Showing posts with label phylogeny. Show all posts
Showing posts with label phylogeny. Show all posts

Tuesday, 27 September 2016

Mayaro virus: a primer and a tree...

UPDATE 11OCT2016
Mayaro virus (MAYV) is a member of the Family Togaviridae. Genetically its divided into two genotypes, "D" (widely Dispersed), "N" (?New) and "L" (Limited) - shown in the tree below.

MAYV is an arthropod-borne virus (arbovirus) that can cause Mayaro fever. 

Disease may can include 4 days of viraemia, a rash that may appear after a 3-5 day fever, headache, photophobia, inguinal lymphadenopathy, myalgia, vomiting, diarrhoea and arthralgia which can affect ankles, wrists and toes and less often, other joints. Joint pain may continue for weeks and maybe very painful. 

Disease is clinically similar to that due to primary dengue virus or chikungunya virus infection. MAYV was first described in 1954 after its discovery in in Mayaro County, Trinidad.[2,3]

Recently, a MAYV infection by a rare member of the L lineage was identified in a dengue virus coinfection in a child in Haiti (sequence shown in bold below) during investigations of sera collected from children with unspecified fever between May 2014 and February 2015.[1]
Mayaro viruses and other Genus Alphavirus and 
Genus Rubivirus complete genome sequences. 
Aligned using MAAFT in Geneious v7. 
Tree made using Mega v7.
Click on image to enlarge

While the Haitian case triggered the usual media sirens, this is a virus well worth watching - and testing for. 

An incredibly prescient 2010 review by Weaver & Reisen on future threats is well worth a read.[4] 

Findings of infection and occasional flaccid paralysis in suckling mice (adult mice were not obviously infectable) that had been injected intracerebrally with low passage virus preparations [2,5] - well, in the new Zika virus reality, it really wouldn't pay to underestimate the potential of yet another tropical virus would it?

Human cases of MAYV infection have most often been reported in working males in forested areas near rivers in countries from Mexico down to Bolivia. All of that knowledge is, of course, based on visible disease outbreaks. I have yet to read every paper, but so  far I have not seen anything that delves deeply into rates of mild or asymptomatic disease. 

MAYV was also isolated in 1967 (reported in 1974 [6]) from a migrating bird (orchard oriole - Icterus spurius) detected in Louisiana, USA. Because it was such a rare event, the authors concluded that these birds probably didn't play a role as natural hosts to MAYV. Apparently it was found in a lizard too - but I'm still chasing down that paper.[7]

References...
  1. http://wwwnc.cdc.gov/eid/article/22/11/16-1015_article
  2. Casals J, Whitman L. Mayaro virus: a new human disease agent. I. Relationship to other arbor viruses. Am J Trop Med Hyg. 1957;6(6):1004-11. PubMed PMID: 13487972.
  3. Anderson CR, Downs WG, Wattley GH, Ahin NW, Reese AA. Mayaro virus: a new human disease agent. II. Isolation from blood of patients in Trinidad, B.W.I. Am J Trop Med Hyg. 1957;6(6):1012-6. PubMed PMID: 13487973.
  4. Scott C. Weaver and William K. Reisen. Present and Future Arboviral Threats. Antiviral Res.
    http://www.ncbi.nlm.nih.gov/pubmed/19857523
  5. Schmidt JR, Gajdusek DC, Schaffer M, Gorrie RH. Epidemic jungle fever among Okinawan colonists in the Bolivian rain forest. II. Isolation and characterization of Uruma virus, a newly recognized human pathogen. Am J Trop Med Hyg. 1959;8(4):479-87. PubMed PMID: 13670375.
  6. Charles H. Calisher, Ph.D.; Ernest0 Gutikez V., M.D.; Kathryn S. C. Maness, B.S., and Rexford D. Lord, SC.D. ISOLATION OF MAYARO VIRUS FROM A MIGRATING BIRD CAPTURED IN LOUISIANA IN 1967. Bull Pan Am Health Organ. 1974;8(3):243-8.
    https://www.ncbi.nlm.nih.gov/pubmed/4418030
  7. Woodall JP Virus research in Amazonia. Atas do Simposia sobre a Biota Amazónia 1967; 6(Patologia):31–63.
  8. Albert J. Auguste, Jonathan Liria, Naomi L. Forrester, Dileyvic Giambalvo, Maria Moncada, KC Long, D Morón, N de Manzione, RB Tesh, ES Halsey, TJ Kochel, R Hernandez, J-C Navarro, SC Weaver. Evolutionary and Ecological Characterization of Mayaro Virus Strains Isolated during an Outbreak, Venezuela, 2010
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593426/

Wednesday, 13 August 2014

Behind the naming of ebolaviruses... [UPDATE 2]

This post has been moved to the new Virology Down Under platform on Wordpress.

You can get to this specific post by clicking on the link below...

http://virologydownunder.com/behind-the-naming-of-an-ebolavirus/

Please adjust your bookmarks.


Apologies for any inconvenience.
-Ian

Thursday, 29 May 2014

Updated MERS-CoV full genome tree...

With thanks to @arambaut for some tips, and for tying my home computer up for 2-days running PHYML on the sequences (super-computer it ain't) - this is a slightly more robust tree of the MERS-CoV complete (or near-complete) genome nucleotide sequences published to date. This follows from my previous post and tree here.

Very little from 2014 despite the majority of MERS-CoV variants circulating then. But of course we have to wait because next generation sequencing is the main way we roll with MERS-CoV.

Alignment of 56 complete or near complete MERS-CoV genomes and an Egyptian divergent variant from a camel. Alignment made using Geneious v6.1.7. The PHYML v2.2.0 plug-in was added to make this tree, using 1000 bootstraps. Red stars indicate 
virus which is reportedly from the same patient (seems doubtful). Vertical bars to the right indicate Clade A (dark blue) and B (pale blue). Sequences from the the 2013 Al-Ahsa hospital outbreak are boxed in pink; from the Jeddah 2014 hospital outbreak in blue; from  the Hafr Al-Batin community cluster in green. Camel icons indicate genomes from camel variants for MERS-CoV. GenBank accession numbers are indicated at the end of each sequence name which also includes region of detection, host (human if not specified) and year of sample collection.
Click on image to enlarge.

The tree really highlights how remarkably interwoven the camel and human MERS-CoV genome sequences are; remembering that these 30,000nt genomes don't differ from each other by more than 1% at the nucleotide level.

Some new sequence analyses from the Netherlands cases should be coming out in the next issue of Eurosurveillance so get a tab ready and keep hitting refresh. Or, ya know, go get a life or something (I'm hitting refresh).

Monday, 26 August 2013

T.perforatus MERS-CoV strain sequence, and others, online...

If you're a bit of a sequence collector/hoarder/nut then you'll be interested to know that the recent bat CoV RNA-dependent RNA polymerase (RdRp) sequences are now online on GenBank.

These seem to include the primer regions judging by their length. Consider that when using them.

The MERS-CoV strain from T.perfortaus is CII_KSA_287 - highlighted in bold. Please note, that at writing, it is erroneously identified on GenBank as originating from Rhinopoma hardwickii. It should be Taphozous perforatus.

Tuesday, 20 August 2013

Understanding phylogeny....how virus sequence relate to each other through time

Over at Edinburgh University, there is an awesome Molecular evolution, phylogeneticis and epidemiology's website. 

On it's "epidemic" blog, run by Prof. Andrew Rambaut, there is a fantastic new primer on how to read a phylogenetic tree.


I highly recommend this for all levels of skill. It provides a great and colourful background to what a phylogenetic tree does, and does not, convey. 


Of particular interest, an example includes bat and camel virus sequences. Also relevant to interpreting future MERS-CoV trees as part of the infection source/animal host debate.


These trees were drawn in FigTree (Mac and Windows versions avail,able) and polished using Adobe Illustrator.

Monday, 12 August 2013

Coronavirus family tree....

The phylogenetic tree below shows the relationships among the four genera of coronaviruses (CoVs); Genus Alphacoronavirus, Betacoronavirus, Deltacoronavirus, Gammacoronavirus. 

This tree is based on full length genomes (nucleotides; aligned using Geneious Pro; Neighbor-Joining tree built using Mega with 500 bootstraps). 

The MERS-CoV clade of betacoronaviruses is marked on the left and the endemic human CoVs are indicated with yellow triangles.