By March 2014 — about the time the epidemic was detected, but some 3 months after the first case actually occurred — the sequences had split into two distinct lineages, one of which was characterized by a single amino
acid change in a region of the virus's surface protein and allows it to bind to cells.
Given that most amino
acid changes are slightly deleterious [12] and assuming that most genes
in the genome are relatively conserved, one would expect that
regions of the genome with a low recombination rate, when compared to those with a high rate, would show i) a higher ratio of non-synonymous (amino
acid replacing) to synonymous (silent) substitutions (ω) and ii) a higher degree of protein divergence (dA) due,
in both cases, to the reduced effectiveness of selection against slightly deleterious mutations.