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Acute gastroenteritis associated with diarrhea is considered a serious disease in Africa and South Asia. In this study, we examined the trends in the causative pathogens of diarrhea and the corresponding gut microbiota in Ghana using microbiome analysis performed on diarrheic stools via 16S rRNA sequencing. In total, 80 patients with diarrhea and 34 healthy adults as controls, from 2017 to 2018, were enrolled in the study. Among the patients with diarrhea, 39 were norovirus-positive and 18 were rotavirus-positive. The analysis of species richness (Chao1) was lower in patients with diarrhea than that in controls. Beta-diversity analysis revealed significant differences between the two groups. Several diarrhea-related pathogens (e.g., Escherichia-Shigella, Klebsiella and Campylobacter) were detected in patients with diarrhea. Furthermore, co-infection with these pathogens and enteroviruses (e.g., norovirus and rotavirus) was observed in several cases. Levels of both Erysipelotrichaceae and Staphylococcaceae family markedly differed between norovirus-positive and -negative diarrheic stools, and the 10 predicted metabolic pathways, including the carbohydrate metabolism pathway, showed significant differences between rotavirus-positive patients with diarrhea and controls. This comparative study of diarrheal pathogens in Ghana revealed specific trends in the gut microbiota signature associated with diarrhea and that pathogen-dependent dysbiosis occurred in viral gastroenteritis. [ABSTRACT FROM AUTHOR]

Rhesus macaque is one of the most widely used primate model animals for immunological research of infectious diseases including human immunodeficiency virus (HIV) infection. It is well known that major histocompatibility complex (MHC) class I genotypes affect the susceptibility and disease progression to simian immunodeficiency virus (SIV) in rhesus macaques, which is resembling to HIV in humans. It is required to convincingly determine the MHC genotypes in the immunological investigations, that is why several next-generation sequencing (NGS)-based methods have been established. In general, NGS-based genotyping methods using short amplicons are not often applied to MHC because of increasing number of alleles and inevitable ambiguity in allele detection, although there is an advantage of short read sequencing systems that are commonly used today. In this study, we developed a new high-throughput NGS-based genotyping method for MHC class I alleles in rhesus macaques and cynomolgus macaques. By using our method, 95% and 100% of alleles identified by PCR cloning-based method were detected in rhesus macaques and cynomolgus macaques, respectively, which were highly correlated with their expression levels. It was noted that the simulation of new-allele detection step using artificial alleles differing by a few nucleotide sequences from a known allele could be identified with high accuracy and that we could detect a real novel allele from a rhesus macaque sample. These findings supported that our method could be adapted for primate animal models such as macaques to reduce the cost and labor of previous NGS-based MHC genotyping. [ABSTRACT FROM AUTHOR]

Anti-retroviral therapy (ART) can inhibit HIV proliferation but not achieve virus eradication from HIV-infected individuals. Under ART-based HIV control, virus-specific CD8+ T-cell responses are often reduced. Here, we investigated the impact of therapeutic vaccination inducing virus-specific CD8+ T-cell responses under ART on viral control in a macaque AIDS model. Twelve rhesus macaques received ART from week 12 to 32 after simian immunodeficiency virus (SIV) infection. Six of them were vaccinated with Sendai virus vectors expressing SIV Gag and Vif at weeks 26 and 32, and Gag/Vif-specific CD8+ T-cell responses were enhanced and became predominant. All macaques controlled viremia during ART but showed viremia rebound after ART cessation. Analysis of in vitro CD8+ cell ability to suppress replication of autologous lymphocytes-derived SIVs found augmentation of anti-SIV efficacy of CD8+ cells after vaccination. In the vaccinated animals, the anti-SIV efficacy of CD8+ cells at week 34 was correlated positively with Gag-specific CD8+ T-cell frequencies and inversely with rebound viral loads at week 34. These results indicate that Gag-specific CD8+ T-cell induction by therapeutic vaccination can augment anti-virus efficacy of CD8+ cells, which may be insufficient for functional cure but contribute to more stable viral control under ART. [ABSTRACT FROM AUTHOR]

Non-human primates such as rhesus macaque and cynomolgus macaque are important animals for medical research fields and they are classified as Old World monkey, in which genome structure is characterized by gene duplications. In the present study, we investigated polymorphisms in two genes for ULBP2 molecules that are ligands for NKG2D. A total of 15 and 11 ULBP2.1 alleles and 11 and 10 ULBP2.2 alleles were identified in rhesus macaques and cynomolgus macaques, respectively. Nucleotide sequences of exons for extra cellular domain were highly polymorphic and more than 70 % were non-synonymous variations in both ULBP2.1 and ULBP2.2. In addition, phylogenetic analyses revealed that the ULBP2.2 was diverged from a branch of ULBP2.1 along with ULBP2s of higher primates. Moreover, when 3D structural models were constructed for the rhesus ULBP2 molecules, residues at presumed contact sites with NKG2D were polymorphic in ULBP2.1 and ULBP2.2 in the rhesus macaque and cynomolgus macaque, respectively. These observations suggest that amino acid replacements at the interaction sites with NKG2D might shape a specific nature of ULBP2 molecules in the Old World monkeys. [ABSTRACT FROM AUTHOR]

T-cell immunoglobulin domain and mucin domain containing protein 1 (TIM1), also known as a cellular receptor for hepatitis A virus (HAVCR1) or a molecule induced by ischemic injury in the kidney (KIM1), is involved in the regulation of immune responses. We investigated a natural selection history of TIM1 by comparative sequencing analysis in 24 different primates. It was found that TIM1 had become a pseudogene in multiple lineages of the New World monkey. We also investigated T cell lines originated from four different New World monkey species and confirmed that TIM1 was not expressed at the mRNA level. On the other hand, there were ten amino acid sites in the Ig domain of TIM1 in the other primates, which were suggested to be under positive natural selection. In addition, mucin domain of TIM1 was highly polymorphic in the Old World monkeys, which might be under balanced selection. These data suggested that TIM1 underwent a lineage-specific evolutionary pathway in the primates. [ABSTRACT FROM AUTHOR]

Cynomolgus macaques are widely used as a primate model for human diseases associated with an immunological process. Because there are individual differences in immune responsiveness, which are controlled by the polymorphic nature of the major histocompatibility (MHC) locus, it is important to reveal the diversity of MHC in the model animal. In this study, we analyzed 26 cynomolgus macaques from five families for MHC class I genes. We identified 32 Mafa-A, 46 Mafa-B, 6 Mafa-I, and 3 Mafa-AG alleles in which 14, 20, 3, and 3 alleles were novel. There were 23 MHC class I haplotypes and each haplotype was composed of one to three Mafa-A alleles and one to five Mafa-B alleles. Family studies revealed that there were two haplotypes which contained two Mafa-A1 alleles. These observations demonstrated further the complexity of MHC class I locus in the Old World monkey. [ABSTRACT FROM AUTHOR]

Natural-killer group 2 member D (NKG2D) is an activating receptor that plays an important role in the immune response mediated by NK cells, γδ T cells, and CD8 T cells. In humans, MHC class I chain-related genes and UL-16 binding protein (ULBP)/retinoic acid early transcript 1 (REAT1) gene family encode ligands for NKG2D. The rhesus and crab-eating macaques, which belong to the Old World monkeys, are widely used as non-human primate models in medical researches on the immunological process. In the present study, we investigated the polymorphisms of ULBP4/ RAET1E, a member of the ULBP/RAET1 family, and found 25 and 14 alleles from the rhesus and crab-eating macaques, respectively, of which diversities were far more extended than in humans. A phylogenetic study suggested that the allelic diversification of ULBP4/RAET1E predated the divergence of rhesus and crab-eating macaques. [ABSTRACT FROM AUTHOR]

Rhesus macaques ( Macaca mulatta) are widely used in developing a strategy for vaccination against human immunodeficiency virus by using simian immunodeficiency virus infection as a model system. Because the genome diversity of major histocompatibility complex (MHC) is well known to control the immune responsiveness to foreign antigens, MHC loci in Indian- and Chinese-origin macaques used in the experiments have been characterized, and it was revealed that the diversity of MHC in macaques was larger than the human MHC. To further characterize the diversity of Mamu-A and Mamu-B loci, we investigated a total of 73 different sequences of Mamu-A, 83 sequences of Mamu-B, and 15 sequences of Mamu-I cDNAs isolated from Burmese-origin macaques. It was found that there were one to five expressing genes in each locus. Among the Mamu-A, Mamu-B, and Mamu-I sequences, 44 (60.2%), 45 (54.2%), and 8 (53.3%), respectively, were novel, and most of the other known alleles were identical to those reported from Chinese- or Indian-origin macaques, demonstrating a genetic mixture between the geographically distinct populations of present day China and India. In addition, it was found that a Mamu haplotype contained at least two highly transcribed Mamu-A genes, because multiple Mamu-A1 cDNAs were obtained from one haplotype. These findings further revealed the diversity and complexity of MHC locus in the rhesus macaques. [ABSTRACT FROM AUTHOR]