HTLV-II ~1E-07: HTLV-II populations that are experiencing rapid epidemic transmission >1E-04 substitution/site/year
||human T-cell lymphotropic virus type II (HTLV-II)
||Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet. 2008 Apr9(4):267-76 p.271 right column top paragraphPubMed ID18319742
|| Salemi, M. et al. Different population dynamics of human T-cell lymphotropic virus type II in intravenous drug users compared with endemically infected tribes. Proc. Natl Acad. Sci. USA 96, 13253–13258 (1999).  Vandamme, A. M., Bertazzoni, U. & Salemi, M. Evolutionary strategies of human T-cell lymphotropic virus type II. Gene 261, 171–180 (2000).PubMed ID10557307, 11164048
||P.271 right column top paragraph: "A reduced rate of replication associated with latency has also been proposed to explain the low rate of approximately 10^−7 subs/site/year that is observed in another retrovirus — human T-cell lymphotropic virus type II (HTLV-II). In this case, low substitution rates are thought to be associated with low rates of inter-host transmission and correspondingly long periods of time within a single host, so that viruses largely spread through the clonal expansion of infected cells (in which the virus is integrated into host DNA), rather than active replication (primary sources). More recent and precise estimates of substitution rates in HTLV-II and its relative HTLV-I similarly revealed low rates of nucleotide substitution, although rates were higher when analyses were based on family-level transmissions compared with those that were based on virus–host co-divergence (ref 44). Indeed, far higher rates (>10^−4 subs/site/year) are observed among HTLV-II populations that are experiencing rapid epidemic transmission because, in this case, active replication is required to initiate infection of each new host (primary sources). Together, both SFV [Simian foamy virus, BNID 112773] and HTLV-I/II reveal how differences in viral generation time combine with mutation to shape overall rates of nucleotide substitution."