Alphaviruses are positive-sense RNA arboviruses that can cause either a chronic arthritis or a 24 potentially lethal encephalitis. Like other RNA viruses, alphaviruses produce truncated, defective 25 genomes featuring large deletions during replication. Defective RNAs (D-RNAs) have primarily been 26 isolated from virions after high-multiplicity of infection passaging. Here, we aimed to characterize both 27 intracellular and packaged viral D-RNA populations during early passage infections under the 28 hypothesis that D-RNAs arise de novo intracellularly that may not be packaged and thus have remained 29 undetected. To this end, we generated NGS libraries using RNA derived from passage 1 (P1) stock 30 chikungunya virus (CHIKV) 181/clone 25, intracellular virus, and encapsidated P2 virus and analyzed 31 samples for D-RNA expression, followed by diversity and differential expression analyses. We found 32 that the diversity of D-RNA species is significantly higher for intracellular D-RNA populations than 33 encapsidated and specific populations of D-RNAs are differentially expressed between intracellular and 34 encapsidated compartments. Importantly, these trends were likewise observed in a murine model of 35 CHIKV 15561 infection, as well as in vitro studies using related Mayaro, Sindbis, and Aura viruses.
36Additionally, we identified a novel subtype of subgenomic D-RNA that are conserved across 37 arthritogenic alphaviruses. D-RNAs specific to intracellular populations were defined by recombination 38 events specifically in the subgenomic region, which was confirmed by direct RNA nanopore sequencing 39 of intracellular CHIKV RNAs. Together, these studies show that only a portion of D-RNAs generated 40 intracellularly are packaged and D-RNAs readily arise de novo in the absence of transmitted template. 41 3 IMPORTANCE 42 Our understanding of viral defective RNAs (D-RNAs), or truncated viral genomes, comes largely from 43 passaging studies in tissue culture under artificial conditions and/or packaged viral RNAs. Here, we 44 show that specific populations of alphavirus D-RNAs arise de novo and that they are not packaged into 45 virions, thus imposing a transmission bottleneck and impeding their prior detection. This raises 46 important questions about the roles of D-RNAs, both in nature and in tissue culture, during viral infection 47 and whether their influence is constrained by packaging requirements. Further, during the course of 48 these studies, we found a novel type of alphavirus D-RNA that is enriched intracellularly; dubbed 49 subgenomic D-RNAs (sgD-RNAs), they are defined by deletion boundaries between capsid/E3 and 50 E1/3'UTR regions and are common to chikungunya, Mayaro, Sindbis, and Aura viruses. These sgD-51 RNAs are enriched intracellularly and do not appear to be selectively packaged, and additionally may 52 exist as subgenome-derived transcripts. 53 Although D-RNAs have been considered an epi-phenomenon of cell-culturing practices, emerging deep 79 sequencing technologies have enabled researchers t...