Xapuri virus, a novel mammarenavirus: natural reassortment and increased diversity between New World viruses

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Abstract

Mammarenavirus RNA was detected in Musser’s bristly mouse ( Neacomys musseri) from the Amazon region, and this detection indicated that rodents were infected with a novel mammarenavirus, with the proposed name Xapuri virus (XAPV), which is phylogenetically related to New World Clade B and Clade C viruses. XAPV may represent the first natural reassortment of the Arenaviridae family and a new unrecognized clade within the Tacaribe serocomplex group.

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Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.

K Lole, R Bollinger, R S Paranjape … (1999)

The development of an effective human immunodeficiency virus type 1 (HIV-1) vaccine is likely to depend on knowledge of circulating variants of genes other than the commonly sequenced gag and env genes. In addition, full-genome data are particularly limited for HIV-1 subtype C, currently the most commonly transmitted subtype in India and worldwide. Likewise, little is known about sequence variation of HIV-1 in India, the country facing the largest burden of HIV worldwide. Therefore, the objective of this study was to clone and characterize the complete genome of HIV-1 from seroconverters infected with subtype C variants in India. Cocultured HIV-1 isolates were obtained from six seroincident individuals from Pune, India, and virtually full-length HIV-1 genomes were amplified, cloned, and sequenced from each. Sequence analysis revealed that five of the six genomes were of subtype C, while one was a mosaic of subtypes A and C, with multiple breakpoints in env, nef, and the 3' long terminal repeat as determined by both maximal chi2 analysis and phylogenetic bootstrapping. Sequences were compared for preservation of known cytotoxic T lymphocyte (CTL) epitopes. Compared with those of the HIV-1LAI sequence, 38% of well-defined CTL epitopes were identical. The proportion of nonconservative substitutions for Env, at 61%, was higher (P < 0.001) than those for Gag (24%), Pol (18%), and Nef (32%). Therefore, characterized CTL epitopes demonstrated substantial differences from subtype B laboratory strains, which were most pronounced in Env. Because these clones were obtained from Indian seroconverters, they are likely to facilitate vaccine-related efforts in India by providing potential antigens for vaccine candidates as well as for assays of vaccine responsiveness.

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Estimating maximum likelihood phylogenies with PhyML.

Stéphane Guindon, Frédéric Delsuc, Jean-François Dufayard … (2009)

Our understanding of the origins, the functions and/or the structures of biological sequences strongly depends on our ability to decipher the mechanisms of molecular evolution. These complex processes can be described through the comparison of homologous sequences in a phylogenetic framework. Moreover, phylogenetic inference provides sound statistical tools to exhibit the main features of molecular evolution from the analysis of actual sequences. This chapter focuses on phylogenetic tree estimation under the maximum likelihood (ML) principle. Phylogenies inferred under this probabilistic criterion are usually reliable and important biological hypotheses can be tested through the comparison of different models. Estimating ML phylogenies is computationally demanding, and careful examination of the results is warranted. This chapter focuses on PhyML, a software that implements recent ML phylogenetic methods and algorithms. We illustrate the strengths and pitfalls of this program through the analysis of a real data set. PhyML v3.0 is available from (http://atgc_montpellier.fr/phyml/).

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Reordering contigs of draft genomes using the Mauve Aligner

Anna Rissman, Bob Mau, Bryan Biehl … (2009)

Summary: Mauve Contig Mover provides a new method for proposing the relative order of contigs that make up a draft genome based on comparison to a complete or draft reference genome. A novel application of the Mauve aligner and viewer provides an automated reordering algorithm coupled with a powerful drill-down display allowing detailed exploration of results. Availability: The software is available for download at http://gel.ahabs.wisc.edu/mauve. Contact: rissman@wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online and http://gel.ahabs.wisc.edu

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Author and article information

Contributors

Jorlan Fernandes:

ORCID: http://orcid.org/0000-0002-5039-0604

jorlan@ioc.fiocruz.br

Elba Regina Sampaio de Lemos: elba.lemos@ioc.fiocruz.br

Journal

Journal ID (nlm-ta): Emerg Microbes Infect

Journal ID (iso-abbrev): Emerg Microbes Infect

Title: Emerging Microbes & Infections

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2222-1751

Publication date (Electronic): 29 June 2018

Publication date PMC-release: 29 June 2018

Publication date Collection: 2018

Volume: 7

Electronic Location Identifier: 120

Affiliations

[1 ]ISNI 0000 0001 0723 0931, GRID grid.418068.3, Laboratory of Hantaviruses and Rickettsiosis, Oswaldo Cruz Foundation, , Oswaldo Cruz Institute, ; Rio de Janeiro – RJ, 21040-360 Brazil

[2 ]ISNI 0000 0001 2196 8713, GRID grid.9004.d, National Infection Service, , Public Health England, Porton Down, ; Salisbury, Wiltshire SP4 0JG UK

[3 ]ISNI 0000 0001 0723 0931, GRID grid.418068.3, Laboratory of Biology and Parasitology of Wild Mammals Reservoirs, Oswaldo Cruz Foundation, , Oswaldo Cruz Institute, ; Rio de Janeiro – RJ, 21040-360 Brazil

[4 ]Federal Institute of Acre, Rio Branco – AC, 69900-640 Brazil

[5 ]ISNI 0000 0001 0723 0931, GRID grid.418068.3, Postgraduate Program in Biodiversity and Health, Oswaldo Cruz Foundation, , Oswaldo Cruz Institute, ; Rio de Janeiro – RJ, 21040-360 Brazil

[6 ]GRID grid.419166.d, Nacional Cancer Institute, ; Rio de Janeio – RJ, 20230-130 Brazil

Author information

Jorlan Fernandes http://orcid.org/0000-0002-5039-0604

Article

Publisher ID: 119

DOI: 10.1038/s41426-018-0119-9

PMC ID: 6026159

PubMed ID: 29959319

SO-VID: a1790baa-81d2-4ca0-bc7c-37133b04da9a

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Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 2 April 2018

Date revision received : 21 May 2018

Date accepted : 27 May 2018

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Xapuri virus, a novel mammarenavirus: natural reassortment and increased diversity between New World viruses

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Most cited references 42

Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.

Estimating maximum likelihood phylogenies with PhyML.

Reordering contigs of draft genomes using the Mauve Aligner

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