Analysis of intrapatient heterogeneity uncovers the microevolution of Middle East respiratory syndrome coronavirus

Park, Donghyun; Huh, Hee Jae; Kim, Yeon Jeong; Son, Dae-Soon; Jeon, Hyo-Jeong; Im, Eu-Hyun; Kim, Jong-Won; Lee, Nam Yong; Kang, Eun-Suk; Kang, Cheol In; Chung, Doo Ryeon; Ahn, Jin-Hyun; Peck, Kyong Ran; Choi, Sun Shim; Kim, Yae-Jean; Ki, Chang-Seok; Park, Woong-Yang

Although we could not provide a clear picture of the functional interactions among distinct genetic variants in the population, the high ratio of nonsynonymous to synonymous substitutions offered a clue to their functional impact. The 14 variants consisted of 12 nonsynonymous and two synonymous substitutions. Assuming that the unit of selection might not be an individual variant but the population as a whole, we calculated d N (the number of nonsynonymous changes per nonsynonymous site) and d S (the number of synonymous changes per synonymous site) by the Pamilo-Bianchi-Li method (Li 1993; Pamilo and Bianchi 1993) . The d N /d S ratio was 1.03, hinting at the possibility of positive selection. Notably, six of the 12 nonsynonymous substitutions were found in the spike glycoproteincoding region. As quasispecies theory proposes, the unit of selection might not be an individual virus but the population as a whole. Our data showed that the frequencies of the single mutants (D510G, I529 and D510, I529T) significantly fluctuated among specimens, but the combined frequency of the single mutants was consistently high in most samples, suggesting a combination of variants as the unit of selection.