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Chapter 2 : Genomics and Evolution of the

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Abstract:

This chapter briefly overviews some of the recent advancements and challenges in nidovirus research concerning the genetic diversity of nidoviruses and selected aspects of nidovirus classification and evolution. Although being nidovirus-wide in scope, most of the discussion concerns coronaviruses, which have been characterized most extensively. The chapter has benefited from a recently published review to which the reader is referred, for details concerning protein domains and the molecular biology of nidoviruses. The genomes of nidoviruses include untranslated regions at their genome termini. These flank an array of multiple genes whose number may vary in and among the families of the order . As in other organisms, two evolutionary mechanisms—mutation and recombination—have been implicated in the generation of nidovirus genome diversity and the maintenance of genome stability. Furthermore, a comprehensive understanding of the parameters of nidovirus adaptability may result in the identification of the driving forces that have shaped nidovirus evolution. In this context, it will be essential to continue the sampling of the natural diversity of nidoviruses, also to see whether the genome size gap between the small and large nidoviruses will be filled with viruses with intermediate-size genomes, and whether nidoviruses infecting other phyla, e.g., plants and insects, can be identified. Ultimately, we may hope to learn whether the large nidoviruses have reached the theoretical genome size limit that nature may have set for RNA viruses. Finally, our progress in understanding the fundamental aspects of RNA virus genome expansion may help to monitor and control infections caused by nidoviruses.

Citation: Gorbalenya A. 2008. Genomics and Evolution of the , p 15-28. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch2

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Figure 1

Distribution of genome sizes of ssRNA+ viruses. Box-and-whisker graphs were used to plot the family/group-specific distribution of genome sizes of all ssRNA+ viruses whose genome sequences have been placed in the NCBI Viral Genome Resource ( ) by 7 December 2005 (J. Faase and A. E. Gorbalenya, unpublished data). The four major groups of nidoviruses are highlighted with the Nido- prefix, and the family is split into the Nido-Coronavirus and Nido-Torovirus groups. The box spans from the first to the third quartiles and includes the median, indicated by the bold line. The whiskers extend to the extreme values that are distant from the box at most 1.5 times the interquartile range. Values beyond this distance are indicated by circles (outliers). Viruses that do not encode a helicase are indicated by black squares. Adapted from reference .

Citation: Gorbalenya A. 2008. Genomics and Evolution of the , p 15-28. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch2
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Figure 2

phylogeny. A tree depicting the evolutionary relationships between the five major groups of nidoviruses (coronaviruses, toroviruses, bafiniviruses, roniviruses, and arteriviruses) is shown. The dotted line separates large and small nidoviruses as defined in the text. This unrooted maximum parsimonious tree was inferred by using multiple nucleotide alignments of the RdRp-HEL region of a representative set of nidoviruses with the help of the PAUP* v.4.0b10 software ( ; A. E. Gorbalenya, unpublished data). Support for all bifurcations from 100 bootstraps is indicated. The coronaviruses analyzed were HCoV-229E, -HKU1, -OC43, and -NL63; transmissible gastroenteritis virus (TGEV); feline coronavirus (FCoV); porcine epidemic diarrhea virus (PEDV); mouse hepatitis virus (MHV); bovine coronavirus (BCoV); bat corona-viruses (BtCoV) HKU3, HKU5, HKU9, 133, and 512 (the last two isolated in 2005); PHEV; IBV; and SARS-CoV. The toroviruses analyzed were equine torovirus (EToV) and bovine torovirus (BToV). The bafinivirus analyzed was WBV. The arteriviruses analyzed were equine arteritis virus (EAV); simian hemorrhagic fever virus (SHFV); lactate dehydrogenase-elevating virus (LDV); and three porcine reproductive and respiratory syndrome viruses (PRRSV), Euro, HB1, and MLV. The ronivirus analyzed was gill-associated virus (GAV). SARS-CoV is highlighted with larger type than the other viruses. Due to the very large scale of the tree, three pairs of nodes formed by very closely related viruses (SARS-CoV and BtCoV-HKU3, BCoV and HCoV-OC43, and BToV and EToV) were collapsed. For coronaviruses, major groups and subgroups are highlighted and labeled ( ); internal nodes defining group and subgroup bifurcations are indicated with black squares and circles, respectively. Subgroup 2b viruses may have been classified differently by other researchers (see the text and references , and ). For arteriviruses, four major clusters, prototyped by EAV, SHFV, LDV, and PRRSV, are highlighted.

Citation: Gorbalenya A. 2008. Genomics and Evolution of the , p 15-28. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch2
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Figure 3

RNA-processing enzymes of nidoviruses: possible cooperation and virus distribution. (A) Cellular pathways for processing of pre-U16 small nucleolar RNA (snoRNA) and pre-tRNA splicing in which homologs of five nidovirus RNA-processing enzymes are involved. Note that both pathways produce intermediates with the 2’-3’-cyclic phosphate termini (black circles), indicating the structural basis for possible cooperation of the nidovirus homologs in a single pathway ( ). XendoU is a cellular homolog of NendoU discussed with other enzymes in the text. (B) Table summarizing the conservation of five (putative) RNA-processing enzymes among representatives of large and small nidoviruses. This figure, updated from reference , is based on Fig. 5 in reference .

Citation: Gorbalenya A. 2008. Genomics and Evolution of the , p 15-28. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch2
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Figure 4

Origin and evolution of the nidovirus genome plan. A tentative evolutionary scenario leading to the origin of the MRCAs of nidoviruses and large nidoviruses from a progenitor with an astrovirus-like genome organization is illustrated. The three shown genomes are fictitious, although they are drawn to a relative common size scale and include major replicative domains found in genomes of respective contemporary viruses, as discussed in the text. Adapted from reference .

Citation: Gorbalenya A. 2008. Genomics and Evolution of the , p 15-28. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch2
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