Evolutionary rate shifts suggest species-specific adaptation events in HIV-1 and SIV

Maoz Gelbart; Adi Stern

How viruses are able to cross species barrier is a subject of much interest, since many pandemic 37 human viruses arose from zoonosis events such as the influenza strain of "Spanish flu" H1N1, 38 measles virus (MeV), and SARS coronavirus [13] . Due to genetic differences between the hosts, 39 virus adaptation occurs at multiple levels: at the level of entry to target cells; interaction with 40 happened [17] . This is due to new roles gained by these protein sites that constrain their 45 evolution. A reciprocal phenomenon where amino acids are less conserved in one clade than in 46 other clades is also possible, and may either reflect a loss of function or a gain of function 47 manifested as positive diversifying selection. Identification of such "rate shifting sites" can thus 48 reveal virus adaptation events, and is expected to promote a better understanding of cross-49 species transmissions in general and in the HIV pandemic in particular in this study. 50