Phylogenetic relationships of a rabies virus isolate in Costa Rica

Introduction: The sylvatic cycle of rabies is a significant sanitary burden in Central America. The Costa Rican government monitors cases since 1985 and infections from bats are still reported for wild animals, livestock, and humans, generating a need of further pathogen characterization in the region. Objective: To compare rabies phylogenetic analyses from complete genomes with nucleoprotein gene studies. Methods: For the phylogenetic analyses we used four rabies tissue samples collected in 2018, and generated complete genomes by Next-Generation sequencing (NGS). We also extracted RNA from tissues of confirmed cases and generated ssDNA using several primers. Double-stranded DNA was generated and used to generate genomic libraries. Results: We describe, for the first-time, the complete genome of four sequences of the rabies virus isolated in Costa Rica in 2018. Complete genome trees resembled the topology of nucleoprotein gene trees. All isolates were related to Desmodus rotundus. One sample group into Lineage (L)2, and the remaining samples group in L1, matched previous reports from regional rabies viruses. Conclusion: Our method produces valid viral assemblies from clinical specimens without target enrichment or viral isolation.

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Diagnosis and molecular typing of rabies virus in samples stored in inadequate conditions

The Journal of Infection in Developing Countries ◽

10.3855/jidc.4136 ◽

2014 ◽

Vol 8 (08) ◽

pp. 1016-1021 ◽

Cited By ~ 8

Author(s):

Fernando J Beltran ◽

Federico Gury Dohmen ◽

Horacio Del Pietro ◽

Daniel M Cisterna

Keyword(s):

Rabies Virus ◽

Molecular Typing ◽

Diagnostic Tests ◽

Limit Of Detection ◽

Antibody Test ◽

Rt Pcr ◽

Tissue Samples ◽

Nucleoprotein Gene ◽

Three Samples

Introduction: The exposure of nervous tissue samples to high temperatures affects the sensitivity of rabies virus diagnostic tests, causing degradation of the viral structure. This study evaluated reverse transcriptase polymerase chain reaction (RT-PCR) for the diagnosis and molecular characterization of brain tissue samples in an advanced state of decomposition and poorly conserved viral isolates by comparing it with routine diagnostic tests. Methodology: A panel of three canine brain samples exposed to controlled decomposition for 7, 15, 30, and 120 days were evaluated using fluorescence antibody test (FAT), mouse inoculation test (MIT), and RT-PCR. In addition, 14 isolates of rabies variants, representing the largest circulation in Argentina, preserved in inadequate cooling for six to eight years were analyzed. Molecular typing of strains was performed using a 159-nucleotide region corresponding to the nucleoprotein gene. Results: The three samples analyzed were positive by RT-PCR at all the decomposition times evaluated, in contrast to results observed with FAT and MIT, which rapidly became negative. In addition, 100% of the inadequately preserved samples were characterized molecularly. The limit of detection of RT-PCR was 0.5 MICDL50/0.03 mL. Conclusion: RT-PCR can be useful for rabies diagnosis and typing of putrefying samples or rabies isolates stored in inadequate conditions.

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Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin

ISME Communications ◽

10.1038/s43705-021-00027-x ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Rui Zhao ◽

Jennifer F. Biddle

Keyword(s):

Costa Rica ◽

Metabolic Pathways ◽

Phylogenetic Analyses ◽

Sulfate Reducing Bacteria ◽

Sulfate Reducing ◽

Hydrocarbon Emission ◽

Costa Rica Margin ◽

Reducing Bacteria ◽

Electron Transfers ◽

Deep Sediments

AbstractDeep sediments host many archaeal lineages, including the Asgard superphylum which contains lineages predicted to require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and the co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Phylogenetic analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore have the capacity to transfer the reducing equivalents (in the forms of hydrogen and formate) generated from alkane oxidation to external partners. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilization and could facilitate electron transfers from other organisms by means of these reduced substances. Their co-occurrence and metabolic features suggest that Helarchaeota may metabolize synergistically with some SRB, and together exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.

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Complete Genome Sequences of Six Novel Macaca mulatta Papillomavirus Types Isolated from Genital Sites of Rhesus Monkeys in Hong Kong SAR, China

Microbiology Resource Announcements ◽

10.1128/mra.01414-18 ◽

2018 ◽

Vol 7 (22) ◽

Cited By ~ 1

Author(s):

Teng Long ◽

Po Yee Wong ◽

Wendy C. S. Ho ◽

Robert D. Burk ◽

Paul K. S. Chan ◽

...

Keyword(s):

Hong Kong ◽

Macaca Mulatta ◽

Complete Genome ◽

Rhesus Monkeys ◽

Genome Sequences ◽

Content Type ◽

Complete Genomes ◽

Hong Kong Sar

The complete genomes of six Macaca mulatta papillomavirus types isolated from genital sites of rhesus monkeys were characterized, and less than 72% identity with the complete L1 genes of known papillomaviruses was found. Macaca mulatta papillomavirus type 2 (MmPV2), MmPV3, and MmPV6 cluster into the genus Alphapapillomavirus, and MmPV4, MmPV5, and MmPV7 cluster into the genus Gammapapillomavirus.

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Complete Genome Sequence of a Vampire Bat Rabies Virus from French Guiana

Genome Announcements ◽

10.1128/genomea.00188-16 ◽

2016 ◽

Vol 4 (2) ◽

Cited By ~ 2

Author(s):

Anne Lavergne ◽

Edith Darcissac ◽

Hervé Bourhy ◽

Sourakhata Tirera ◽

Benoît de Thoisy ◽

...

Keyword(s):

Rabies Virus ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

French Guiana ◽

Genomic Sequence ◽

Amazon Region ◽

Desmodus Rotundus ◽

Bat Rabies ◽

Vampire Bat

A rabies virus was detected in a common vampire bat ( Desmodus rotundus ) in French Guiana. Its genomic sequence was obtained and found to be closely related to other hematophagous bat-related viruses that widely circulate in the northern Amazon region. This virus is named AT6.

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Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004936 ◽

2021 ◽

Vol 71 (8) ◽

Author(s):

Ran Li ◽

Wenbao Zhuang ◽

Congcong Wang ◽

Hamed El-Serehy ◽

Saleh A. Al-Farraj ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Small Subunit ◽

The Yellow Sea ◽

Rrna Gene ◽

Ssu Rrna ◽

Gene Trees ◽

Ssu Rrna Gene ◽

Anaerobic Ciliate ◽

Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

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Correction to: Sequence analysis of nucleoprotein gene reveals the co-circulation of lineages and sublineages of rabies virus in herbivorous in Rio Grande do Sul state, Brazil

Brazilian Journal of Microbiology ◽

10.1007/s42770-020-00258-5 ◽

2020 ◽

Vol 51 (2) ◽

pp. 849-850

Author(s):

Gisane L. de Almeida ◽

Juliana F. Cargnelutti ◽

Ananda S. Ries ◽

José C. Ferreira ◽

Júlio C. A. Rosa ◽

...

Keyword(s):

Sequence Analysis ◽

Rabies Virus ◽

Rio Grande ◽

Rio Grande Do Sul ◽

Nucleoprotein Gene

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Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

Systematic Biology ◽

10.1093/sysbio/syaa063 ◽

2020 ◽

Author(s):

Matthew H Van Dam ◽

James B Henderson ◽

Lauren Esposito ◽

Michelle Trautwein

Keyword(s):

Marine Invertebrates ◽

Phylogenetic Analyses ◽

Single Gene ◽

Gene Tree ◽

Single Copy ◽

Species Tree ◽

Bootstrap Support ◽

Gene Trees ◽

Species Trees ◽

Tree Reconstruction

Abstract Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

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Typing of the rabies virus in Chile, 2002–2008

Epidemiology and Infection ◽

10.1017/s0950268812000520 ◽

2012 ◽

Vol 140 (12) ◽

pp. 2157-2162 ◽

Cited By ~ 7

Author(s):

V. YUNG ◽

M. FAVI ◽

J. FERNANDEZ

Keyword(s):

Phylogenetic Analysis ◽

Monoclonal Antibodies ◽

Rabies Virus ◽

Tadarida Brasiliensis ◽

Insectivorous Bats ◽

Nucleoprotein Gene ◽

Nucleoprotein N

SUMMARYIn Chile, dog rabies has been controlled and insectivorous bats have been identified as the main rabies reservoir. This study aimed to determine the rabies virus (RABV) variants circulating in the country between 2002 and 2008. A total of 612 RABV isolates were tested using a panel with eight monoclonal antibodies against the viral nucleoprotein (N-mAbs) for antigenic typing, and a product of 320-bp of the nucleoprotein gene was sequenced from 99 isolates. Typing of the isolates revealed six different antigenic variants but phylogenetic analysis identified four clusters associated with four different bat species. Tadarida brasiliensis bats were confirmed as the main reservoir. This methodology identified several independent rabies enzootics maintained by different species of insectivorous bats in Chile.

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PROKARYOTIC PHYLOGENY BASED ON COMPLETE GENOMES WITHOUT SEQUENCE ALIGNMENT

Modern Physics Letters B ◽

10.1142/s0217984903004968 ◽

2003 ◽

Vol 17 (03) ◽

pp. 91-94 ◽

Cited By ~ 14

Author(s):

BAILIN HAO ◽

JI QI ◽

BIN WANG

Keyword(s):

Sequence Alignment ◽

Complete Genome ◽

New Method ◽

Systematic Bacteriology ◽

Bacterial Phylogeny ◽

Genome Data ◽

Complete Genomes

We present a brief review of a series of on-going work on bacterial phylogeny. We propose a new method to infer relatedness of prokaryotes from their complete genome data without using sequence alignment, leading to results comparable with the bacteriologist's systematics as reflected in the latest 2001 edition of Bergey's Manual of Systematic Bacteriology.1 We only touch on the mathematical aspects of the method. The biological implications of our results will be published elsewhere.

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