Phylogenetic associations of human and simian T-cell leukemia/lymphotropic virus type I strains: evidence for interspecies transmission.

Homologous env sequences from 17 human T-leukemia/lymphotropic virus type I (HTLV-I) strains from throughout the world and from 25 simian T-leukemia/lymphotropic virus type I (STLV-I) strains from 12 simian species in Asia and Africa were analyzed in a phylogenetic context as an approach to resolving the natural history of these related retroviruses. STLV-I exhibited greater overall sequence variation between strains (1 to 18% compared with 0 to 9% for HTLV-I), supporting the simian origin of the modern viruses in all species. Three HTLV-I phylogenetic clusters or clades (cosmopolitan, Zaire, and Melanesia) were resolved with phenetic, parsimony, and likelihood analytical procedures. Seven phylogenetic clusters of STLV-I were resolved with the most primitive (deeply rooted) divergence involving several STLV-I strains from Asian primate species. Combined analysis of HTLV-I and STLV-I revealed that neither STLV-I clusters nor HTLV-I clusters recapitulated host species specificity; rather, multiple clades from the same species were closer to clades from other species than to each other. We interpret these evolutionary associations as support for the occurrence of multiple discrete interspecies transmissions of ancestral viruses between primate species (including human) that led to recognizable phylogenetic clades that persist in modern species. Geographic concordance of divergent host species that harbor closely related viruses reinforces that physical feasibility for hypothesized interspecies virus transmission in the past and in the present.     

Identical consensus sequence and conserved genomic polymorphism of hepatitis E virus during controlled interspecies transmission

High-throughput sequencing of bile and feces from two pigs experimentally infected with human hepatitis E virus (HEV) of genotype 3f revealed the same full-length consensus sequence as in the human sample. Twenty-nine percent of polymorphic sites found in HEV from the human sample were conserved throughout the infection of the heterologous host. The interspecies transmission of HEV quasispecies is the result of a genomic negative-selection pressure on random mutations which can be deleterious to the viral population. HEV intrahost nucleotide diversity was found to be in the lower range of other human RNA viruses but correlated with values found for zoonotic viruses. HEV transmission between humans and pigs does not seem to be modulated by host-specific mutations, suggesting that adaptation is mainly regulated by ecological drivers.     

Adaptation and selection of prion protein strain conformations following interspecies transmission of transmissible mink encephalopathy

Interspecies transmission of the transmissible spongiform encephalopathies (TSEs), or prion diseases, can result in the adaptation and selection of TSE strains with an expanded host range and increased virulence such as in the case of bovine spongiform encephalopathy and variant Creutzfeldt-Jakob disease. To investigate TSE strain adaptation, we serially passaged a biological clone of transmissible mink encephalopathy (TME) into Syrian golden hamsters and examined the selection of distinct strain phenotypes and conformations of the disease-specific isoform of the prion protein (PrP(Sc)). The long-incubation-period drowsy (DY) TME strain was the predominate strain, based on the presence of its strain-specific PrP(Sc) following interspecies passage. Additional serial passages in hamsters resulted in the selection of the hyper (HY) TME PrP(Sc) strain-dependent conformation and its short incubation period phenotype unless the passages were performed with a low-dose inoculum (e.g., 10(-5) dilution), in which case the DY TME clinical phenotype continued to predominate. For both TME strains, the PrP(Sc) strain pattern preceded stabilization of the TME strain phenotype. These findings demonstrate that interspecies transmission of a single cloned TSE strain resulted in adaptation of at least two strain-associated PrP(Sc) conformations that underwent selection until one type of PrP(Sc) conformation and strain phenotype became predominant. To examine TME strain selection in the absence of host adaptation, hamsters were coinfected with hamster-adapted HY and DY TME. DY TME was able to interfere with the selection of the short-incubation HY TME phenotype. Coinfection could result in the DY TME phenotype and PrP(Sc) conformation on first passage, but on subsequent passages, the disease pattern converted to HY TME. These findings indicate that during TSE strain adaptation, there is selection of a strain-specific PrP(Sc) conformation that can determine the TSE strain phenotype.     

B型流感病毒B/Guangxi-Jiangzhou/1352/2018毒株的遗传进化及其对小鼠的致病性分析北大核心CSCD

B型流感病毒(influenza B virus,IBV)比A型流感病毒(influenza A virus,IAV)更易引发并发症,在一定季节内造成的疾病负担甚至超过IAV,但目前人们对IBV的关注较少。为了分析IBV临床毒株B/Guangxi-Jiangzhou/1352/2018的遗传进化特点,本研究构建了系统进化树,并以世界卫生组织推荐的疫苗株为参考,对其血凝素(hemagglutinin,HA)和神经氨酸酶(neuraminidase,NA)进行了氨基酸序列同源性及突变位点分析。分析结果发现B/Guangxi-Jiangzhou/1352/2018毒株无谱系间重配现象,与同年疫苗株B/Colorado/06/2017匹配性较差。另外,测定了B/Guangxi-Jiangzhou/1352/2018毒株感染小鼠的半数致死量(median lethal dose,LD_(50))及其对小鼠的致病性。结果表明,B/Guangxi-Jiangzhou/1352/2018毒株感染小鼠的LD_(50)为10^(5.9) TCID_(50)(median tissue culture infective dose),小鼠肺脏中病毒滴度在感染后1 d达到高峰,炎性细胞因子的mRNA水平在感染后12 h达到高峰,且感染后肺脏中的肺泡损伤严重,有大量炎性细胞浸润。本研究证明了IBV临床毒株B/Guangxi-Jiangzhou/1352/2018可以感染小鼠并诱发典型的肺脏炎症,为研究IBV致病及传播机制奠定了基础,为评价新型流感疫苗、抗病毒和抗炎症药物提供了理想的动物模型。     

Cloning, sequencing and distribution of the Salmonella typhimurlum LT2 siaiidase gene, nanH, provides evidence for interspecies gene transfer

The Salmonella typhimurium LT2 sialidase (neuraminidase, EC 3.2.1.18) structural gene, nanH, has been cloned and sialidase overproduced from multicopy plasmids in Escherichia coli. Sialidase expression was regulated positively by cAMP. In contrast, certain Tn1000 insertions located upstream of nanH coding sequences reduced sialidase activity. A nanH chromosomal insertion mutation constructed by marker exchange demonstrated a single sialidase gene copy in S. typhimurium LT2. The complete nucleotide sequence of nanH, encoding a 41,300 dalton polypeptide, was determined and the derived primary structure was similar to sialidases from Clostridium perfringens, Clostridium sordellii, Bacteroides fragilis, and Trypanosoma cruzi. Comparative sequence analysis, including codon usage and secondary structure predictions, indicated that the S. typhimurium and clostridial sialidases are homologous, strongly suggestive of an interspecies gene transfer event. At least two primary sequence motifs of the bacterial enzymes were detected in influenza A virus sialidases. The predicted secondary structure of the bacterial enzymes was strikingly similar to viral sialidase. From the population distribution of nanH detected within a collection of salmonellae, it was apparent that S. typhimurium obtained its nanH copy most recently from Salmonella arizonae. S. typhimurium LT2 is thus a genetic mosaic that differs from other strains of even the same serotype by nanH plus potentially additional characters linked to nanH. These results have relevance to the evolution and function of sialidases in pathogenic microbes, and to the origin of the sialic acids.     

Genetic analysis of testis weight and fertility in an interspecies hybrid congenic strain for Chromosome X

A hybrid congenic strain, C57BL/6J.SPRET-Hprt ^a , carrying 17 map units of Chromosome (Chr) X from Mus spretus on a background of C57BL/6J, has the novel phenotype of low fertility associated with small testis weight. In histological cross-section, many of the tubules in the testes of these congenic mice are empty except for Sertoli cells, while the other tubules appear to be normal. The gene, interspecific hybrid testis weight 1 (Ihtw1) causing this phenotype, has been fine mapped by using the strategy of generating subcongenic strains from recombinants within the congenic region. Genetic and phenotypic analysis of the subcongenic strains has defined a critical region of 1.8 map units for Ihtw1. This region of the genetic map is orthologous to the region on human Chr X containing the gene for the Borjeson-Forssman-Lehman syndrome, an inherited disease in which males show microorchidism. Received: 12 June 2000 / Accepted: 8 September 2000     

Isolation and molecular characterization of a serotype 9 human rotavirus strain.

A human rotavirus strain, designated AU32, that belongs to serotype 9 was isolated and was compared by RNA-RNA hybridization with recently established two serotype 9 strains (WI61 and F45) as well as other prototype human strains. These three strains exhibited a very high degree of homology with one another and shared a high degree of homology with strains belonging to the Wa genogroup but not with strains belonging to either the DS-1 or AU-1 genogroup. These results suggest that genetic constellation of the serotype 9 strains is similar to that of the commonest human rotavirus despite the recent recognition of this serotype.     

Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish lineage

A whole-genome duplication in the ray-finned fish lineage has been supported by the analyses of the genome sequence of the Japanese pufferfish, Fugu rubripes. Recently, genome sequence of a second teleost fish, the freshwater pufferfish, Tetraodon nigroviridis, was completed. Comparisons of long-range synteny between the Tetraodon and human genomes provided additional evidence for the whole-genome duplication in the ray-finned fish lineage. In the present study, we conducted phylogenetic analysis of the Tetraodon and human proteins to identify ray-finned fish lineage-specific (‘fish-specific’) duplicate genes in the Tetraodon genome. Our analyses provide evidence for 1087 well defined fish-specific duplicate genes in Tetraodon. We also analyzed the Fugu proteome that was predicted in the recent Fugu genome assembly, and identified 346 duplicate genes in addition to the 425 duplicates previously identified. We estimated the ages of duplicate genes using the molecular clock. The ages of duplicate genes in the two pufferfishes independently support a large-scale gene duplication around 380–400 Myr ago. In addition, a burst of recent gene duplications was evident in the Tetraodon lineage. These findings provide further evidence for a whole-genome duplication early in the evolution of ray-finned fishes, and suggest that independent gene duplications have occurred recently in the Tetraodon lineage.     

Comparative genome analysis provides shreds of molecular evidence for reclassification of Leuconostoc mesenteroides MTCC 10508 as a strain of Leu. suionicum

This study presents the whole-genome comparative analysis of a Leuconostoc sp. strain, previously documented as Leu. mesenteroides MTCC 10508. The ANI, dDDH, dot plot, and MAUVE analyses suggested its reclassification as a strain of Leu. suionicum. Functional annotation identified a total of 1971 genes, out of which, 265 genes were mapped to CAZymes, evincing its carbohydrate transforming capability. The genome comparison with 59 Leu. mesenteroides and Leu. suionicum strains generated the core and pan-genome profiles, divulging the unique genes in Leuconostoc sp. MTCC 10508. For the first time, this study reports the genes encoding alpha-xylosidase and copper oxidase in a strain of Leu. suionicum. The genetic information for any possible allergenic molecule could not be detected in the genome, advocating the safety of the strain. The present investigation provides the genomic evidence for reclassification of the Leuconostoc sp. strain and also promulgates the molecular insights into its metabolic potential.     

Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains

Group A rotavirus classification is currently based on the molecular properties of the two outer layer proteins, VP7 and VP4, and the middle layer protein, VP6. As reassortment of all the 11 rotavirus gene segments plays a key role in generating rotavirus diversity in nature, a classification system that is based on all the rotavirus gene segments is desirable for determining which genes influence rotavirus host range restriction, replication, and virulence, as well as for studying rotavirus epidemiology and evolution. Toward establishing such a classification system, gene sequences encoding VP1 to VP3, VP6, and NSP1 to NSP5 were determined for human and animal rotavirus strains belonging to different G and P genotypes in addition to those available in databases, and they were used to define phylogenetic relationships among all rotavirus genes. Based on these phylogenetic analyses, appropriate identity cutoff values were determined for each gene. For the VP4 gene, a nucleotide identity cutoff value of 80% completely correlated with the 27 established P genotypes. For the VP7 gene, a nucleotide identity cutoff value of 80% largely coincided with the established G genotypes but identified four additional distinct genotypes comprised of murine or avian rotavirus strains. Phylogenetic analyses of the VP1 to VP3, VP6, and NSP1 to NSP5 genes showed the existence of 4, 5, 6, 11, 14, 5, 7, 11, and 6 genotypes, respectively, based on nucleotide identity cutoff values of 83%, 84%, 81%, 85%, 79%, 85%, 85%, 85%, and 91%, respectively. In accordance with these data, a revised nomenclature of rotavirus strains is proposed. The novel classification system allows the identification of (i) distinct genotypes, which probably followed separate evolutionary paths; (ii) interspecies transmissions and a plethora of reassortment events; and (iii) certain gene constellations that revealed (a) a common origin between human Wa-like rotavirus strains and porcine rotavirus strains and (b) a common origin between human DS-1-like rotavirus strains and bovine rotaviruses. These close evolutionary links between human and animal rotaviruses emphasize the need for close simultaneous monitoring of rotaviruses in animals and humans.     

Identification of non-functional human VNO receptor genes provides evidence for vestigiality of the human VNO.

In mammals, the vomeronasal organ (VNO) contains chemosensory receptor cells that bind to pheromones and induce a variety of social and reproductive behaviors. It has been traditionally assumed that the human VNO (Jacobson's organ) is a vestigial structure, although recent studies have shown minor evidence for a structurally intact and possibly functional VNO. The presence and function of the human VNO remains controversial, however, as pheromones and VNO receptors have not been well characterized. In this study we screened a human Bacterial Artificial Chromosome (BAC) library with multiple primer sets designed from human cDNA sequences homologous to mouse VNO receptor genes. Utilizing these BAC sequences in addition to mouse VNO receptor sequences, we screened the High Throughput Genome Sequence (HTGS) database to find additional human putative VNO receptor genes. We report the identification of 56 BACs carrying 34 distinct putative VNO receptor gene sequences, all of which appear to be pseudogenes. Sequence analysis indicates substantial homology to mouse V1R and V2R VNO receptor families. Furthermore, chromosomal localization via FISH analysis and RH mapping reveal that the majority of the BACs are localized to telomeric and centromeric chromosomal localizations and may have arisen through duplication events. These data yield insight into the present state of pheromonal olfaction in humans and into the evolutionary history of human VNO receptors.     

Parental origin of triploidy in human fetuses: evidence for genomic imprinting

Two distinct phenotypes of triploid fetuses have been previously described and a correlation with parental origin of the triploidy has been suggested. We have studied the parental origin of the extra haploid set of chromosomes in nine triploid fetuses using analysis of DNA polymorphisms at a variety of loci. Maternal origin of the triploidy (digyny) was demonstrated in six fetuses with type II phenotype, paternal origin (diandry) in two cases with type I phenotype, and nonpaternity in one case. The predominance of digynic triploids in our study contrasts with the results reported in previous studies in which, through analysis of cytogenetic polymorphisms, paternal origin was found to account for the majority of triploid conceptuses. This difference may be accounted for by a combination of factors — the different methods of parental assignment used and analysis of a different subset of triploid conceptuses. The correlation between the observed phenotypes and the parental origin of triploidy may represent another example of imprinting in human development.     

Natural recombination event within the capsid genomic region leading to a chimeric strain of human enterovirus B

Recombination between two strains is a known phenomenon for enteroviruses replicating within a single cell. We describe a recombinant strain recovered from human stools, typed as coxsackievirus B4 (CV-B4) and CV-B3 after partial sequencing of the VP1 and VP2 coding regions, respectively. The strain was neutralized by a polyclonal CV-B3-specific antiserum but not by a CV-B4-specific antiserum. The nucleotide sequence analysis of the whole structural genomic region showed the occurrence of a recombination event at position 1950 within the VP3 capsid gene, in a region coding for the 2b antigenic site previously described for CV-B3. This observation evidences for the first time the occurrence of an interserotypic recombination within the VP2-VP3-VP1 capsid region between two nonpoliovirus enterovirus strains. The neutralization pattern suggests that the major antigenic site is located within the VP2 protein.     

Infectivity and antigenicity reduction rates of human rotavirus strain Wa in fresh waters

The rates of inactivation of human rotavirus type 2 (strain Wa) (HRV-Wa) and poliovirus type 1 (strain CHAT) were compared in polluted waters (creek water and secondary effluent before chlorination) and nonpolluted waters (lake water, groundwater, and chlorinated tap water). Viral infectivity titers were determined by plaque assays, while HRV-Wa antigenicity also was monitored by an enzyme-linked immunosorbent assay. Both viruses persisted longest in lake water and shortest in tap water. The actual inactivation times (i.e., times required for two-log10 reductions of initial viral titers) for the two viruses were significantly different in all waters except tap water. With the exception of the groundwater and secondary effluent results, the HRV-Wa inactivation times in the fresh waters tested were significantly different. Owing perhaps to aggregation, HRV-Wa appeared less susceptible to the effects of chlorine than previously reported for this virus and for the simian rotavirus SA11. HRV-Wa displayed prolonged survival in lake water and groundwater exceeding that previously reported for the SA11 virus. The HRV-Wa infectivity reduction rate (ki) was significantly correlated with the water pH (i.e., as pH increased, ki increased). The water pH may have influenced viral aggregation and thereby HRV-Wa susceptibility to other virucidal factors in the water. Enzyme-linked immunosorbent assay results showed similar inactivation patterns with the most significant reduction in HRV-Wa antigenicity occurring in polluted waters and tap water. In all waters, particularly tap water, infectivity declined at a faster rate than antigenicity. It is proposed that HRV-Wa can be used as a model for future studies of rotaviral persistence in the aquatic environment.     

Comparative genomic analysis of human and chimpanzee proteases

Proteolytic enzymes are implicated in multiple physiological and pathological processes. The availability of the sequence of the chimpanzee genome has allowed us to determine that the chimpanzee degradome-the repertoire of protease genes from this organism-is composed of at least 559 protease and protease-like genes and is virtually identical to that of human, containing 561 genes. Despite the high degree of conservation between both genomes, we have identified important differences that vary from deletion of whole genes to small insertion/deletion events or single nucleotide changes that lead to the specific gene inactivation in one species, mostly affecting immune system genes. For example, the genes encoding PRSS33/EOS, a macrophage serine protease conserved in most mammals, and GGTLA1 are absent in chimpanzee, while the gene for metalloprotease MMP23A, located in chromosome 1p36, has been specifically duplicated in the human genome together with its neighbor gene CDC2L1. Other differences arise from single nucleotide changes in protease genes, such as NAPSB and CASP12, resulting in the presence of functional genes in chimpanzee and pseudogenes in human. Finally, we have confirmed that the Trypanosoma lytic factor HPR is inactive in chimpanzee, likely contributing to the susceptibility of chimpanzees to T. brucei infection. This study provides the first analysis of the chimpanzee degradome and might contribute to the understanding of the molecular bases underlying variations in host defense mechanisms between human and chimpanzee.     

Preferential retention of paternal alleles in human retinoblastoma: evidence for genomic imprinting

The origins of the initial mutations in sporadic retinoblastoma were explored using polymorphic markers from chromosome 13q. The paternal chromosome was maintained in 3 of 3 informative bilateral tumors which had undergone reduction to homozygosity for regions of this chromosome. The paternal chromosome was maintained in 7 of 8 informative unilateral tumors which likewise demonstrated a reduction of homozygosity. These data are in contrast to previously published studies of chromosome retention in unilateral retinoblastoma [Dryja, T. P., Mukai, S., Petersen, R., Rapaport, J. M., Walton, D., and Yandel, D. W. Nature (Lond.), 339: 556-558, 1989; Zhu, Z., Dunn, J. M., Phillips, R. A., Goddard, A. D., Paton, K. E., Becker, A., and Gallie, B. L. Nature (Lond.), 340: 312-313, 1989] and provide the first evidence that genomic imprinting may play a role in this disease.     

Species and interspecies radioimmunoassays for rat type C virus p30: interviral comparisons and assay of human tumor extracts.

The major internal protein, p30, of rat type C virus (RaLV) was purified and utilized to establish intra- and interspecies radioimmunoassays. Three rat viruses were compared in homologous and heterologous intraspecies assays with no evidence of type specificity. The only heterologous viruses to give inhibition in these species assays were the feline (FeLV) and hamster (HaLV) type C viruses; these reactions were incomplete and required high virus concentrations. An interspecies assay using a goat antiserum prepared after sequentially immunizing with FeLV, RD 114, and woolly monkey virus p30's and labeled RaLV p30 was inhibited by all mammalian type C viruses, although preferentially by RaLV, FeLV, and HaLV. Thus, as in a previously reported assay developed with HaLV p30, rat, hamster, and cat p30's seem more closely related to each other than to mouse type C virus p30. High levels of specific antigen were found in all cell lines producing rat virus, whereas embryonic tissues from several rat strains and cell lines considered virus-free based on other tests were negative for p30. Rats bearing tumors containing Moloney murine sarcoma virus (RaLV) did not contain free circulating antibody to RaLV p30. Fifty-one human tumor extracts (including two tumor cell lines) were tested for activity in the RaLV species and 47 in the interspecies assays after Sephadex gel filtration and pooling of material in the 15,000- to 40,000-molecular-weight range. At a sensitivity level of 7 ng/ml (0.7 ng/assay) in the interspecies assay, all human tissues, with one exception, were negative. The one positive result is considered nonspecific based on proteolysis of the labeled antigen. Input tissue protein of the purified tumor extracts averaged 1.9 mg/ml with a range of less than 0.025 to 22 mg/ml. Tissues from NIH Swiss mice processed in the same manner were positive in the interspecies assay but negative in the intraspecies RaLV assay.     

Infectivity and antigenicity reduction rates of human rotavirus strain Wa in fresh waters.

The rates of inactivation of human rotavirus type 2 (strain Wa) (HRV-Wa) and poliovirus type 1 (strain CHAT) were compared in polluted waters (creek water and secondary effluent before chlorination) and nonpolluted waters (lake water, groundwater, and chlorinated tap water). Viral infectivity titers were determined by plaque assays, while HRV-Wa antigenicity also was monitored by an enzyme-linked immunosorbent assay. Both viruses persisted longest in lake water and shortest in tap water. The actual inactivation times (i.e., times required for two-log10 reductions of initial viral titers) for the two viruses were significantly different in all waters except tap water. With the exception of the groundwater and secondary effluent results, the HRV-Wa inactivation times in the fresh waters tested were significantly different. Owing perhaps to aggregation, HRV-Wa appeared less susceptible to the effects of chlorine than previously reported for this virus and for the simian rotavirus SA11. HRV-Wa displayed prolonged survival in lake water and groundwater exceeding that previously reported for the SA11 virus. The HRV-Wa infectivity reduction rate (ki) was significantly correlated with the water pH (i.e., as pH increased, ki increased). The water pH may have influenced viral aggregation and thereby HRV-Wa susceptibility to other virucidal factors in the water. Enzyme-linked immunosorbent assay results showed similar inactivation patterns with the most significant reduction in HRV-Wa antigenicity occurring in polluted waters and tap water. In all waters, particularly tap water, infectivity declined at a faster rate than antigenicity. It is proposed that HRV-Wa can be used as a model for future studies of rotaviral persistence in the aquatic environment.     

Integrative analysis provides multi‐omics evidence for the pathogenesis of placenta percreta

Pernicious placenta previa with placenta percreta (PP) is a catastrophic condition during pregnancy. However, the underlying pathogenesis remains unclear. In the present study, the placental tissues of normal cases and PP tissues of pernicious placenta previa cases were collected to determine the expression profile of protein‐coding genes, miRNAs, and lncRNAs through sequencing. Weighted gene co‐expression network analysis (WGCNA), accompanied by miRNA target prediction and correlation analysis, were employed to select potential hub protein‐coding genes and lncRNAs. The expression levels of selected protein‐coding genes, Wnt5A and MAPK13, were determined by quantitative PCR and immunohistochemical staining, and lncRNA PTCHD1‐AS and PAPPA‐AS1 expression levels were determined by quantitative PCR and fluorescence in situ hybridization. The results indicated that 790 protein‐coding genes, 382 miRNAs, and 541 lncRNAs were dysregulated in PP tissues, compared with normal tissues. WGCNA identified coding genes in the module (ME) black and ME turquoise modules that may be involved in the pathogenesis of PP. The selected potential hub protein‐coding genes, Wnt5A and MAPK13, were down‐regulated in PP tissues, and their expression levels were positively correlated with the expression levels of PTCHD1‐AS and PAPPA‐AS1. Further analysis demonstrated that PTCHD1‐AS and PAPPA‐AS1 regulated Wnt5A and MAPK13 expression by interacting with specific miRNAs. Collectively, our results provided multi‐omics data to better understand the pathogenesis of PP and help identify predictive biomarkers and therapeutic targets for PP.