DNA from isolates of monkeypox virus, when digested with the endonuclease I, gave fragment-size profiles which correlated with the geographic area from which the isolate originated. Although some of the differences were located subterminally in the genome, others mapped to the central conserved region. Further differentiation of the viral genomes was sought by analysis of a short region within the central conserved part of the genome that appeared to be a partially deleted counterpart of an intact 1024 bp open reading frame (ORF) present in variola and vaccinia virus genomes. We reasoned that this region would not be conserved by functional selection and would therefore be likely to show more variation between isolates of monkeypox virus. The deletions found in monkeypox virus isolates from Liberia and from Benin were almost the same as that which we had previously found in the Denmark strain. A much shortened ORF, potentially coding for a product of 133 amino acids, was retained in all three West African isolates, but three Zairean isolates each showed an identical series of small insertions and deletions which effectively abolish the ORF. Three deletions, present in all isolates, must pre-date the geographical separation of monkeypox virus lineages; other, presumably more recent, changes differ between the Zairean and West African isolates. In contrast, the base similarity was found to be more than 99% when all the monkeypox virus sequences were appropriately aligned. This, in a disrupted and presumably non-functional gene also indicates that the changes described are recent. It is suggested that insertions and deletions occur regularly during poxvirus DNA replication, but are preserved only in sequences that are not required for continued transmission in the natural host.


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