The polyhedrin (polh) gene of nucleopolyhedroviruses (NPVs) encodes for the matrix protein of the virus occlusion body and is one of the most conserved baculovirus genes. Previous analyses of different NPV genes and polh genes provided conflicting results indicating that the Autographa californica nucleopolyhedrovirus (AcMNPV) is generally a member of the so-called group I NPVs and is most closely related to Rachiplusia ou (Ro) NPV, whereas the AcMNPV polh is more similar to the polh of the group II NPVs. A comparative analysis of the AcMNPV polh and its closest neighbours within group I and group II NPV, the RoMNPV and the Thysanoplusia orichalcea (Thor) NPV, was performed using Hidden Markov Models for detecting recombination. The result provided strong evidence that the AcMNPV polh is a chimerical gene which consists of a mosaic of group I and group II NPV specific sequences.
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