The genome of Thogoto (THO) virus, an unclassified tick-borne virus, comprises six segments of single-stranded RNA. The complete sequence of the third largest RNA segment has been determined from overlapping cDNA clones and by primer extension studies. Segment 3 RNA consists of 1865 nucleotides (approx. 6.2 x 10(5) Mr). It has a large open reading frame (ORF1;597 amino acids, 68.6K) in its virus-complementary sequence, confirming that the RNA has a negative-sense coding strategy. A transcription termination (polyadenylation) site located after the end of ORF1 has been identified. A second ORF (ORF2;98 amino acids in length), overlapping ORF1, is also present in the virus-complementary sequence although whether it is translated is not known. The 3' and 5' sequences of the segment 3 RNA are complementary and similar to those of the tick-borne Dhori (DHO) and the mammalian and avian influenza viruses. Protein database searches have identified regions of homology between the sequence of the THO ORF1 gene product and regions of the PA protein of influenza virus strain A/NT/60/68 (approx. 20% aligned homology) and the corresponding protein of influenza B/Sing/222/79 virus (approx. 15% aligned homology). Although the THO protein sequence is not as closely related to those of the influenza viruses as they are to each other (40% aligned homology), the indicated sequence data provide further evidence of relationships between the tick-borne THO and DHO viruses and the vertebrate orthomyxoviruses.