaire was administered to physicians who are currently, or have the experience of, providing care and treatment for PLHIV in Japan.

Results

The questionnaire was sent to a total of 83 physicians, of which 59 responded (response rate; 71.1%). 52.5% (31/59) conducted routine screening and 44.0% (26/59) conducted selectively screening for active TB among HIV/AIDS patients. As for LTBI, 54.2% (32/59) conducted routine screening and 35.6% (21/59) conducted selective screening for LTBI among PLHIV. “T-SPOT only” was the most frequently used method of screening (n = 33), followed by “QFT only” (n = 11). Criteria for LTBI screening included TB burden in the country of birth of the patient, previous contact with a TB patient, and CD4+ cell count. 83.1% (49/59) either “always” or “selectively” offered TPT to PLHIV diagnosed with LTBI, and among the 49 respondents who did provide TPT, 77.6% (38/49) chose 9-months isoniazid as their first choice. None chose regimen including rifampicin.

Conclusions

Our study revealed that practices regarding TB and LTBI screening and treatment for PLHIV among HIV physicians were mixed and not necessarily in accordance with the various published guidelines. Building and disseminating scientific evidence that takes into consideration the local epidemiology of TB and HIV in Japan is urgently needed to assist physicians make decisions.

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., cloning or single-genome amplification, to distinguish them from dual- or multiple-infection variants. However, these processes are time-consuming and labor-intensive. Here, we constructed a new nanopore sequencing-based platform that enables us to obtain distinctive genetic information for intersubtype RFs and dual-infection HIV-1 variants by using amplicons of HIV-1 near-full-length genomes or two overlapping half-length genome fragments. Repeated benchmark tests of HIV-1 proviral DNA revealed consensus sequence inference with a reduced error rate, allowing us to obtain sufficiently accurate sequence data. In addition, we applied the platform for sequence analyses of 9 clinical samples with suspected HIV-1 RF infection or dual infection according to Sanger sequencing-based genotyping tests for HIV-1 drug resistance. For each RF infection case, replicated analyses involving our nanopore sequencing-based platform consistently produced long consecutive analogous consensus sequences with mosaic genomic structures consisting of two different subtypes. In contrast, we detected multiple heterologous sequences in each dual-infection case. These results demonstrate that our new nanopore sequencing platform is applicable to identify the full-length HIV-1 genome structure of intersubtype RFs as well as dual-infection heterologous HIV-1. Since the genetic diversity of HIV-1 continues to gradually increase, this system will help accelerate full-length genome analysis and molecular epidemiological surveillance for HIV-1. IMPORTANCE HIV-1 is characterized by large genetic differences, including HIV-1 recombinant forms (RFs). Conventional genetic analyses require time-consuming pretreatments, i.e., cloning or single-genome amplification, to distinguish RFs from dual- or multiple-infection cases. In this study, we developed a new analytical system for HIV-1 sequence data obtained by nanopore sequencing. The error rate of this method was reduced to ~0.06%. We applied this system for sequence analyses of 9 clinical samples with suspected HIV-1 RF infection or dual infection, which were extracted from 373 cases of HIV patients based on our retrospective analysis of HIV-1 drug resistance genotyping test results. We found that our new nanopore sequencing platform is applicable to identify the full-length HIV-1 genome structure of intersubtype RFs as well as dual-infection heterologous HIV-1. Our protocol will be useful for epidemiological surveillance to examine HIV-1 transmission as well as for genotypic tests of HIV-1 drug resistance in clinical settings.

Molecular-Epidemiological Features of SARS-CoV-2 in Japan, 2020-2021

There were five epidemic waves of coronavirus disease 2019 in Japan between 2020 and 2021. It remains unclear how the domestic waves arose and abated. To better understand this, we analyzed the pangenomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and characterized the molecular epidemiological features of the five epidemic waves in Japan. In this study, we performed deep sequencing to determine the pangenomic SARS-CoV-2 sequences of 1,286 samples collected in two cities far from each other, Tokyo Metropolis and Nagoya. Then, the spatiotemporal genetic changes of the obtained sequences were compared with the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. A total of 873 genotypes carrying different sets of mutations were identified in the five epidemic waves. Phylogenetic analysis demonstrated that sharp displacements of lineages and genotypes occurred between consecutive waves over the 2 years. In addition, a wide variety of genotypes were observed in the early half of each wave, whereas a few genotypes were detected across Japan during an entire wave. Phylogenetically, putative descendant genotypes observed late in each wave displayed regional clustering and evolution in Japan. The genetic diversity of SARS-CoV-2 displayed uneven dynamics during each epidemic wave in Japan. Our findings provide an important molecular epidemiological basis to aid in controlling future SARS-CoV-2 epidemics.

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

The early initiation of antiretroviral therapy (ART) in HIV-infected patients shortly after the initiation of treatment for Pneumocystis 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). We compared the incidence of AIDS progression or death, the virological suppression rate, and changes in the CD4⁺ cell count at 24 weeks after the initiation of ART between the two groups. In addition, we analyzed the incidences of immune reconstitution inflammatory syndrome and grade 3 or 4 laboratory and clinical adverse events within 24 weeks as safety outcomes. Ninety-one HIV-PCP patients (36 in the early ART group and 55 in the deferred group) were included in this study. We found no significant difference in the incidence of AIDS progression or death between the two groups. Virological outcomes tended to be better in the early ART group but were not significantly different. Increases in the CD4⁺ cell counts at 24 weeks were comparable in both groups, suggesting that the safety was not significantly different. Analysis of the propensity-score matched cohort was performed to adjust for selection bias, and no significant difference was found in any outcome. Our results suggest that early ART introduction can be considered for untreated HIV-positive patients with PCP on the basis of efficacy and safety.

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. A log-rank test was conducted to compare the lost-to-follow-up rates by patients’ nation of origin and medical interpreter use. Of the 931 participants, 114 were foreign patients, whose overall attendance rate at 5 years was 75.5%, which was significantly lower than that of Japanese patients (94.1%, p < 0.001). There was no significant difference in regular attendance with respect to medical interpreter use (p = 0.09). Social support in addition to a medical interpreter may be needed to improve attendance rates in the study population.

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. Here, we reveal the 2.20-Å crystal structure of the chimpanzee A3H (cpzA3H) dimer bound to a short double-stranded RNA (dsRNA), which appears to be similar to two recently reported structures of pig-tailed macaque A3H and human A3H. In the structure, the dsRNA-binding interface forms a specialized architecture with unique features. The analysis of the dsRNA nucleotides in the cpzA3H complex revealed the GC-rich palindrome-like sequence preference for dsRNA interaction, which is largely determined by arginine residues in loop 1. In cells, alterations of the cpzA3H residues critical for the dsRNA interaction severely reduce intracellular protein stability due to proteasomal degradation. This suggests that cpzA3H stability is regulated by the dsRNA-mediated dimerization as well as by unknown cellular machinery through proteasomal degradation in cells. Taken together, these findings highlight unique structural features of primate A3Hs that are important to further understand their cellular functions and regulation.

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. Respondent-driven sampling was used to collect data from YMSM aged 16-29 in Houston, Texas and Chicago, Illinois. Social network data from 746 respondents and 2035 social and/or sexual partners were collected from 2014 to 2016, of whom 27.9% were HIV seropositive, with 9.4% of their partners being both sexually and socially connected to respondents (overlapping network status), and 90.6% either sexually or socially connected. Generalized estimating equation analysis was conducted based on respondents' knowledge of their sexual partners' HIV status. Results showed that respondents with overlapping sexual and social relationships with their partners were less likely to not know their partners' HIV status (AOR = 0.26 95% CI: 0.18-0.40). Results highlight the association between overlapping partnership and knowledge of partner's HIV status among YMSM. These findings are useful when selecting potential network members to disclose HIV status and support YMSM's health and well-being.

Identifying integration sites of the HIV-1 genome with intact and aberrant ends through deep sequencing

Paired-end deep sequencing is a powerful tool to investigate integration sites of the HIV-1 genome in infected cells. Integration sites of HIV-1 proviral DNA carrying intact LTR ends have been well documented. In contrast, integration sites of proviral DNA with aberrant ends, which emerge infrequently but can also induce replication-competent viruses, have not been extensively examined, in part, because of the lack of a suitable bioinformatics method for deep sequencing. Here, we report a novel bioinformatics protocol, named the VINSSRM, to search for integration sites of proviral DNA carrying intact and aberrant LTR ends using paired-end deep sequencing data. The protocol incorporates split-read mapping to assign viral and human genome parts within read sequences and overlapping paired-end read merging to construct long error-corrected sequences. The VINSSRM not only consistently detects integration sites similar to the conventional method but also provides information on additional integration sites, including those of proviral DNA with aberrant ends, which were mainly found in non-exonic regions of the human genome. Therefore, the VINSSRM may help us to understand HIV-1 integration, persistence of infected cells, and viral latency.

APOBEC3G genotypes and proviral DNA hypermutations on HIV/AIDS disease progression in Thai and Cambodian children

Aim: To evaluate the effect of APOBEC3G host factor on HIV/AIDS progression in perinatally HIV-infected Thai and Cambodian children with distinct clinical patterns; rapid progressors (RPs) and long-term nonprogressors (LTNPs). Materials & methods: APOBEC3G genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism in DNA samples. APOBEC3G-mediated G-to-A hypermutations were analyzed by sequencing of the vif/vpu genes from proviral DNA. Results: Frequency of APOBEC3G 186H/R genotypes, AA:AG:GG, in the RPs was 100:0:0% and 83:17:0% (p = 0.3) in LTNPs. Hypermutation of the vif-coding region was observed in none of the RPs and 8.3% of LTNPs (p = 0.5). Hypermutations at the vpu genes were not detected in either groups’ proviral DNA. Conclusion: We observed no significant association of APOBEC3G genotypes and hypermutation rates between children with different profiles of HIV/AIDS disease progression.

Crystal structure of the Vif-interaction domain of the anti-viral APOBE3F

Human cells express a family of cytidine deaminases, called APOBEC3 (A3) (A3A, B, C, D, F, G, and H). The family enzymes, especially A3G and A3F potentially inhibit replication of retroviruses including HIV-1. However, HIV-1 overcomes the A3-mediated antiviral system by expressing a virus-encoded antagonist, viral infectivity factor (Vif) protein. In HIV-1-infected cells, Vif specifically binds with A3 followed by proteasomal degradation of A3. Hence, inhibition of the interaction between A3 and Vif is an attractive strategy for developing novel anti-HIV-1 drugs. To date, we have determined the first crystal structure of A3 with Vif-binding interface, A3C (PDB ID: 3VOW). In addition, our extensive mutational analysis, based on the A3C structure, revealed that structural features of the Vif-binding interface are highly conserved among A3C, DE, and F [1]. However, more recently, Bohn et al. and Karen et al. have shown the crystal structures of mutant A3F C-terminal domain (CTD) which is responsible for the Vif interaction, and have predicted more extended area, including our identified residues, for the interface on the A3F CTD [2][3]. To clarify the Vif-binding interface of A3F, we sought to determine the crystal structure of the wild-type A3F CTD and evaluated contributions of the additional residues for the Vif-interaction interface by virological method. First, we have successfully determined the crystal structure of A3F CTD at 2.75 Å resolution. Furthermore, we have identified four additional residues unique on the A3F CTD but not A3C for Vif interaction, which are located in the vicinity of our previously reported interface. These results demonstrated that the structural features of Vif-binding interface are indeed conserved between A3C and A3F. Taken together, these results will provide the fine-tuned structure information to understand the binding between A3 and Vif and to facilitate a development of novel anti-HIV-1 compounds targeting A3 proteins.

Lack of association between intact/deletion polymorphisms of the APOBEC3B gene and HIV-1 risk

Objective

The human APOBEC3 family of proteins potently restricts HIV-1 replication APOBEC3B, one of the family genes, is frequently deleted in human populations. Two previous studies reached inconsistent conclusions regarding the effects of APOBEC3B loss on HIV-1 acquisition and pathogenesis. Therefore, it was necessary to verify the effects of APOBEC3B on HIV-1 infection in vivo.

Methods

Intact (I) and deletion (D) polymorphisms of APOBEC3B were analyzed using PCR. The syphilis, HBV and HCV infection rates, as well as CD4⁺ T cell counts and viral loads were compared among three APOBEC3B genotype groups (I/I, D/I, and D/D). HIV-1 replication kinetics was assayed in vitro using primary cells derived from PBMCs.

Results

A total of 248 HIV-1-infected Japanese men who have sex with men (MSM) patients and 207 uninfected Japanese MSM were enrolled in this study. The genotype analysis revealed no significant differences between the APOBEC3B genotype ratios of the infected and the uninfected cohorts (p = 0.66). In addition, HIV-1 disease progression parameters were not associated with the APOBEC3B genotype. Furthermore, the PBMCs from D/D and I/I subjects exhibited comparable HIV-1 susceptibility.

Conclusion

Our analysis of a population-based matched cohort suggests that the antiviral mechanism of APOBEC3B plays only a negligible role in eliminating HIV-1 in vivo.

Association of APOBEC3G genotypes and CD4 decline in Thai and Cambodian HIV-infected children with moderate immune deficiency

INTRODUCTION

Human APOBEC3G is a host defense factor that potently inhibits HIV replication. We hypothesize that HIV-infected children with a genetic variant of APOBEC3G will have a more rapid disease progression.

METHODS

Antiretroviral therapy (ART)-naïve children, aged 1-12 years old with CD4 15-24% and without severe HIV-related symptoms were enrolled. The children had CD4% and absolute CD4 counts every 12 weeks and HIV-RNA every 24 weeks until 144 weeks. ART was started when CD4% declined to < 15% or AIDS-related events developed.APOBEC3G genetic variants were performed by PCR-based restriction fragment length polymorphism techniques from peripheral blood mononuclear cells. Random-effect linear regression analysis was performed to correlate APOBEC3G genotypes and disease progression.

RESULTS

147 children, 35% male, with a median (IQR) age of 6.5 (4.3-8.8) years were enrolled. CDC N:A:B were 1:63:36%. Median baseline values were 20% for CD4% 605 cells/mm3 for CD4 count and 4.7 log10copies/mL for HIV-RNA.The frequencies of APOBEC3G genotypes AA (186H/H), AG (186H/R), GG (186R/R) were 86%, 12%, and 2% respectively. The APOBEC3G genotype GG was associated with a significant decline in CD4% -5.1% (-8.9 to -1.2%), p<0.001, and CD4 counts -226 (-415 to -34) cells/mm3, p<0.001 by random-effect liner regression analysis. No significant associations of APOBEC3G genotypes with HIV-RNA changes overtime (p=0.16) or progression to CDC B and C (p=0.49) were observed.

CONCLUSIONS

APOBEC3G genotype GG was significantly associated with a more rapid decline in CD4. APOBEC3G's antiviral effects on HIV disease progression in children should be further explored.

Antiviral Mechanism and Biochemical Basis of the Human APOBEC3 Family

The human APOBEC3 (A3) family (A, B, C, DE, F, G, and H) comprises host defense factors that potently inhibit the replication of diverse retroviruses, retrotransposons, and the other viral pathogens. HIV-1 has a counterstrategy that includes expressing the Vif protein to abrogate A3 antiviral function. Without Vif, A3 proteins, particularly APOBEC3G (A3G) and APOBEC3F (A3F), inhibit HIV-1 replication by blocking reverse transcription and/or integration and hypermutating nascent viral cDNA. The molecular mechanisms of this antiviral activity have been primarily attributed to two biochemical characteristics common to A3 proteins: catalyzing cytidine deamination in single-stranded DNA (ssDNA) and a nucleic acid-binding capability that is specific to ssDNA or ssRNA. Recent advances suggest that unique property of A3G dimer/oligomer formations, is also important for the modification of antiviral activity. In this review article we summarize how A3 proteins, particularly A3G, inhibit viral replication based on the biochemical and structural characteristics of the A3G protein.

[A case of Wegener's granulomatosis with episcleritis, mediastinal lesions, and pleural effusion and without serum anti-neutrophil cytoplasmic antibodies]

We report a 63-year-old male case of Wegener's granulomatosis. His complaints were cough and fever, and chest X-ray showed subpleural infiltrative opacities in the bilateral lungs and small nodular lesions in the middle portion of the right lung. He had been treated as bacterial pneumonia at another hospital without any improvement and was referred to this hospital. Chest CT scan disclosed several small nodular lesions in the subpleural region of the right lung, consolidation in the posterior mediastinum, and the left pleural effusion. Transbronchial lung biopsy revealed inflammatory granulation with predominantly lymphocytes and micro-necrosis in the peribronchiolar region. Although these findings suggested Wegener's granulomatosis, open lung biopsy was performed because both antineutrophil cytoplasmic antibodies (ANCA) and antibodies to proteinase-3 were negative and ear, nose, and throat abnormalities were not found. Pathologic findings consisted mainly of granulomatous inflammation with lymphocytes, histiocytes, and multinucleated giant cells, and granulomatous vasculitis with micro-necrosis. Furthermore, the patient was diagnosed as having bilateral episcleritis by an ophthalmologist. No renal involvement was found. Standard treatment with cyclophosphamide and glucocorticoid resulted in marked improvement within a couple of weeks, and the patient was in complete remission eight months after initiation of therapy. This case is of interest in that the distribution of lesions was not typical and ANCA was negative.

[Diffuse large cell lymphoma with spontaneous regression in the lung and lymph nodes. Case report]

An 84-year-old woman was admitted to our hospital because of swelling of the cervical lymph nodes and multiple tumorous lesions observed on radiographic studies. Transcutaneous lung biopsy was performed, but necrosis of the tissue was too marked to make a diagnosis. The diagnosis of diffuse large-cell lymphoma was made based on a biopsy of the pretracheal lymph node. During the first two months after admission, the left cervical lymph nodes and most of the pulmonary lesions regressed not withstanding of special treatment for lymphoma. The patient eventually died of generalized peritonitis. At autopsy, metastasis of systemic organs by malignant lymphoma was observed. Most of the lung regions were cicatrized, but clusters of atypical lymphocytes were observed in the necrotic tissue. The tumor in the mucosa of the small intestine showed necrosis, which accounted for the intestinal perforation. The total clinical course after admission was about six months. Spontaneous regression of diffuse large cell lymphoma is rare, and this is the second reported case in Japan.

[A case of primary antiphospholipid syndrome with fever, pulmonary thromboembolism and endocardial lesion]

A previously healthy 16-year-old girl complaining of fever, hemosputum, chest pain and dyspnea was hospitalized. On admission, physical examination revealed mental confusion, holosystolic heart murmur, and swelling of the left foot. Laboratory investigations showed anemia, leukocytosis, thrombocytopenia, activation of inflammatory reactions, prolongation of PT and APTT, and hypoxia. Antinuclear antibody test was negative. There were no other findings suggestive of collagen diseases such as SLE. Chest X-ray showed consolidation in the left lower lung field and pleural effusion. Echocardiography disclosed a mass lesion in the left atrium in contact with the mitral valve, and mitral regurgitation. No findings indicative of an infectious etiology were present. The patient rapidly improved with high dose corticosteroid and anticoagulant therapy. A venogram of the lower extremity disclosed deep venous thrombosis. A lung ventilation-perfusion scan revealed multiple pulmonary thromboemboli. Elevation of anticardiolipin antibody was noted. Based on these findings, the diagnosis of primary antiphospholipid syndrome was made. Further administration of steroid and anticoagulant resulted in decrease of the titer of anticardiolipin antibody. This is the second report of primary antiphospholipid syndrome in Japan. The clinical significance of this disease is also discussed.

[Study on postoperative perforation in patients with chronic empyema--reoperated cases]

In 18 cases undergone reoperation because of perforation after the initial operation for primary and secondary chronic empyema during the period from 1974 through August 1986, we evaluated findings of fistula, procedures and causes of failure of the initial operation, and procedures and results of reoperation. Subjects consisted of 16 cases of chronic empyema complicated with pulmonary tuberculosis, 1 case of group III nontuberculous mycobacteriosis, and 1 case of chronic empyema secondary to pulmonary fibrosis. All patients had fistula at the initial operation. The initial operation was performed by Kinchu method in 8 cases, pulmonary detachment in 6 cases, and thoracic cavity reduction chiefly by a modification of Grow's method in 4 cases. The initial operation failed because of incomplete closure of the fistula in 11 cases (61%) and appearance of new fistula in 7 cases (39%). In reoperation, the fistula was closed by pedicle muscle plombage in 1 case undergone the initial operation by Kinchu method, while thoracic cavity reduction chiefly by a modification of Grow's method in all of the other 17 cases. After the operation, 15 patients (83%) were cured, 16 patients (89%) could be socially rehabilitated and 2 patients (11%) had recurrence of empyema. Two recurrent patients died from hepatitis and exacerbation of nontuberculous mycobacteriosis, respectively. Out of 10 patients undergone pedicle muscle plombage, 8 patients (80%) were cured. From these findings, we consider that the results of one stage operation can be improved by applying pedicle muscle plombage for closure of fistula after the initial operation following treatment with effective antibiotics.(ABSTRACT TRUNCATED AT 250 WORDS)

[A study on selection of operative technique for chronic empyema based on findings obtained from reoperated cases]

In 13 patients undergone reoperation for chronic empyema during 9 years period from 1975 to 1983, the operative technique employed for the initial treatment, number of operations, findings of fistula and residual cavity and complications associated with each technique were reviewed with following results. Among these reoperated patients, the initial operation was thoracic cavity reduction in 5 cases, pulmonary detachment in 6 cases and air-plombage (Kinchu method) in 2 cases. Reoperation was carried out in a total of 27 times. There were 6 cases (46%) which were operated more than 3 times. These 6 cases included none of the cases which underwent air plombage. At the time of the first reoperation, fistula was observed in 11 out of 13 cases. At the final operation the residual cavity was accompanied with fistula in 7 cases and empyema in 5 cases. As the final operation, chest wall plombage chiefly by a modification of Grow's method combined with pedicle muscle plombage was employed. In cases indicated for more than two times of operations of thoracic cavity reduction, chest wall plombage was useful for reoperation. On the basis of these results, indication of each operation to improve results of surgical treatment of chronic empyema was discussed by taking into consideration advantages and complications of each operative technique.

[Two cases of Hermansky-Pudlak syndrome with interstitial pneumonia]

Two cases of Hermansky-Pudlak syndrome with interstitial pneumonia were reported. Both patients had evidence of pulmonary involvement characterized by diffuse bilateral infiltrates. They had oculocutaneous albinism. Case 1 was a 55 year-old female who had a history of easy bruising. Her two sisters were albino and had died of pulmonary fibrosis. One of them was diagnosed as Hermansky-Pudlak syndrome on autopsy. Bone marrow aspirate disclosed typical macrophages with ceroid-like pigment. Transbronchial lung biopsy showed alveolar wall thickening. Lumi-aggregometer showed a decrease of platelet aggregation and an absence of ATP release. Case 2 was a 43 year-old female and had a bleeding tendency during a surgical procedure. Lumi-aggregometer showed normal platelet aggregation but an absence of ATP release. BALF analysis did not disclose macrophages with ceroid-like pigment.

[A case of primary pulmonary sporotrichosis]

We report the first case of primary pulmonary sporotrichosis in Japan. A 53-year-old man was admitted to our hospital for further examination of the abnormal shadows on chest X-ray film. Six months before admission, he was admitted to another hospital because of alcoholic liver disease and diabetes mellitus. Since the initial chest film showed cavities with infiltration in the left upper lung field, he was treated with antituberculous drugs despite negative sputum cultures for mycobacterium. In spite of the medication, his chest X-ray film revealed another cavitary lesion, so he was referred to our hospital. He had been asymptomatic during this period. Chest X-ray on admission disclosed multiple cavities in the left upper lobe and a cavity in the right lower lobe. Repeated sputum specimens, bronchial washings and brushings for cytology and cultures were all negative. In an attempt to clarify the pathogen, percutaneous lung aspiration (PLA) was performed. The PLA sample yielded a positive culture of Sporothrix shenckii. After the diagnosis, S. schenckii was also cultured from sputa. A sporothrix skin test and yeast agglutination test for S. schenckii were positive. In the absence of a history for skin lesion, the patient was diagnosed as a primary pulmonary sporotrichosis. As iodide therapy was ineffective, he was started on a regimen of intravenous amphotericin B. However his renal function progressively deteriorated, so amphotericin B was discontinued. Now he receives miconazole intravenously and is still under careful observation. As far as we know, this is the first report of primary pulmonary sporotrichosis in Japan. The possibility of sporotrichosis should be considered in any cases of undiagnosed cavitary lung diseases.