Genomic analysis of two novel human enterovirus C genotypes found in respiratory samples from Peru

We report the discovery of two enteroviruses detected in nasopharyngeal samples obtained from subjects with respiratory disease in Peru. Phylogenetic analysis indicated that both viruses belong to a clade within the species Human enterovirus C, which includes the recently characterized human enteroviruses 109 and 104. Members of this clade have undergone significant genomic rearrangement, as indicated by deletions in the hypervariable region of the 5′ UTR and the VP1 protein, as well as recombination within the non-structural genes. Our findings and review of published sequences suggests that several novel human enterovirus C serotypes are currently circulating worldwide.

Download Full-text

Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C

Journal of General Virology ◽

10.1099/vir.0.053462-0 ◽

2013 ◽

Vol 94 (9) ◽

pp. 1995-2004 ◽

Cited By ~ 19

Author(s):

Rafal Tokarz ◽

Saddef Haq ◽

Stephen Sameroff ◽

Stephen R. C. Howie ◽

W. Ian Lipkin

Keyword(s):

Phylogenetic Analysis ◽

Sequence Analysis ◽

Genomic Analysis ◽

The Other ◽

High Rate ◽

Structural Genes ◽

Genome Sequences ◽

Capsid Region ◽

High Degree ◽

Degree Of Similarity

Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease.

Download Full-text

Worldwide emergence of multiple clades of enterovirus 68

Journal of General Virology ◽

10.1099/vir.0.043935-0 ◽

2012 ◽

Vol 93 (9) ◽

pp. 1952-1958 ◽

Cited By ~ 153

Author(s):

Rafal Tokarz ◽

Cadhla Firth ◽

Shabir A. Madhi ◽

Stephen R. C. Howie ◽

Winfred Wu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

North America ◽

Respiratory Disease ◽

Respiratory Illness ◽

Genetic Differences ◽

Human Enterovirus ◽

The Past ◽

The Usa

Human enterovirus 68 (EV-D68) is a historically rarely reported virus linked with respiratory disease. In the past 3 years, a large increase in respiratory disease associated with EV-D68 has been reported, with documented outbreaks in North America, Europe and Asia. In several outbreaks, genetic differences were identified among the circulating strains, indicating the presence of multiple clades. In this report, we analyse archived and novel EV-D68 strains from Africa and the USA, obtained from patients with respiratory illness. Phylogenetic analysis of all EV-D68 sequences indicates that, over the past two decades, multiple clades of the virus have emerged and spread rapidly worldwide. All clades appear to be currently circulating and contributing to respiratory disease.

Download Full-text

Genomic Analysis of Avian Infectious Bronchitis Viruses Recently Isolated in South Korea Reveals Multiple Introductions of GI-19 Lineage (QX Genotype)

Viruses ◽

10.3390/v13061045 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1045

Author(s):

Hyuk-Chae Lee ◽

Sol Jeong ◽

Andrew Y. Cho ◽

Kyu-Jik Kim ◽

Jun-Young Kim ◽

...

Keyword(s):

Phylogenetic Analysis ◽

South Korea ◽

Infectious Bronchitis Virus ◽

Economic Burden ◽

Genomic Analysis ◽

Multiple Introductions ◽

Infectious Bronchitis ◽

South Korean ◽

Phylogeographic Analysis ◽

The Past

Infectious bronchitis virus (IBV) was first identified in the 1930s and it imposes a major economic burden on the poultry industry. In particular, GI-19 lineage has spread globally and has evolved constantly since it was first detected in China. In this study, we analyzed S1 gene sequences from 60 IBVs isolated in South Korea. Two IBV lineages, GI-15 and GI-19, were identified in South Korea. Phylogenetic analysis suggested that there were six distinct subgroups (KM91-like, K40/09-like, and QX-like I to IV) of the South Korean GI-19 IBVs. Among them, QX-type III and IV subgroups, which are phylogenetically different from those reported in South Korea in the past, accounted for more than half of the total. Moreover, the phylogeographic analysis of the QX-like subgroups indicated at least four distinct introductions of GI-19 IBVs into South Korea during 2001–2020. The efficacy of commercialized vaccines against the recently introduced QX-like subgroups should be verified, and continuous international surveillance efforts and quarantine procedures should be enhanced to prevent the incursion of viruses.

Download Full-text

Isolation, identification, and phylogenetic analysis of subgroup III strain of bovine respiratory syncytial virus contributed to outbreak of acute respiratory disease among cattle in Northeast China

Virulence ◽

10.1080/21505594.2021.1872178 ◽

2021 ◽

Vol 12 (1) ◽

pp. 404-414

Author(s):

Shuo Jia ◽

Xin Yao ◽

Yaqi Yang ◽

Chao Niu ◽

Yi Zhao ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Respiratory Syncytial Virus ◽

Respiratory Disease ◽

Northeast China ◽

Bovine Respiratory Syncytial Virus ◽

Acute Respiratory Disease ◽

Syncytial Virus

Download Full-text

Genomic Analysis of the Glutathione S-Transferase Family in Pear (Pyrus communis) and Functional Identification of PcGST57 in Anthocyanin Accumulation

International Journal of Molecular Sciences ◽

10.3390/ijms23020746 ◽

2022 ◽

Vol 23 (2) ◽

pp. 746

Author(s):

Bo Li ◽

Xiangzhan Zhang ◽

Ruiwei Duan ◽

Chunhong Han ◽

Jian Yang ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Developmental Stages ◽

Genomic Analysis ◽

Pyrus Communis ◽

Anthocyanin Content ◽

Anthocyanin Accumulation ◽

Rna Seq ◽

Virus Induced Gene Silencing ◽

Functional Identification ◽

Glutathione S Transferase

Anthocyanin accumulation in vacuoles results in red coloration in pear peels. Glutathione S-transferase (GST) proteins have emerged as important regulators of anthocyanin accumulation. Here, a total of 57 PcGST genes were identified in the European pear ‘Bartlett’ (Pyrus communis) through comprehensive genomic analysis. Phylogenetic analysis showed that PcGST genes were divided into 10 subfamilies. The gene structure, chromosomal localization, collinearity relationship, cis-elements in the promoter region, and conserved motifs of PcGST genes were analyzed. Further research indicated that glutamic acid (Glu) can significantly improve anthocyanin accumulation in pear peels. RNA sequencing (RNA-seq) analysis showed that Glu induced the expression of most PcGST genes, among which PcGST57 was most significantly induced. Further phylogenetic analysis indicated that PcGST57 was closely related to GST genes identified in other species, which were involved in anthocyanin accumulation. Transcript analysis indicated that PcGST57 was expressed in various tissues, other than flesh, and associated with peel coloration at different developmental stages. Silencing of PcGST57 by virus-induced gene silencing (VIGS) inhibited the expression of PcGST57 and reduced the anthocyanin content in pear fruit. In contrast, overexpression of PcGST57 improved anthocyanin accumulation. Collectively, our results demonstrated that PcGST57 was involved in anthocyanin accumulation in pear and provided candidate genes for red pear breeding.

Download Full-text

Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes

10.1101/374165 ◽

2018 ◽

Cited By ~ 5

Author(s):

Mingwei Cai ◽

Yang Liu ◽

Zhichao Zhou ◽

Yuchun Yang ◽

Jie Pan ◽

...

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Genomic Analysis ◽

Phylogenetic Position ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Group D ◽

Origin Of Eukaryotes

AbstractAsgard is a newly proposed archaeal superphylum. Phylogenetic position of Asgard archaea and its relationships to the origin of eukaryotes is attracting increasingly research interest. However, in-depth knowledge of their diversity, distribution, and activity of Asgard archaea remains limited. Here, we used phylogenetic analysis to cluster the publicly available Asgard archaeal 16S rRNA gene sequences into 13 subgroups, including five previously unknown subgroups. These lineages were widely distributed in anaerobic environments, with the majority of 16S rRNA gene sequences (92%) originating from sediment habitats. Co-occurrence analysis revealed potential relationships between Asgard, Bathyarchaeota, and Marine Benthic Group D archaea. Genomic analysis suggested that Asgard archaea are potentially mixotrophic microbes with divergent metabolic capabilities. Importantly, metatranscriptomics confirmed the versatile lifestyles of Lokiarchaeota and Thorarchaeota, which can fix CO2using the tetrahydromethanopterin Wood-Ljungdahl pathway, perform acetogenesis, and degrade organic matters. Overall, this study broadens the understandings of Asgard archaea ecology, and also provides the first evidence to support a transcriptionally active mixotrophic lifestyle of Asgard archaea, shedding light on the potential roles of these microorganisms in the global biogeochemical cycling.

Download Full-text

Natural Merodiploidy of the lux-rib Operon of Photobacterium leiognathi from Coastal Waters of Honshu, Japan

Journal of Bacteriology ◽

10.1128/jb.00672-07 ◽

2007 ◽

Vol 189 (17) ◽

pp. 6148-6158 ◽

Cited By ~ 17

Author(s):

Jennifer C. Ast ◽

Henryk Urbanczyk ◽

Paul V. Dunlap

Keyword(s):

Phylogenetic Analysis ◽

Sequence Analysis ◽

Coastal Waters ◽

Efflux Pump ◽

Bacterial Species ◽

Genomic Analysis ◽

Multidrug Efflux Pump ◽

Photobacterium Leiognathi ◽

Content Organization ◽

Luminous Bacteria

ABSTRACT Sequence analysis of the bacterial luminescence (lux) genes has proven effective in helping resolve evolutionary relationships among luminous bacteria. Phylogenetic analysis using lux genes, however, is based on the assumptions that the lux genes are present as single copies on the bacterial chromosome and are vertically inherited. We report here that certain strains of Photobacterium leiognathi carry multiple phylogenetically distinct copies of the entire operon that codes for luminescence and riboflavin synthesis genes, luxCDABEG-ribEBHA. Merodiploid lux-rib strains of P. leiognathi were detected during sequence analysis of luxA. To define the gene content, organization, and sequence of each lux-rib operon, we constructed a fosmid library of genomic DNA from a representative merodiploid strain, lnuch.13.1. Sequence analysis of fosmid clones and genomic analysis of lnuch.13.1 defined two complete, physically separate, and apparently functional operons, designated lux-rib 1 and lux-rib 2. P. leiognathi strains lelon.2.1 and lnuch.21.1 were also found to carry lux-rib 1 and lux-rib 2, whereas ATCC 25521T apparently carries only lux-rib 1. In lnuch.13.1, lelon.2.1, lnuch.21.1, and ATCC 25521T, lux-rib 1 is flanked upstream by lumQ and putA and downstream by a gene for a hypothetical multidrug efflux pump. In contrast, transposase genes flank lux-rib 2 of lnuch.13.1, and the chromosomal location of lux-rib 2 apparently differs in lnuch.13.1, lelon.2.1, and lnuch.21.1. Phylogenetic analysis demonstrated that lux-rib 1 and lux-rib 2 are more closely related to each other than either one is to the lux and rib genes of other bacterial species, which rules out interspecies lateral gene transfer as the origin of lux-rib 2 in P. leiognathi; lux-rib 2 apparently arose within a previously unsampled or extinct P. leiognathi lineage. Analysis of 170 additional strains of P. leiognathi, for a total of 174 strains examined from coastal waters of Japan, Taiwan, the Philippine Islands, and Thailand, identified 106 strains that carry only a single lux-rib operon and 68 that carry multiple lux-rib operons. Strains bearing a single lux-rib operon were obtained throughout the geographic sampling range, whereas lux-rib merodiploid strains were found only in coastal waters of central Honshu. This is the first report of merodiploidy of lux or rib genes in a luminous bacterium and the first indication that a natural merodiploid state in bacteria can correlate with geography.

Download Full-text

Cocirculation of Two Distinct Genetic and Antigenic Lineages of Proposed Influenza D Virus in Cattle

Journal of Virology ◽

10.1128/jvi.02718-14 ◽

2014 ◽

Vol 89 (2) ◽

pp. 1036-1042 ◽

Cited By ~ 77

Author(s):

Emily A. Collin ◽

Zizhang Sheng ◽

Yuekun Lang ◽

Wenjun Ma ◽

Ben M. Hause ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Influenza Virus ◽

Respiratory Disease ◽

New Genus ◽

Cross Reactivity ◽

Surface Glycoprotein ◽

Clinical Samples ◽

Genome Sequences ◽

Antigenic Analysis ◽

Pathogenic Potential

ABSTRACTViruses with approximately 50% homology to human influenza C virus (ICV) have recently been isolated from swine and cattle. The overall low homology to ICV, lack of antibody cross-reactivity to ICV in hemagglutination inhibition (HI) and agar gel immunodiffusion assays, and inability to productively reassort with ICV led to the proposal that these viruses represented a new genus of influenza virus, influenzavirus D (IDV). To further our understanding of the epidemiology of IDV, real-time reverse transcription-PCR was performed on a set of 208 samples from bovines with respiratory disease. Ten samples (4.8%) were positive and six viruses were successfully isolatedin vitro. Phylogenetic analysis of full-genome sequences of these six new viruses and four previously reported viruses revealed two distinct cocirculating lineages represented by D/swine/Oklahoma/1334/2011 (D/OK) and D/bovine/Oklahoma/660/2013 (D/660), which frequently reassorted with one another. Antigenic analysis using the HI assay and lineage-representative D/OK and D/660 antiserum found up to an approximate 10-fold loss in cross-reactivity against heterologous clade antiserum. One isolate, D/bovine/Texas/3-13/2011 (D/3-13), clustered with the D/660 lineage, but also had high HI titers to heterologous (D/OK) clade antiserum. Molecular modeling of the hemagglutinin esterase fusion protein of D/3-13 identified a mutation at position 212 as a possible antigenic determinant responsible for the discrepant HI results. These results suggest that IDV is common in bovines with respiratory disease and that at least two genetic and antigenically distinct clades cocirculate.IMPORTANCEA novel bovine influenza virus was recently identified. Detailed genetic and antigenic studies led to the proposal that this virus represents a new genus of influenza, influenzavirus D (IDV). Here, we show that IDV is common in clinical samples of bovine respiratory disease complex (BRDC), with a prevalence similar to that of other established BRDC etiological agents. These results are in good agreement with the near-ubiquitous seroprevalence of IDV previously found. Phylogenetic analysis of complete genome sequences found evidence for two distinct cocirculating lineages of IDV which freely reassort. Significant antigenic differences, which generally agreed with the surface glycoprotein hemagglutinin esterase phylogeny, were observed between the two lineages. Based on these results, and on the ability of IDV to infect and transmit in multiple mammalian species, additional studies to determine the pathogenic potential of IDV are warranted.

Download Full-text