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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.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of coronavirus disease (COVID-19) which has spread rapidly worldwide to cause a global pandemic. The SARS-CoV-2 genome shows a lower mutation rate than other RNA viruses. However, because of the ongoing rapid worldwide transmission among humans, the genetic diversity of the SARS-CoV-2 genome has increased. In Japan, a previous study suggested that the distinct viral clades L, S, G and GR of SARS-CoV-2 had been imported from overseas and begun to circulate domestically by April 2020. However, little is known about molecular epidemiology of SARS-CoV-2 since then, because of the lack of sufficient information on the viral genome sequence information in Japan. Herein, to probe the molecular epidemiological trends in Japan, we determined the full genome sequences of SARS-CoV-2 (n=55) derived from patients admitted to our hospital and performed a comparative analysis with domestic and international sequence information available from GISAID and GenBank. The results showed that the dominant domestic genotypes, including our determined sequences, had shifted from clades S and L to clades G and GR, and dispersed widely during the first infection peak period (March to April). In contrast, all the SARS-CoV-2 genotypes after May 2020 are highly clustered as unique clade GR genotypes that are not detected outside Japan. This genetic clustering occurred during the period under which restrictions were placed on overseas travel in Japan. Similar trends of viral genotype clustering have also been observed worldwide, with regional disparities. Under these circumstances, we should adopt adequate preventive measures to prevent the viral genetic diversity from increasing, and also further extend the molecular epidemiological survey of SARS-CoV-2 genotypes in Japan. These efforts will aid in ensuring successful use of the novel vaccines and antiviral drugs in the near future.

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.

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.A total of 57 plasma samples, including three panels (Ⅰ: HIV-2-positive samples [n=9], Ⅱ: HIV-1 infection with HIV-2 antibody cross-reactivity samples [n=37], and Ⅲ: HIV negative with biological false-positive HIV-2 samples [n=11]) were tested by Geenius.Geenius determined Panel I to be "HIV-2 positive with/without HIV-1 cross-reactivity (n=4, respectively)", including HIV-2 group A and CRF01_AB. In the case with HIV-2 group B, all bands were detected, resulting in a Geenius interpretation of "HIV positive untypable". Geenius classified Panels II and III as "HIV-1 positive (n=37)" or "HIV negative (n=9)", "HIV indeterminate (n=1)" and "HIV-2 indeterminate (n=1)", suggesting 95.8% HIV-2 differentiation by Geenius.With Geenius, there were fewer false-positives for HIV-1/-2 negativity and fewer cross-reactions with HIV-2 among HIV-1-positive samples. Additionally, the assay could detect HIV-2 genetic group CRF01_AB. Geenius can be expected to be a useful diagnostic tool that is an alternative to conventional Western blotting.

Background: To explore the perspectives and approaches of primary care physicians in Japan and the US on diagnosing dementia.Methods: Qualitative comparison conducted in ethnographic tradition using semi-structured interviews and thematic analysis. Primary care settings across Japan and in the Midwest State of Michigan, US. Participants were a total of 48 primary care physicians, 24 each from Japan and the US participated. Both groups contained a mixture of the practice area (rural/urban), gender, age, and years of experience as a primary care physician. Results: Participants in Japan and the US voiced similar approaches for making the diagnosis of dementia and held similar views about the desire benefits of diagnosing dementia. Differences were found in attitudes about the appropriate timing of formally diagnosing dementia. Japanese physicians tended to make a formal diagnosis when problems that would benefit from long-term care services emerged for family members. US physicians were more proactive in diagnosing dementia in the early stages by screening for dementia in health check-ups and promoting advance directives when the patients were still capable of decision-making. Views about appropriate timing of diagnostic testing for dementia in the two systems reflect what medical or nursing care services physicians can use to support dementia patients and caregivers.Conclusions: Testing to establish an early diagnosis of dementia by primary care physicians only partly relates to testing options available. Benefits of making the diagnosis included the need to activate the long-term care services in Japan and for early intervention and authoring advance directives in the US.

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. We found that ART, especially conventional nucleotide/nucleoside reverse transcriptase inhibitor (NRTI)-based ART, has remarkable impacts on fecal microbial diversity: decreased α-diversity and increased ß-diversity over time. In contrast, dynamic diversity changes in the salivary microbiome were not observed. Comparative analysis of bacterial genus compositions showed a propensity for Prevotella-enriched and Bacteroides-poor gut microbiotas in patients with ART over time. In addition, we observed a gradual reduction in Bacteroides but drastic increases in Succinivibrio and/or Megasphaera under conventional ART. These results suggest that ART, especially NRTI-based ART, has more suppressive impacts on microbiota composition and diversity in the gut than in the mouth, which potentially causes intestinal dysbiosis in patients. Therefore, NRTI-sparing ART, especially integrase strand transfer inhibitor (INSTI)- and/or non-nucleotide reverse transcriptase inhibitor (NNRTI)-containing regimens, might alleviate the burden of intestinal dysbiosis in HIV-1-infected patients under long-term ART.

ObjectivesWe investigated the prevalence and patterns of pre-treatment and acquired HIV drug resistance mutations (DRMs) in Tanzania as a ‘treat all’ strategy, virological monitoring and the progressive increase in usage of tenofovir are being implemented in HIV treatment programmes.MethodsViral RNA was isolated from plasma of 60 ART-naive and 166 treated-but-viraemic (>400 copies/mL) HIV-1-infected adults attending a care and treatment clinic at Muhimbili National Hospital, Dar es Salaam, Tanzania, between June and October 2017. Viral genes encoding protease and reverse transcriptase were amplified by PCR and directly sequenced.ResultsViral genotyping of successfully amplified samples revealed pre-treatment DRMs in 14/47 (29.8%) ART-naive subjects. Of these, 7/47 (14.9%) harboured mutations that confer high-level resistance to at least one drug of the default first-line regimen. In treated-but-viraemic subjects, DRMs were found in 100/111 (90%), where DRMs against NNRTI, NRTI and PI were observed in 95/100 (95%), 92/100 (92%) and 13/100 (13%), respectively. Tenofovir-resistance mutations K65R and K70G/E or ≥3 thymidine analogue resistance mutations including M41L and L210W were found in 18/36 (50%) subjects on a tenofovir-containing regimen at failure. Four patients harboured multiple DRMs, which can confer resistance to all available ART regimens in Tanzania.ConclusionsTaken together, pre-treatment and acquired DRMs were highly prevalent, which represents a major risk for the efficacy of ART programmes in Tanzania. Availability of a newer generation of antiretroviral drugs with a higher genetic barrier to resistance and robust treatment monitoring is warranted for effective and sustainable HIV treatment.

HIV-1 CRF01_AE and subtype B (B) have dominated and their different circulating recombinant forms (CRFs) have emerged in East and Southeast Asian countries. Here, we report a novel drug-resistant HIV-1 CRF. Five independent recombinant specimens exhibiting discordant subtype results for the gag, pol, and env sequences were isolated. These recombinants had the CRF01_AE (gag p17)/B (pol PR-RT and IN)/CRF01_AE (env C2-V3) pattern similar to CRF69_01B. Sequence analysis of four near full-length HIV-1 genomes revealed a unique phylogenetic cluster distinct from previously reported CRFs. Of the four recombinants, three shared an identical mosaic structure including seven breakpoints in the gag, pol, vif, and env regions, designated CRF76_01B. The one remaining recombinant had additional recombination breakpoints in the vpu region and exhibited another unique recombinant form composed of CRF76_01B and B. These findings provide important insight into the transmission dynamics of HIV-1 in Asia that may be important for its effective prevention.

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.

To design appropriate antiretroviral therapy regimens and avoid the emergence of human immunodeficiency virus (HIV)-1 variants with reduced susceptibility to antiretroviral drugs, genotypic drug-resistance testing (HIV genotyping) is strongly recommended. To monitor the quality of HIV genotyping in Japan, we performed an external quality assessment (EQA), named the Japanese external quality assessment program, to standardize HIV genotyping (JEQS). To accurately evaluate the quality of HIV genotyping, we employed as reference material (RM) a well-characterized sample, in vitro transcribed RNA (trRNA) that includes the HIV gag–pol sequence, and created a JEQS2010 panel consisting of three single variant and three mixed trRNA samples. All 11 participating laboratories showed high concordance rates (>96%) for the single variant samples. Eight laboratories also showed good rates of detecting minor variants, but three laboratories failed to detect the variants comprising one-half of the sample. These three laboratories used a common primer that had four internal mismatches to the minor trRNA clone. This program showed the usefulness of trRNA as RM, the high quality of HIV genotyping, and extensive interlaboratory variation in the ability to detect minor variants. These results suggest that improving the quality of HIV genotyping in Japan requires regularly implementing the EQA program and improving the HIV genotyping protocol in each laboratory.

A novel HIV-1 integrase mutation pattern, L74F V75I, which conferred resistance to first-generation integrase strand transfer inhibitors (INSTIs), was identified in a clinical case with virological failure under a raltegravir-based regimen. Addition of L74F V75I to N155H or G140S Q148H increased resistance levels to the second-generation INSTIs dolutegravir (>385- and 100-fold, respectively) and cabotegravir (153- and 197-fold, respectively). These findings are important for the development of an accurate system for interpretation of INSTI resistance and the rational design of next-generation INSTIs.

The emergence and transmission of drug-resistant human immunodeficiency virus-1 (HIV-1) compromises antiretroviral treatment for HIV-1. Thus, testing for drug resistance is recommended at diagnosis and before initiating highly active antiretroviral treatment. We conducted an epidemiological study enrolling newly diagnosed patients between 2003 and 2008 in our nationwide surveillance network. In the 6-year study period, the prevalence of drug-resistant HIV-1 among 2573 patients, consisting mainly of Japanese men in their late-30s and infected through male-to-male sexual contacts, followed an increasing trend from 5.9% (16/273) in 2003 to 8.3% (50/605) in 2008. Nucleoside reverse transcriptase inhibitor-associated mutations predominated in each year, with T215 revertants being the most abundant. The predictive factor for drug-resistant HIV-1 transmission was subtype B (OR=2.36; p=0.004), and those for recent HIV-1 infection were male gender (OR=3.79; p=0.009), MSM behavior (OR=1.67; p=0.01), Japanese nationality (OR=2.31; p=0.008), and subtype B (OR=5.64; p

1989年から2005年までの17年間に当科にて経験した痔瘻癌7例の臨床病理組織学的特徴と治療成績の検討を行った. 男性5例, 女性2例, 平均年齢67歳. 痔瘻から癌発見までの平均期間は26.4年. 全例に肛門部痛を認め, 痔瘻分類はII Ls症例4例, 他は不明であった. 平均腫瘍最大径は55mm, 組織型は粘液癌が5例, stage II以上の進行例が6例で, 仙・尾骨, 肛門挙筋などへの浸潤のためradial marginが不十分となったものは3例に及んだ. 全症例に腹会陰式直腸切断術を施行し, 術後化学療法3例, 術後放射線治療も3例に行われた. 無再発生存例はわずか2例で, 肺転移のみの1例に化学療法を施行中である. 局所再発例の4例は全例死亡し, 平均生存期間は2.3年であった. 局所再発は予後不良因子であり, 治療成績向上のためには早期発見と十分な断端確保を目指した治療方法の選択が肝要である. 断端確保が困難な症例には術前放射線化学療法の展開が望まれる.

Under programs organized by the government of Thailand, HIV-1-infected patients have been treated since 2002 with several regimens, including a tablet known as GPOvir, which contains lamivudine, stavudine, and nevirapine. The aim of this study was to establish an effective assay, based on mutagenically separated PCR (MS-PCR), with the goal of surveying GPOvir-resistant HIV-1 cases. To determine the target mutation point for the assay, we analyzed the patterns of acquired drug resistance in plasma samples from GPOvir-failed cases. Of 428 HIV-1-infected individuals treated with GPOvir at Lampang Hospital in northern Thailand from 2002 to 2004, 66 had detectable viral loads after 3 months of treatment. The HIV-1 sequences of these 66 GPOvir-failed cases and 55 pre-GPOvir baseline samples were analyzed. The most prevalent drug resistance mutation among the samples was the lamivudine resistance M184I/V mutation. Based on this finding, we developed a new MS-PCR assay to detect the M184I/V mutation, and evaluated the assay performance for detecting GPOvir-resistant CRF01_AE cases. Comparing the results of M184I/V MS-PCR and sequence analyses, we found a concordance rate of 95% and an overall sensitivity of the M184I/V MS-PCR for detecting GPOvir-resistant cases of 79%. Considering the relatively low price of the assay, approximately $12.50 per sample, M184I/V MS-PCR may be a candidate for monitoring a large number of GPOvir-treated patients, particularly in developing nations.

To understand the predominant HIV subtype and drug-resistant viruses in northwest Ethiopia, isolates from 92 antiretroviral drug-naive HIV-1-infected tuberculosis patients were analyzed. Of these patients, 90 (97.8%) were found to be infected with viral subtype C. Other isolates had subtype A (1.1%) and subtype D (1.1%). No primary mutations were associated with protease inhibitor drug resistance. One case (1.1%) had the reverse-transcriptase mutation, V75I. Two patients (2.2%) had the G190A mutation, which confers resistance to the nonnucleoside reverse transcriptase inhibitor, nevirapine. Our study demonstrates that subtype C is the major HIV-1 subtype in northwest Ethiopia. Our results also reveal that the population in the study area had been exposed to antiretrovirals and that treatment-naive patients had drug resistance mutations. Thus, our results emphasize the need for routine drug resistance monitoring in northwest Ethiopia.

The major circulating HIV-1 strains in Japan have been subtype B (B) followed by CRF01_AE (AE) in newly diagnosed HIV/AIDS cases. These two subtypes have distinct epidemiological characteristics; B predominates in men who have sex with men, while AE is observed mostly in heterosexuals engaging in high-risk sex. However, transmission networks of these two high-risk populations appear to be crossing over and diffusing. Here we report the emergence of previously unidentified HIV-1 AE/B recombinants in Japan. We initially identified 13 cases with discordant subtyping results with AE (gag MA)/B (pol PR-RT)/AE (env C2V3) by molecular phylogenetic analysis of 1,070 cases who visited Nagoya Medical Center from 1997 to 2012. Genetic characterization of full-length sequences demonstrated that they shared an identical recombinant structure, and was designated as CRF69_01B by the Los Alamos HIV National Laboratory. By reviewing gag, pol, and env sequences collected in the Japanese Drug Resistance HIV-1 Surveillance Network, we found five other CRF69_01B probable cases from different areas in Japan, suggesting that the strain is transmitted widely throughout the country. The time of the most recent common ancestor analyses estimated that CRF69_01B emerged between 1991 and 1995, soon after AE was introduced from neighboring countries in the mid-1990s. Understanding the current epidemic strains is important for the diagnosis and treatment of HIV/AIDS, as well as for the development of globally effective HIV vaccines.

Integrase strand transfer inhibitors (INSTIs), which block proviral DNA integration into the host chromosome, are clinically effective against HIV-1 isolates exhibiting resistance to other classes of antiretroviral agents. Although naturally occurring amino acid variation has been less frequently observed in the integrase region, the functional constraints of this variation on primary INSTI resistance-associated mutations are not fully understood. In the present study, we focused on the S119G/R/P/T (S119X) polymorphisms, which are frequently observed in HIV-1 sequences derived from clinical specimens (naive, n=458, 26%). The frequency of the S119X polymorphism together with Q148H/R (n=8, 63%) or N155H (n=12, 83%) was relatively high compared with that of naive group. Our in vitro assays revealed that S119G/P/T alone exerted no effect on the susceptibility to INSTIs, whereas S119R enhanced the level of INSTI resistance induced by well-known INSTI resistance-associated mutations (Y143C, Q148H or N155H). Notably, the S119R polymorphism contributed to a significant (5.9-fold) increase in dolutegravir resistance caused by G140S/Q148H. Analysis of two cases of virological failure during raltegravir-based therapy showed that the accumulation and the rapid evolution of primary INSTI resistance-associated mutations coincided with the S119R mutation. These data highlight the role of the S119X polymorphism in INSTI resistance, and this polymorphism might be linked to the potential treatment outcome with INSTI-based therapy.

BACKGROUND Drug-resistant HIV are more prevalent and persist longer than previously demonstrated by bulk sequencing due to the ability to detect low-frequency variants. To clarify a clinical benefit to monitoring minority-level drug resistance populations as a guide to select active drugs for salvage therapy, we retrospectively analyzed the dynamics of low-frequency drug-resistant population in antiretroviral (ARV)-exposed drug resistant individuals. MATERIALS AND METHODS Six HIV-infected individuals treated with ARV for more than five years were analyzed. These individuals had difficulty in controlling viremia, and treatment regimens were switched multiple times guided by standard drug resistance testing using bulk sequencing. To detect minority variant populations with drug resistance, we used a highly sensitive allele-specific PCR (AS-PCR) with detection thresholds of 0.3-2%. According to ARV used in these individuals, we focused on the following seven reverse transcriptase inhibitor-resistant mutations: M41L, K65R, K70R, K103N, Y181C, M184V, and T215F/Y. Results of AS-PCR were compared with bulk sequencing data for concordance and presence of additional mutations. To clarify the genetic relationship between low-frequency and high-frequency populations, AS-PCR amplicon sequences were compared with bulk sequences in phylogenetic analysis. RESULTS The use of AS-PCR enabled detection of the drug-resistant mutations, M41L, K103N, Y181C, M184V and T215Y, present as low-frequency populations in five of the six individuals. These drug resistant variants persisted for several years without ARV pressure. Phylogenetic analysis indicated that pre-existing K103N and T215I variants had close genetic relationships with high-frequency K103N and T215I observed during treatment. DISCUSSION AND CONCLUSION Our results demonstrate the long-term persistence of drug-resistant viruses in the absence of drug pressure. The rapid virologic failures with pre-existing mutant viruses detectable by AS-PCR highlight the clinical importance of low-frequency drug-resistant viruses. Thus, our results highlight the usefulness of AS-PCR and support its expanded evaluation in ART clinical management.

As the number of HIV-1-infected individuals receiving antiretroviral drugs has been rapidly increasing in developing countries, there is an urgent need for drug resistance genotype information of non-B subtype HIV-1 and for the establishment of a practical system of monitoring drug-resistant viruses. This study first sequenced the reverse transcriptase region of HIV-1 in 112 infected individuals who had been treated with zidovudine (AZT)/didanosine or AZT/zalcitabine as dual therapy at a government hospital in northern Thailand and then compared the above sequence method with mutagenically separated polymerase chain reaction (MS-PCR) for detecting M41L and K70R mutations. Concordant rates of detecting M41L and K70R mutations by the 2 methods were 96.9% (93/96) and 92.7% (89/96), respectively. The M41L and K70R MS-PCR could detect 86.4% of AZT-resistant strains with any resistance mutation, which was determined by the sequencing method. Then 292 drug-naive individuals were screened for the presence of drug-resistant HIV-1 by the MS-PCR assay and it was found that 2 individuals (0.7%) carried viruses with either the M41L or K70R mutation. It is feasible to test a large number of samples with MS-PCR, which is sensitive, cheap, and easy to perform and does not require sophisticated equipment. The M41L and K70R MS-PCR is potentially a useful tool to monitor the spread of AZT-resistant HIV-1 in resource-limited countries.

It is well documented that human immunodeficiency virus type 1 (HIV-1) Gag cleavage site mutations (CSMs) emerge in conjunction with various HIV-1 mutations for protease inhibitor (PI) resistance and improve viral replication capacity, which is reduced by acquisition of the resistance. However, CSMs are not the only mutations that emerge in Gag during treatment; many mutations other than CSMs (non-CSMs) have been found to accumulate in the Gag region. In the present study we demonstrate the important role of Gag non-CSMs with regard to viral fitness recovery. We selected three Gag-protease sequences with different PI resistance-associated mutations and CSMs from patients with antiretroviral treatment failure. To clarify the significance of CSMs and non-CSMs, four types of recombinant viruses with different patterns in each sequence were constructed. These were the GP type (patient-derived Gag and protease), the P type (HXB2 Gag and patient-derived protease), the GP −c type (CSMs removed from the GP type), and the P +c type (CSMs in the HXB2 Gag frame and patient-derived protease). By comparison of these four types of recombinant viruses in each patient-derived Gag-protease sequence, we found that non-CSMs, which had no systematic pattern, make a significant contribution to viral fitness recovery. Our findings demonstrate a delicate interaction between the in vivo evolution of Gag and protease to evade drug selective pressure and the importance of Gag in evaluating drug-resistant viruses.

Meckel's diverticulum has been known to occur in 2% of the general population and is usually asymptomatic; it causes complications in 4% of cases. We have recently experienced a rare case of perforation of Meckel's diverticulum in a neonate delivered to a mother who had been treated with methimazole for hyperthyroidism during pregnancy. A 2-day-old neonate who was delivered by Cesarean section at 39 weeks' gestation underwent an emergency operation; he was diagnosed with gastrointestinal perforation, showing a large amount of air within the gastrointestinal tract, and pneumoperitoneum radio graphically. Laparotomy showed a perforated Meckel's diverticulum in the jejunum with a moderate amount of serous ascitic fluid. Segmental resection of the small bowel and intraperitoneal drainage were performed. A pathological examination for Meckel's diverticulum revealed a partially thinned muscular layer suggesting the existence of an increase in pressure within the diverticulum. The neonate needed to be administrated thyroid hormone for a hypothyroid state, which was possibly due to the maternal treatment with methimazole during pregnancy. We hypothesize that maternal treatment with methimazole during pregnancy may be associated with the formation of Meckel's diverticulum in a neonate; and it may be associated with an abdominal distention and subsequent perforation of Meckel's diverticulum with secondary hypothyroidism.

An increasing number of HIV-1-infected patients living in developing countries now have access to antiretroviral drugs. Information regarding the drug-resistant mutations of non-B subtype HIV-1 remains limited, however. The authors cross-sectionally compared patterns of the drug-resistant point mutations in patients infected with either subtype B or CRF01_AE (subtype E) among patients who acquired HIV by sexual transmission in Japan. Protease sequence data were available from 216 patients with a detectable level of RNA copies in plasma. Based on phylogenetic analysis of the protease and the C2V3 regions, 162 subtype B and 45 CRF01_AE cases were identified; 82 subtype B and 24 CRF01_AE patients had a treatment failure with nucleoside reverse transcriptase inhibitors; and 69 subtype B and 19 CRF01_AE patients had a treatment failure with a protease inhibitor. Antiretroviral drug history was similar in subtype B-infected and CRF01_AE-infected patients. The mutations T69N and V75M in reverse transcriptase and L10F, K20I, L33I, and N88S in protease were seen more frequently in patients infected with CRF01_AE than in patients with subtype B. The mutations, D30N, A71V, and N88D were found exclusively in patients with subtype B. Most of the characteristic mutation patterns were associated with a history of receiving nelfinavir. The pattern of drug resistance mutations differs between the subtypes. Data derived from subtype B drug-resistant genotypes may not always be applicable to non-B subtypes.

Strictures of the alimentary tract are conventionally treated by fluoroscopically guided bouginage and endoscopic balloon dilation, which is often very effective. However, severe and recurrent stenosis associated with ischemic injury in a jejunal segment transpositioned with a vascular anastomosis after reconstruction for cervical esophageal cancer is an intractable problem. We describe a new method using a Steno-Cutter to successfully treat a patient with this type of stricture following surgery for cervical esophageal cancer. The positive results achieved in this case suggest that our new method could represent a promising option of treatment for strictures when conventional modalities fail.

The usefulness of primary chemotherapy has been widely recognized and applied to routine clinical practice to improve prognosis by downstaging. Nevertheless, none of many trials has been able to show a positive effect of primary chemotherapy in terms of prognosis, and predictive factors of outcome have not been defined and are still under investigation. Primary chemotherapy was given to 50 patients with advanced breast cancer. Predictive factors involved in clinical or pathological response to primary chemotherapy (3 cycles of CE(F) therapy) were investigated. The response rate in all patients was 56.0% (CR: 3 patients PR: 25 patients) and 64.1% in patients without distant metastases. MIB-1 was related to the clinical response and EIC (extensive intraductal component) was related to the pathological response; the response was high in patients with EIC negative tumors. Responders had tumors with higher proliferative activity, which decreased significantly after chemotherapy. Patients with a decrease of more than 30% in proliferative activity after chemotherapy had significantly higher disease-free survival rates. The proliferative activity and EIC status were useful predictors of clinical or pathological response to primary chemotherapy. A decrease in proliferative activity by chemotherapy significantly correlated with clinical response and reflected a favorable prognosis. The number of patients benefiting from primary chemotherapy might steadily increase by detecting these predictive factors.

We studied the evolutionary relationships between the two protease inhibitor (PI) resistance mutations, D30N and L90M, of human immunodeficiency virus type 1 (HIV-1). The former is highly specific for nelfinavir resistance, while the latter is associated with resistance to several PIs, including nelfinavir. Among patients with nelfinavir treatment failure, we found that D30N acquisition was strongly suppressed when L90M preexisted. Thus, D30N/L90M double mutations not only were detected in a very limited number of patients but also accounted for a minor fraction within each patient. In the disease course, the D30N and L90M clones readily evolved independently of each other, and later the D30N/L90M double mutants emerged. The double mutants appeared to originate from the D30N lineage but not from the L90M lineage, or were strongly associated with the former. However, their evolutionary pathways appeared to be highly complex and to still have something in common, as they always contained several additional polymorphisms, including L63P and N88D, as common signatures. These results suggest that D30N and L90M are mutually exclusive during the evolutionary process. Supporting this notion, the D30N/L90M mutation was also quite rare in a large clinical database. Recombinant viruses with the relevant mutations were generated and compared for the ability to process p55 gag and p160 pol precursor proteins as well as for their infectivity. L90M caused little impairment of the cleavage activities, but D30N was detrimental, although significant residual activity was observed. In contrast, D30N/L90M demonstrated severe impairment. Thus, the concept of mutual antagonism of the two mutations was substantiated biochemically and functionally.

A 50-year-old woman was referred to our hospital for shoulder joint stiffness. She had a history of polyclonal hypergammaglobulinemia and an elevated C-reactive protein level. Her laboratory data revealed an elevated serum immunoglobulin G4 (IgG4) level, hypergammaglobulinemia, and rheumatoid factor positivity in the absence of anticyclic citrullinated peptide antibody. [18F]-Fluorodeoxyglucose positron emission tomography showed significant [18F]-fluorodeoxyglucose uptake in multiple lymph nodes (axillary, hilar, para-aortic, and inguinal). Biopsy of the inguinal lymph node showed expansion of the interfollicular areas by heavily infiltrating plasma cells, consistent with multicentric Castleman disease (MCD). Immunohistochemical analysis revealed a 37.3% IgG4-positive:IgG-positive plasma cell ratio, indicating overlapping IgG4-related disease. However, serological cytokine analysis revealed elevated levels of interleukin-6 (9.3 pg/ml) and vascular endothelial growth factor (VEGF) (1210 pg/ml), which are compatible with MCD. Corticosteroid treatment resolved the serological and imaging abnormalities. IgG4-related disease can mimic MCD, and it is crucial to distinguish between these two diseases. Serum interleukin-6 and VEGF levels may help to discriminate MCD from IgG4-related disease.

Treatment of advanced or recurrent breast cancer with medroxyprogesterone acetate (MPA) shows high response rates and the accessory effects of appetite stimulation, improvement in performance status (PS) and bone marrow protection. In recent years, interleukin-6 (IL-6) has been reported to cause cachexia. In this study, to clarify the significance of IL-6 in advanced or recurrent breast cancer, the relationship between the IL-6 level and clinical findings or effect of MPA was investigated. Sixty-five patients with recurrent or advanced breast cancer participated in a prospective study. The age of patients ranged from 28 to 79 years with an average age of 51.3 years. IL-6 level was investigated in these patients dosed with 800 mg/day of MPA and in 17 postoperative nonrecurrent patients. Serum MPA level was measured by high-performance liquid chromatography and IL-6 level was measured prior to MPA administration, 4 weeks (in 59 cases) and 12 weeks (in 32 patients) after MPA administration by ELISA. Serum IL-6 level was significantly higher in recurrent cases, especially in those with visceral metastasis. Further, in patients for whom MPA therapy was effective, the IL-6 level prior to the treatment was clearly low. The IL-6 level was significantly increased after 4 weeks. However, response to MPA was significantly higher and PS was improved in those cases demonstrating less increased IL-6 levels after 4 weeks. In addition, the effect of MPA was significantly related to a higher serum concentration of MPA-positive ER, and longer disease-free interval, although there was no significant predictive factor for the clinical effect of MPA therapy in multivariate analysis. In conclusion, MPA therapy was effective in cases demonstrating a low IL-6 level and less increased IL-6 levels after 4 weeks. PS was improved in those cases in which the degree of IL-6 increase was suppressed by MPA, and many such cases showed low IL-6 levels prior to MPA therapy. Furthermore, PS was improved even in nonresponders to MPA. Therefore, it is suggested that MPA therapy might be useful in treating recurrent breast cancer, and its benefits might be mediated by IL-6.

BACKGROUND Bone metastases from breast carcinoma are frequently observed as postoperative pathologic conditions; however, in many cases, diagnosis and treatment are difficult. Although most diagnoses of bone metastases are made by plain radiography (X-P) or bone scintigraphy, the use of magnetic resonance imaging (MRI) has enabled detailed imaging of foci, and many more lesions have become detectable. In the current study, the authors evaluated the relation between the diagnosis of bone metastases of breast carcinoma and clinicopathologic factors, especially those of proliferative activity and effects of treatment. METHODS The subjects consisted of 51 breast carcinoma patients (mean age, 51.2 years) with vertebral metastases diagnosed by plain radiography, bone scintigraphy, or MRI. Twenty-eight of the 51 patients were premenopausal and 27 of the 51 had bone metastases only. The patients were classified into the following groups: Group A, 24 patients who showed similar findings in plain radiography, bone scintigraphy, and MRI; Group C, 14 who showed no abnormalities on radiography or bone scintigraphy but whose lesions were diagnosed by MRI only; and Group B, 13 patients with findings intermediate between Groups A and C. The proliferative activity of tumors was evaluated by determining the level of DNA polymerase α. RESULTS Regarding the relation to clinicopathologic factors, a significant number of patients with estrogen receptor (ER) negative tumors who had a high level of DNA polymerase α, short disease free intervals (DFI), and metastases to other organs were included in Group C. Prognoses of patients in Group C were poor. CONCLUSIONS For the diagnosis of breast carcinoma with bone metastasis, different correlations were noted among the various biologic characteristics, such as ER status and proliferative activity. That is, bone scintigraphy sufficiently reflected foci in patients with ER positive tumors or tumors with low proliferation, whereas bone scintigraphy was false-negative in patients with ER negative or highly proliferative tumors, showing that MRI was useful in diagnosing such patients. Therefore, consideration of malignant features, such as proliferative activity and ER status, is believed necessary during the postoperative follow-up of breast carcinoma patients. Cancer 1999;85:1782–8. © 1999 American Cancer Society.

Medroxyprogesterone acetate (MPA) is one of the most commonly prescribed drugs for endocrine therapy of metastatic breast cancer. In this study, the serum MPA concentration was measured by high-performance liquid chromatography (HPLC) and evaluated for its usefulness in predicting the response in 79 cases of advanced or recurrent breast cancers. Overall, 29 patients (37%) achieved an objective response. The response rate correlated significantly with the oestrogen receptor (ER) status (P = 0.03), proliferative activity determined by DNA polymerase alpha (P = 0.04), the disease-free interval (DFI) (P = 0.05) and the serum MPA concentration (P < 0.001). Patients with ER-positive tumours, lower proliferative activity, a longer (DFI) or a higher serum MPA concentration responded more frequently. The mean serum MPA concentration in the responders with ER-positive tumours (P = 0.01) or tumours with a lower proliferative activity (P = 0.008) were significantly lower than in cases with ER-negative tumours or tumours with a higher proliferative activity, respectively. Cases with soft tissue metastases showed responses at significantly lower MPA concentrations (P = 0.003) than those with bone or visceral metastases. Furthermore, there was a dramatic decrease in the MPA concentration when a responder with a high concentration became unresponsive to the therapy. Thus, the serum MPA concentration is a determining factor for the response to treatment.

ObjectiveDrug-resistant (DR) HIV emerges during combined antiretroviral treatment (cART), creating concern about widespread transmission of DR-HIV as cART is expanded in resource-limited countries. The aim of this study was to determine the predominant HIV-1 subtypes and prevalence of transmitted DR mutations among antiretroviral-naïve patients in Iran.DesignTo monitor transmission of DR HIV, a threshold surveillance based on the world health organization (WHO) guidelines was implemented in Iran.MethodsFor this HIVDR threshold surveillance study, blood samples were collected from 50 antiretroviral-naïve HIV-1-infected patients. Antiretroviral-resistant mutations were determined by sequencing HIV-1 protease, reverse transcriptase and integrase regions. The HIV-1 subtype was determined by sequencing the p17 and C2-V5 regions of the gag and env genes, respectively.ResultsPhylogenetic analyses of the sequenced regions revealed that 45 (95.7%) of 47 samples that were successfully obtained were CRF35_AD. The remaining two cases were subtype B (2.1%) and CRF01_AE (2.1%). Consistent results were obtained also from Env and Gag sequences. Regarding prevalence of transmitted DR viruses, two cases were found to harbor reverse transcriptase-inhibitor-resistant mutations (4.3%). In addition, although not in the WHO list for surveillance of transmitted mutations, 13 minor protease-inhibitor-resistant mutations listed in the International AIDS Society-USA panel of drug resistance mutations were found. No DR mutations were detected in the integrase region.ConclusionsOur study clarified that CRF35_AD is the major subtype among HIV-1-infected patients in Iran. According to the WHO categorization method of HIVDR threshold survey, the prevalence of transmitted drug resistant HIV in Iran was estimated as moderate (5-15%).

OBJECTIVE: A new device of staple cutter was developed to evaluate the clinical effect for the treatment of rectal stricture after the double stapling anastomosis. SUMMARY BACKGROUND DATA: The double stapling technique has become an established reconstruction method for patients with low anterior resection. The major complication of anastomotic stricture associated with circular stapling has been reported to be harmful and distressing. Because underlying mechanisms of stricture are not well understood, no prophylactic means have been developed and this results in postoperative dilation still being the only treatment available. Although various dilation methods are used for the treatment of stricture, none is fully satisfactory. METHODS: Low anterior resection was performed in 30 patients with rectal carcinoma using a double stapling technique. First, the incidence of the anastomotic stricture and the clinical factors that contribute to the stricture formation were studied. Second, the clinical effects and advantages of the treatment of coloproctostomic stricture using the newly developed device (staple cutter) were evaluated. RESULTS: Nine (30%) of 30 patients had anastomotic stricture with the symptom of distressing frequent bowel movement. There was no significant relation between the clinical factors and the stricture when compared with that of nonstricture patients. Excellent dilation was performed in all of the nine strictures using the staple cutter, and the symptom of stricture disappeared dramatically in eight patients (89%) within 1 week. The recurrence of stricture occurred in two patients; however, it has not been observed after one further use of this treatment. The staple cutter is safe and easy to use even at the bedside, and except for a conventional anoscope, no special equipment, including fluoroscope, was needed. CONCLUSIONS: From the significant effects and advantages, the procedure using staple cutter is recommended highly for the treatment of circular stapling anastomotic stricture of the rectum.

An 18-year-old female patient with Crohn's disease presented with left lower lobe pneumonia and pleural effusion which were resistant to treatment with antibiotics. Colo-bronchial fistula had not been recognized until she coughed up yellow sputa with feculent odor and developed acute respiratory distress syndrome. This type of fistula is a rare complication of Crohn's disease, but the present case certainly alerts physicians to search for a fistula between the bronchus and gastrointestinal tract when encountering patients with Crohn's disease accompanied by antibiotic-resistant chronic pneumonia.(Internal Medicine 35: 957-960, 1996)

To understand the molecular epidemiology of HIV-1 infection in Iran, we conducted the first study to analyze the genome sequence of Iranian HIV-1 isolates. For this cross-sectional study, we enrolled 10 HIV-1-infected individuals associated with injection drug use from Tehran, Shiraz, and Kermanshah. Near full-length genome sequences obtained from their plasma samples were used for phylogenetic tree and similarity plotting analyses. Among 10 isolates, nine were clearly identified as CRF35_AD and the remaining one as CRF01_AE. Interestingly, five of our Iranian CRF35_AD isolates made two clusters with 10 Afghan CRF35_AD isolates in a phylogenetic tree, indicating epidemiological connections among injection drug users in Iran and Afghanistan. In contrast, our CRF01_AE isolate had no genetic relationship with any other CRF01_AE isolates worldwide, even from Afghanistan. This study provides the first genomic evidence of HIV-1 CRF35_AD predominance and CRF01_AE infection among individuals associated with injection drug use in Iran.

Among 74 patients with esophageal cancer experienced at the department from 1980 to August 1992, 18 patients (24.3%) also had primary cancers of other organs. Clinicopathological features were investigated in these 18 patients. Multiple cancers that were found within one year were regarded as synchronous, and those that were found at an interval longer than one year as heterochronous. There were 11 cases of synchronous and 7 cases of heterochronous multiple cancers, which included one cases of triple or quartet cancer. Of 11 cases of synchronous multiple cancers, 6 cases were found to have an esophageal cancer during preoperative exploration for other organ cancer, which were pharyngolaryngeal cancer for 4 cases, and rectal and lung cancer for each one case. In the meantime, during examination for esophageal cancer one case was found having gastric cancer; and during operation for esophageal cancer each one case was detected to have lung and thyroid cancer, respectively. And, cancers of the colon, liver, tongue, and gingiva were found within one year after the operation. In all heterochronous multiple cancer cases esophageal cancer was preceded by other organ cancer. These were each 2 cases of gastric and larynx cancer, and each one case of lung, colonic, and bile duct cancer, respectively; the last one was detected at 20 months following the esophageal lesion as a triple cancer case. Excision of the esophageal lesion was carried out in 10 synchronous and 4 heterochronous cases. There were 11 mortal patients, and 9 of them died of esophageal cancer, and each one, of lung and bile duct cancer. Four patients have been free of cancer. It can be said that postoperative patients should be followed up by entertaining not only a possibility recurrence but also possible occurrence of malignancy of other organs.

Twenty-eight cases of primary gastric malignant lymphoma treated in this unit over the last 16 years were clinically evaluated. More male patients were affected than female, with a sex ratio of 1.6: 1. Most of the patients were in their 50′s. rising the Naqvi classification there were 10 patients in stage I and 18 patients in stage II, respectively. About 40% of the patients complained of epigastralgia, 30% of the patients were asymptomatic. The macroscopic type according to Sano's classification system was the ulcerative or protruded type in most of the patients. While most patients with superficial type lesions were in stage I, all of the patients with excavated or giant fold type lesions were in stage II. The lesions were located in area M in the largest number of patients, followed by area C, with these two areas accounting for 80% of the total. The histological type determined according to LSG classification was the diffuse type in about 80% of patients, in whom the large cell type accounted for about 70% of the cases. While the stage was I and II in the same number of patients with follicular type lesions, it was II in 2/3 of patients with diffuse type lesions. The 5-year survival rate was 100% in stage I patients compared to only 35% in stage II patients. The mortality rate of stage II patients increased significantly after 7 years, and the prognosis was significantly better in the stage I patients than in the stage II patients (p < 0. 05).

Intramuscular hemangioma growing invasively into the skeletal muscle rarely occurs comparing to hemangiomas arising in the skin or subcutaneous tissue. Since it frequently occurs in childhood and the most common location is on the lower extremities, it is very often discussed in the region of pediatric surgery or orthopedics. Two cases of intramuscular hemangioma arising in the chest wall are reported. The hemangioma was arising in the right latissimus dorsi muscle in a 16-year-old girl and in the left major pectoral muscle in a 28-year-old lady. The significant sign was a palpating mass which was broad-based, elastic soft often with the vascular murmur audible. CT scan was available in making preoperative diagnosis, demonstrating the lesion of heterogenously enhanced in the muscle tissue and widely attached to the ribs. Angiography might also contribute to the diagnosis by revealing the abnormal vessels of mosaic stain. When a symptom is palpating mass in the breast in a female an intramuscular hemangioma should be included in the differential diagnosis. The treatment of choice is surgical excision and complete excision is recommended so as not to recur.

We experienced a rare case of giant cell tumor of bone arising in the 4th rib which was first diagnosed by operation under a preoperative diagnosis of posterior mediastinal tumor. A 35-year-old woman was pointed out having an abnormal shadow on a chest X-ray film at elsewhere and referred to the hospital. Chest X-ray examination on admission revealed a tumor shadow 12.0cm in diameter in the upper lung field to posterior mediastinum region. Based on chest CT and MRI findings the patient was diagnosed as having a posterior mediastinal tumor and operated on in October 1991. It was found that the tumor had no relation to the mediastinum and strongly adhered to the chest wall and lung, a tumor arising in the lung being suspected. Excision of the tumor as well as right upper lobectomy of the lung and partial resection of the 4th lib was carried out. Histopathologically it was giant cell tumor of bone arising in the 4th rib.

To better understand the mechanism of HIV group-specific antigen (Gag) and protease (PR) co-evolution in drug-resistance acquisition, we analyzed a drug-resistance case by both bioinformatics and virological methods. We especially considered the quality of sequence data and analytical accuracy by introducing single-genome sequencing (SGS) and Spidermonkey/Bayesian graphical models (BGM) analysis, respectively. We analyzed 129 HIV-1 Gag–PR linkage sequences obtained from 8 time points, and the resulting sequences were applied to the Spidermonkey co-evolution analysis program, which identified ten mutation pairs as significantly co-evolving. Among these, we focused on associations between Gag-P453L, the P5′ position of the p1/p6 cleavage-site mutation, and PR-D30N/N88D nelfinavir-resistant mutations, and attempted to clarify their virological significance in vitro by constructing recombinant clones. The results showed that P453L Gag has the potential to improve replication capacity and the Gag processing efficiency of viruses with D30N PR /N88D PR but has little effect on nelfinavir susceptibility. Homology modeling analysis suggested that hydrogen bonds between the 30th PR residue and the R452 Gag are disturbed by the D30N PR mutation, but the impaired interaction is compensated by P453L Gag generating new hydrophobic interactions. Furthermore, database analysis indicated that the P453L Gag /D30N PR /N88D PR association was not specific only to our clinical case, but was common among AIDS patients.