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**gsgs** · February 5, 2008, 03:05 AM

Re: .:.INFLUENZAVIRUS ENVIRONMENTAL RESERVOIR, UPDATE:.:

interesting !

how does that work with the "positive-controls" in the laboratories ?
Might such things have happened elsewhere ?

**Malcolm** · February 5, 2008, 05:29 AM

Re: .:.INFLUENZAVIRUS ENVIRONMENTAL RESERVOIR, UPDATE:.:

Professor Worobey went to Oxford University in England----and is very interested in recombination in viruses.

BIO:

404 - File or directory not found.

http://eebweb.arizona.edu/news/news&views_pdfs/winter04.pdf

Michael Worobey

Michael joined the EEB faculty as an
Assistant Professor in August 2003.
I?m a biologist with an interest in the
evolution of viruses, particularly
rapidly evolving RNA viruses like HIV
and influenza. I use the tool kit of
molecular phylogenetics to investigate
basic questions about how
different viruses evolve, and to make
inferences from viral gene trees
about such things as when, where,
and how particular lineages
crossed into the human population,
and how some viruses manage to
stay one step ahead of their hosts in
a relentless evolutionary arms race.
Although much of my research is
driven by empirical questions about
specific viruses, a good portion of
my work does involve using viral

data as convenient and powerful
means to study evolution in a
broader context. The processes that
shape the evolution of viruses are
surprisingly similar to those that act
in higher organisms, and often the
signal of interest is so much louder
and clearer in viral populations that it
pays to give them a close look.
You?re rarely at a loss for a polymorphic
site in the world of RNA viruses.
I studied biology as an undergraduate
at Simon Fraser University
in Burnaby, BC, breaking up the
academic year with four months of
forest-fire fighting each summer. At
SFU, I applied for a job in Bernie
Crespi?s lab and got a good grounding
in phylogenetics with a project
(which formed my Honors thesis)
that showed how the morphology of
the galls of Australian thrips tracks
the phylogeny of the insects.
From SFU I moved on to the
Department of Zoology at the
University of Oxford on a Rhodes
scholarship, landing in Paul
Harvey?s group. At this point I set off
in a new direction, combining my
interest in phylogenetics, an active
research area in the department,
with the study of infectious disease,
another Oxford specialty. Eddie
Holmes took me under his wing and
together we set about showing that
dengue virus, which was supposed
to be a paragon of clonality, in fact
sometimes undergoes recombination.
This empirical finding opened up
a host of questions about the role of
recombination in viral evolution, and
I spent much of my time as a
graduate student investigating these
questions in one way or another. My
DPhil thesis includes several
empirical investigations of recombination
in viruses such as dengue
and HIV, as well some theoretical
and methodological work developing
new recombination detection
tests and exploring how failing to
account for recombination can bias
phylogenetic inference.

In 2000, I violated ????? the prime
directive of the Harvey group and
started collecting my own data. Bill
Hamilton and I shared a common
interest in the origins of HIV, and he
asked me to accompany him to the
Democratic Republic of the Congo
to collect specimens from wild
chimpanzees there who might
harbor viruses related to HIV. I have
now established a solid research
program there to study SIV, HIV, and
other viruses on their home turf. My
lab here in EEB will be equipped for
working with level 1, 2, and 3
pathogens, and I?m looking forward
to turning on the fieldwork-labworkcomputation
pipeline.
In the meantime, some of the
questions I?m investigating in an
overall phylogenetic framework
include: (1) What facilitates crossspecies
transmission to human
populations of viruses like HIV-2
from West African monkeys, HIV-1
from chimpanzees, or influenza from
birds? (2) Can relatively ?ancient?
genetic material help solve the
riddle of RNA virus origins by
reconciling the apparently fast rate of
evolution in many groups with
patterns of co-divergence with hosts
that suggest much deeper evolutionary
roots? (3) How can molecular
phylogenetics inference improve HIV
vaccine development?

------------------------------------

I wonder what his conclusions on recombination are?

I cannot read the articles listed:

404 - File or directory not found.

http://eebweb.arizona.edu/Faculty/Bios/worobey.html

PubMed list of publications for Mike Worobey
Selected Publications

1. Worobey M. 2005. Anthrax and the art of war (against ascertainment bias). 2005. Heredity, in press.

2. Worobey M, Santiago ML, Keele BF, Ndjango J-BN, Joy JB, Labama BL, Dhed'a BD, Rambaut A, Sharp PM, Shaw GM, Hahn BH. 2004. Origin of AIDS: Contaminated polio vaccine theory refuted Nature 428: 820.

3. Barnett OE, Worobey M, Holmes EC, Cooper A. 2004. Detection of TT virus among chimpanzees in the wild using a noninvasive technique. J Wildlife Dis 40: 230-237.

4. Lemey P, Pybus OG, Rambaut A, Drummond AJ, Roques P, Worobey M, Vandamme1 AM. (2004). The molecular population genetics of HIV-1 group O. Genetics 167: 1059-1068.

5. Damond F, Worobey M, Campa P, Farfara1 I, Colin G, Matheron S, Brun-V?zinet F, Robertson DL, Simon F. 2004. The identification of a highly divergent HIV-2 in France and a proposal for a new HIV-2 classification. AIDS Res Hum Retrov 20: 666-672.

6. van Rij RP, Worobey M, Visser JA, Schuitemaker H. 2003. Evolution of R5 and X4 human immunodeficiency virus type 1 gag sequences in vivo: evidence for recombination. Virology 314: 451-459.

7. Walker PR, Worobey M, Rambaut A, Holmes EC, and Pybus OG. 2003. Sexual transmission of HIV in Africa: other routes of infection are not the dominant contributor to the African epidemic. Nature 422: 679.

8. Worobey M, Rambaut A, Pybus OG, and Robertson DL. 2002. Questioning the evidence for genetic recombination in the 1918 ?Spanish flu? virus. Science 296: 211.

9. Worobey M. 2001. A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria. Mol Biol Evol 18:1425-1434.

10. Jenkins GM, Worobey M, Woelk CH, and Holmes EC. 2001. Evidence for the non-quasispecies evolution of RNA viruses. Mol Biol Evol 18: 987-994.

11. Worobey M, and Holmes EC. 2001. Homologous recombination in GB virus C/hepatitis G virus. Mol Biol Evol 18: 254-261.

12. Worobey M. 2000. Extensive homologous recombination among widely divergent TT viruses. J Virol 74: 7666-7670.

13. Worobey M and Holmes EC. 1999. Evolutionary aspects of recombination in RNA viruses. J Gen Virol 80: 2535-2543.

14. Worobey M, Rambaut A, and Holmes EC. 1999. Widespread intra-serotype recombination in natural populations of dengue virus. Proc Natl Acad Sci USA 96: 7352-7357.

15. Holmes EC, Worobey M. and Rambaut A. 1999. Phylogenetic evidence for recombination in dengue virus. Mol Biol Evol 16: 405-409.

**gsgs** · February 5, 2008, 05:36 AM

Re: .:.INFLUENZAVIRUS ENVIRONMENTAL RESERVOIR, UPDATE:.:

wasn't he the one who had a debate with Gibbs (?) about
recombination in the 1918 virus ?

(I will search the source...)

that was easy to find with those keywords:

Just a moment...

http://www.sciencemag.org/cgi/content/full/296/5566/211a

ahh, you even had it as 8.)

why don't those people participate in public internet forums ?
(is it the "dignity"-thing ?)
I do remember math., physics professors participating.
But with virology I can't even find internet-active students

**AlaskaDenise** · February 12, 2008, 02:47 AM

Re: .:.INFLUENZAVIRUS ENVIRONMENTAL RESERVOIR, UPDATE:.:

I cannot read the articles listed:

Some abstracts can be found with a PubMed search of "Worobey".

see http://www.ncbi.nlm.nih.gov/sites/entrez

for instance:

1: Virology. 2003 Sep 15;314(1):451-9.<SCRIPT language=JavaScript1.2></SCRIPT> Links

<DD class=abstract>Evolution of R5 and X4 human immunodeficiency virus type 1 gag sequences in vivo: evidence for recombination.

van Rij RP, Worobey M, Visser JA, Schuitemaker H.
Sanquin Research at CLB and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, Netherlands.
<DD class=abstract>
Human immunodeficiency virus type 1 (HIV-1) infection is in general established by CCR5-utilizing (R5) virus variants, which persist throughout the course of infection. R5 HIV-1 variants evolve into CXCR4-utilizing (X4) HIV-1 variants in approximately half of the infected individuals. We have previously observed an ongoing genetic evolution with a continuous divergence of envelope gp120 sequences of coexisting R5 and X4 virus variants over time. Here, we studied evolution of gag p17 sequences in two patients who developed X4 variants in the course of infection. In contrast to the envelope gp120 sequences, gag p17 sequences of R5 and X4 virus populations intermingled in phylogenetic trees and did not diverge from each other over time. Statistical evaluation using the Shimodaira-Hasegawa test indicated that the different genomic regions evolved along different topologies, supporting the hypothesis of recombination.
<DD class=abstract>
<DD class=abstract>Therefore, our data imply that recombination between R5 and X4 HIV-1 variants occurs in vivo.
PMID: 14517097
</DD>

.

**HenryN** · February 12, 2008, 03:38 AM

Re: .:.INFLUENZAVIRUS ENVIRONMENTAL RESERVOIR, UPDATE:.:

Originally posted by ironorehopper View Post

ABSTRACT
-
(1.3): J Virol. 2008 Jan 30 [Epub ahead of print]
Phylogenetic evidence against evolutionary stasis and natural abiotic reservoirs of influenza A virus.

Worobey M.
Ecology and Evolutionary Biology, Biosciences West, 1041 E Lowell St., University of Arizona, Tucson, AZ, 85721.

Zhang et al. [J. Virol. 80:12229-12235] claim to have recovered influenza A virus RNA from Siberian lake ice, postulating that ice might represent an important abiotic reservoir for the persistence and re-emergence of this medically important pathogen.

A rigorous phylogenetic analysis of these influenza A hemagglutinin gene sequences, however, indicates that they originated from a laboratory reference strain derived from the earliest human influenza A isolate, "WS/33". Contrary to Zhang et al.'s assertions that the Siberian "ice viruses" are most closely related either to avian influenza virus, or to human influenza strains from Asia from the 1960s [J. Virol. 81:2538], they are clearly contaminants from the WS/33 positive-control used in their laboratory.

There is thus no credible evidence that environmental ice acts as a biologically relevant reservoir for influenza viruses.

Several additional cases with findings that seem at odds with the biology of influenza virus - including modern-looking avian influenza virus RNA sequences from an archival goose specimen collected in 1917 [J. Virol. 76:7860-7862] - can an also be explained by laboratory contamination or other experimental errors.

Many putative examples of evolutionary stasis in influenza A virus appear to be due to laboratory artifacts.

PMID: 18234791 [PubMed - as supplied by publisher]

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