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Virus molluscum contagiosum (MCV), ki ga taksonomsko uvrščamo v raznoliko družino Poxviridae in poddružino Chordopoxvirinae, je eden od dveh predstavnikov rodu Molluscipoxvirus. Od izkoreninjenja virusa črnih koz je MCV edini poksvirus, katerega edini znani gostitelj je človek. Za klinično sliko okužbe z MCV so značilne različno velike čvrste papule (t.i. moluski), ki se navadno pojavljajo v manjšem številu in po določenem času same izzvenijo. Pri imunsko-kompromitiranih bolnikih se moluski lahko pojavijo v večjem številu in vztrajajo daljše časovno obdobje. Prve raziskave raznolikosti MCV so temeljile na restrikcijskih vzorcih MCV DNA in kažejo na obstoj vsaj štirih podtipov MCV (MCV1, 2, 3 in 4). Zaradi pomanjkanja informacij, ni znano ali podtipi MCV dejansko zastopajo genomske različice MCV, genotipe, ki so se iz skupnega prednika razvili po divergentnih evolucijskih poteh. V sodobnih molekularno-epidemioloških raziskavah opredeljevanje podtipov MCV temelji na pomnoževanju in sekveniranju določenih genomskih področij virusne DNA. Kljub temu, da so sodobne molekularne metode v praksi poenostavile izvedbo tipizacije MCV, pa so nabor podtipov MCV, ki jih na ta način lahko določimo, omejile zgolj na podtipa MCV1 in MCV2, saj o nukleotidnih zaporedjih drugih podtipov MCV zaenkrat nimamo podatkov. Namen raziskave je bil prvič natančno opredeliti genomsko raznolikost izolatov MCV1, MCV2 in morebitnih drugih zaznanih podtipov in postaviti temelje sodobni metodologiji za klasifikacijo MCV podtipov, vključno z MCV3 in MCV4. Na podlagi opredeljevanja celotnih in delnih nukleotidnih zaporedij MCV smo želeli opredeliti evolucijsko povezanost posameznih podtipov MCV, preveriti ali na posameznih delih genoma MCV lahko prihaja do rekombinacij ter ali evolucija posameznih genov MCV poteka enakomerno. Dodatno smo želeli ugotoviti morebitno raznolikost virusnih populacij znotraj enega moluska, v več moluskih istega gostitelja ter v moluskih različnih gostiteljev. V raziskavo smo vključili skupno 62 celotnih genomov MCV, med njimi je bilo 43 novo-sestavljenih nukleotidnih zaporedij celotnih genomov MCV1 in 12 novo-sestavljenih celotnih genomov MCV2. Filogenetska analiza sorodnosti je pokazala, da podtipa MCV1 in MCV2 dejansko zastopata različni genomski različici MCV, genotipa MCV1 in MCV2. Sintenična razmerja med genomi MCV1 in MCV2, podobnost nukleotidnih zaporedij celotnih genomov in posameznih genskih področij so nakazovali na pretežno linearen (substitucijski), divergenten evolucijski razvoj iz skupnega prednika. Genomska raznolikost med genomi različnih genotipov MCV je bila večja od genomske raznolikosti med genomi istega genotipa MCV. Med genomi MCV, ki so izhajali iz istega gostitelja, je bila genomska raznolikost nižja od genomske raznolikosti med MCV iz različnih gostiteljev. Genomski raznolikosti MCV1 in MCV2 sta si bili podobni, oba genotipa sta nosila zapise za podobno število večinoma homolognih si beljakovin. MCV1 in MCV2 sta se razlikovala v vsebnosti gvanina in citozina. Rekombinacije med različnimi genotipi MCV smo zaznali na območjih nekaterih MCV genov, ki so povezani z izogibanjem imunskemu odzivu gostitelja. V genih, kjer rekombinacij nismo zaznali, smo zaključili, da evolucija tam sicer poteka linearno, a ne nujno tudi enakomerno, kar se odraža v mozaični genski strukturi MCV. Prisotnost/odsotnost rekombinacij v posameznih genomih MCV je sovpadala z filogenetsko določenimi podskupinami MCV in restrikcijskimi kartami za encime BamHI, ClaI in HindIII, ki so bili opredeljeni in silico. Na osnovi enega od kontekstov: vzorca rekombinacij, filogenetske podskupine ali restrikcijske karte, smo lahko napovedovali druga dva konteksta. Vsem dostopnim celotnim nukleotidnim zaporedjem MCV smo lahko z restrikcijo in silico določili podtip, ki je sovpadal s filogenetsko določenim genotipom. Izsledki naše raziskave bodo pomembno prispevali k razumevanju genomske raznolikosti MCV in njegovih genotipov, patogeneze, epidemiologije, evolucije in razvoja diagnostičnih testov za MCV in razlikovanje med njegovimi genotipi/podtipi. Molluscum contagiosum virus (MCV), a member of the diverse taxonomical family Poxviridae and the subfamily Chordipoxvirinae, is one of the two constituent members of the genus Molluscipoxvirus. Since the successful eradication of smallpox, MCV is the last known, still circulating, uniquely homotropic poxvirus. MCV infection is clinically manifested by firm skin lesions, papules of varied sizes – mollusca, which are normally limited in number and often spontaneously regress over time. In immune-compromised patients mollusca can manifest in greater numbers and may persist during longer time spans. Early studies of the diversity of MCV, based on mapping of MCV DNA restriction patterns, indicated the existence of at least four MCV subtypes (MCV1, 2, 3 and 4). Due to a lack of information, it is currently unknown whether the four subtypes represent specific genomic variants of MCV, which have evolved along divergent evolutionary paths from a common ancestor. In modern molecular-epidemiological studies the characterization of MCV subtypes is often based on amplification and sequencing of specific parts of the viral DNA. On one hand, modern molecular methods, have, in practice, simplified the process of MCV subtype assignment, however, due to the lack of data on other MCV subtypes, by doing so they have also narrowed the range of MCV subtypes that can be determined to MCV1 and MCV2. The aim of our study was to, for the first time, characterize the genomic diversity of MCV1, MCV2 and other potentially detected MCV subtypes, and to develop a modern platform for the classification MCV subtypes, including MCV3 and MCV4. Based on characterization of complete MCV genome sequences we aimed to determine the evolutionary relationships between specific MCV subtypes, to clarify whether the evolutionary history of MCV had been to some degree shaped by recombination and to clarify whether different MCV genes evolve co-linearly at similar rates. In addition, we aspired to illuminate the genomic diversity of MCV populations originating from a single molluscum, multiple mollusca of the same host and from mollusca of multiple hosts. A total of 62 complete MCV genome sequences were interrogated during this study, including 43 novel complete genome sequences of MCV1 and 12 novel sequences of MCV2. Phylogenetic analysis determined that the two subtypes MCV1 and MCV2, do in fact represent distinct genomic entities of MCV, genotypes MCV1 and MCV2. Syntenic relationships between genomes of MCV1 and MCV2, genome- and individual gene-scale similarity analyses indicated a generally co-linear, but divergent evolutionary paths with common ancestry. Greater genomic diversity was found among genomes of different MCV genotypes than among genomes of the same MCV genotype. Genomic diversity among MCV genomes originating from multiple hosts was found greater than among those that originated from the same host. The genomic diversities of the two genotypes assumed similar intervals of values, and both were found to contain similar numbers of homologous genes. On the other hand, we identified a significant difference between the guanosine and cytosine contents of MCV1 and MCV2. We identified evidence of recombination in the genomic regions of some of the MCV genes related to host immune-evasion. On the other hand, non-recombinant genes indicated that they have evolved co-linearly but not necessarily at the same local rates, which is reflected in a mosaic genetic structure of MCV. The presence/absence of recombination in specific genomes coincided with the assignment to sub-genotype groups determined phylogenetically, as well as with the BamHI, ClaI and HindIII restriction maps determined in silico. By knowing one of the three contexts: the recombination pattern, the phylogenetic sub-genotype group or the restriction patterns, the other two contexts could be predicted effectively. By interrogating the in silico BamHI, ClaI in HindIII restriction profiles each MCV genome could be assigned an MCV subtype, coinciding with the genotype, determined phylogenetically. In conclusion, the current study greatly expands the knowledge of MCV genomic diversity and its genotypes and provides a valuable resource for future epidemiological, evolutionary, functional pathogenicity and molecular assay development studies.