Introduction: The Sequences

All retroviruses contain three large genes: gag, pol, and env. The gag gene codes for several structural proteins that form the viral particle (virion) capsid and perform other functions. The pol gene codes for several enzymes, including Reverse Transcriptase. We will be analysing env sequences, which are about 2.5 kilobases (Kb) long. The env gene codes for two viral envelope glycoproteins that are positioned on the virion surface and interact with host cell-surface receptors.

You will be analysing an alignment of 62 env sequences of HIV-1, HIV-2, and various SIVs. The alignment has been made for you because aligning this many long sequences can require considerable computation time.

Click here to open the provided alignment.

When viewing the alignment, note that there are many large gaps, which is characteristic of an alignment of a rapidly evolving gene in divergent species.

The sequences are labelled in the format: virus type; followed by the common name of the primate species for the SIV sequences, or the group or subtype for HIV-1 and HIV-2 sequences; finally followed by the accession number.

This alignment contains sequences from various African primate species known to be infected with different SIVs. There are also three non-African species, all from Asia, that have been infected with SIVs in captivity: the pig-tailed macaque, the rhesus macaque and the stump-tailed macaque. The SIVs from all of these primate species are referred to by the three-letter code given with each picture. For example, the SIV from the sooty mangabey is called SIVSMM and the sequence in the alignment or tree is labelled SIV-SMM.


Mona monkey
Cercopithecus
mona mona
[denti]

MON [DEN]
de Brazza's
monkey
Cercopithecus
neglectus

DEB
Tantalus
monkey
Chlorocebus
tantalus

TAN
Syke's
monkey
Cercopithecus
albogularis

SYK
Greater spot-
nosed monkey
Cercopithecus
nictitans

GSN
Green
monkey
Chlorocebus
sabaeus

SAB
Mustached
guenon
Cercopithecus
cephus
MUS
Vervet monkey
Chlorocebus
pygerythrus
VER
Grivet
Chlorocebus
aethiops
GRV
L'Hoest's
monkey
Cercopithecus
lhoest
LST
Sooty
mangabey
Cercocebus
atys
SMM
Red-capped
mangabey
Cercocebus
torquatus
RCM
Sun-tailed
monkey
Cercopithecus
solatus
SUN
Mandrill
Mandrillu
sphinx
MND
Drill
Mandrillus
leucophaeus
DRL
Pig-tailed
macaque
Macaca
nemestrina
MNE
Stump-tailed
macaque
Macaca
arctoides
STM
Rhesus
macaque
Macaca
mulatta
MAC
Common
chimpanzee
Pan
troglodytes
CPZ

Next Page: Phylogenetics: Build a Phylogeny of HIVs and SIVs

Exercise 2: Molecular Phylogenetics of HIVs and SIVs
Exercise 3: The Origin of the HIV-1 Pandemic