Lots of splits? Use just one:

my $s = 'vif The increase in sensitivity of HIV - infected cells to <G
+ENE> vif Fas </GENE> killing mapped to <GENE> vpu </GENE> , while nef
+ , vif, <GENE> vif </GENE> , <GENE> vpr </GENE> , and second exon of 
+<GENE> tat</GENE> did not appear to contribute';
my @ar = split m%(</?GENE>)%, $s;
for my $i (0 .. @ar/4) {
    $ar[4*$i]=~ s%vif%<PGENE>vif</PGENE>%;
}
$s = join q[],@ar;
print "$s\n";
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