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November 20123Playing with the pros

4Food security: an urgent issue for B.C.

7A university library for the 21st century

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"

HIV subtype B

HIV within a single patient Hepatitis C virus 6a

Influenza A virus H3N2

Hepatitis B virus genotype C

All trees depicted are approximately on the same scale.

"

IAS–USA Topics in Antiviral Medicine

158

MUTATIONS IN THE REVERSE TRANSCRIPTASE GENE ASSOCIATED WITH RESISTANCE TO REVERSE TRANSCRIPTASE INHIBITORS

Nucleoside and Nucleotide Analogue Reverse Transcriptase Inhibitors (nRTIs)a

Nonnucleoside Analogue Reverse Transcriptase Inhibitors (NNRTIs)a,m

Multi-nRTI Resistance: 69 Insertion Complexb (affects all nRTIs currently approved by the US FDA)

Multi-nRTI Resistance: 151 Complexc (affects all nRTIs currently approved by the US FDA except tenofovir)

Multi-nRTI Resistance: Thymidine Analogue-Associated Mutationsd,e (TAMs; affect all nRTIs currently approved by the US FDA)

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Zidovudined,e,j,k

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Efavirenz

Nevirapine

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tip

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time

MAXIMUM LIKELIHOOD

METHOD

A method that selects the treethat has the highest probabilityof explaining the sequence data,under a specific model ofsubstitution (changes in thenucleotide or amino-acidsequence).

54 | JANUARY 2004 | VOLUME 5 www.nature.com/reviews/genetics

R E V I EW S

itself a composite of viruses, the descendants of whichare now found in red-capped mangabeys (Cercocebustorquatus, SIVrcm) and greater spot-nosed monkeys(Cercocebus nictitans, SIVgsn)8.

Dating the evolution of primate lentiviruses. To fullyunderstand the evolutionary history of HIV, it is alsonecessary to determine its timescale. At face value, thewide host-species range of the SIVs, as well as their lowVIRULENCE and strong association with specific species9,argues for an ancient evolutionary history, perhapsrepresenting virus–host co-divergence over severalmillion years. Indeed, in some cases the phylogeny ofthe SIVs matches that of their primate hosts, asexpected under a co-divergence model10. However,there are an increasing number of instances in whichhost and virus phylogenies are mismatched, implyingmore recent cross-species transfer in the SIVs8,11,12. Ifcross-species transfer is in fact the main mode of evo-lution, then any resemblance between host and virustrees might be because related primate species areoften found in adjacent geographical ranges, orbecause host switching is most likely to occur betweenclosely related host species13.

The timescale of evolution inferred from viralMOLECULAR CLOCKS also seems incompatible with long-term co-divergence. If co-divergence were true, thenthe divergence times of SIVs should broadly matchthose of their hosts, going back millions of years.However, all molecular clock estimates of primatelentivirus evolution are orders of magnitude morerecent than this14, and the rates of mutation and repli-cation are similar among these viruses15,16. Therefore, ifmolecular clocks are accurate, then the evolutionarytimescale for each epidemic of HIV-1 and HIV-2 ismeasured only in decades. Several methods are avail-able to measure substitution rates, and thereforedivergence times, in RNA viruses, although the mostreliable estimates come from analysing the temporaldistribution of nodes on trees (BOX 2). Application ofthese (and similar) methods have led to suggestionsthat the M group of HIV-1 originated in the 1930s,with a range of ~10 years on either side17–19 (but seeBOX 2). A broadly similar evolutionary timescale hasbeen proposed for HIV-2 (REF. 20).

Although most estimates for the time of origin ofHIV-1 are consistent, all can be subject to the same sys-tematic bias. Once again, recombination might con-tribute to this error. Recombination has complex effectson the estimation of divergence times, by increasingapparent variation in rates among nucleotide sites andreducing genetic distances between sequences21,22. Inthese circumstances, perhaps the only reliable indicatorsof the timescale of HIV evolution are archival viral sam-ples. The earliest HIV-1 M group sequence that is avail-able was sampled in the Democratic Republic of Congoin 1959 (REF. 23). That this sequence falls some distancefrom the root of the M group tree is strong evidencethat the diversification of these viruses occurred beforethis time (BOX 2). Accurately dating HIV evolution willrequire the analysis of more such ‘fossil’ viruses.

humans are thought to explain the current diversity ofHIV-1, such that groups M, N and O each have an inde-pendent origin3,6. However, inter-specific recombina-tion, which might be common among the primatelentiviruses, greatly complicates this analysis7. For exam-ple, HIV-1 group N seems to be a recombinant betweena SIVcpz strain and a virus related to the ancestor ofgroup M (REF. 3), but this event occurred before theestablishment of group M and N in humans. SIVcpz is

A

A

A

B

B

C

B

D

H

F

G

HIV-1 group M

HIV-2

HIV-2

HIV-1 group O

HIV-1 group N

SIVcpz

SIVcpz

SIVcpzSIVdrl

SIVmnd

SIVrcm

SIVsab

SIVsmSIVmac

SIVsyk

SIVgsnSIVmon

SIVver

SIVtan

SIVlhoestSIVsun

SIVmnd

SIVcol

SIVcpz

SIVcpz Pan troglodytes troglodytes

Pan troglodytes schweinfurthii

0.05 substitutions per site

Figure 2 | Evolutionary history of the primate lentiviruses. Because both the humanimmunodeficiency virus type 1 (HIV-1) and HIV-2 lineages (red branches) fall within the simian immunodeficiency viruses (SIVs) that are isolated from other primates, they representindependent cross-species transmission events. The tree and other evidence also indicate that HIV-1 groups M, N and O represent separate transfers from chimpanzees (SIVcpz), againbecause there is a mixing of the HIV-1 and SIV lineages. Similarly, HIV-2 seems to have beentransferred from sooty mangabey monkeys (SIVsm) on many occasions, although this is best documented in other phylogenetic analyses2. The tree was reconstructed using a MAXIMUM LIKELIHOOD METHOD on an alignment of 34 published nucleotide sequences of the viral polymerase (pol) gene (FIG. 1), excluding third codon positions (full details from the authors on request). Other abbreviations for viruses and their primate hosts are as follows: SIVcol, blackand white colobus; SIVdrl, drill; SIVgsn, greater spot-nosed monkey; SIVlhoest, L’Hoest monkey;SIVmac, macaque; SIVmnd, mandrill; SIVmon, Campbell’s mona monkey; SIVrcm, red-cappedmonkey; SIVsab, Sabaeus monkey; SIVsun, sun-tailed monkey; SIVsyk, Sykes’ monkey; SIVtan,tantalus monkey; SIVver, vervet monkey. For clarity, only some subtypes of HIV-1 and HIV-2 areshown. All gene sequences were taken from GenBank (see online links box).

HIV within a single host

Global influenza A virus (H3N2)

1 base pair

400 bps 1 read 100 reads

~2500 reads48 samples

approximate size of a landmark HIV

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~48,000,000 bps

approximate length of a bulk

sequence

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BCCfE Forefront Lecture Series - April 13, 2011

The time of HIV infection is predicted by the TMRCA from 454 data.

200 300 400 500 600

200

300

400

500

600

Estimated date of infection (non-genetic)

Day

s si

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3

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6

7

8

9

10

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14

15

16

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New infection

TMRCA of new infection

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1995 1996 1997 1998 1999 2000 2001

1995

1996

1997

1998

1999

2000

2001

Known date of seroconversion

Estim

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dat

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infe

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Mean difference = +1.2 months25%, 75% = –1.8, +6.5 months

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ConsensusConsensus

Later samples

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The majority of HIV variants use CCR5

Progression to AIDS is associated with switching to CXCR4.

R5 X4

fitne

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Genotype spaceCCR5-using CXCR4-using

0.0

0.2

0.4

0.6

0.8

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Frequency

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0.0

0.2

0.4

0.6

0.8

1.0

Replications (x1000)

Frequency

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0 5000 10000 15000 20000

"

0 5 10 15 20 25 30 35

0.00

0.04

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Amino acid position

Scor

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1991 1992 1993

03.5102050100

g2p false positive rate

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Year

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Positive MT-2MRCA

MRCA

CCR5 CXCR4

TIME

g2p

FPR

(log

sca

le)

0.1

3.5

100

range(tbins)

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range(tbins)

log(range(fbins))

DS2

range(tbins)

log(range(fbins))

DS3

range(tbins)

log(range(fbins))

DS4

DS5

log(range(fbins))

DS6

log(range(fbins))

DS7

log(range(fbins))

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Advice on Applying for a Grant, Writing Papers, Setting up a Research Team and Managing Your Time

Institute of Genetics, CIHRRoderick McInnes • Brenda Andrews • Richard Rachubinski

Guidebook for New Principal Investigators

C anadian Institutesof Health Re searc h

Instituts de rec herc heen santé du C anada