Recombination shapes the 2022 monkeypox outbreak

Supplemental File 1. The Newick tree of the MPXV sequence dataset for Supplemental File 2. Supplemental File 2. Rooted phylogenetic tree of MPXV genomes during 2022 pandemics. Alignments of viral sequences were generated using MAFFT, and the phylogenetic tree was visualized using FigTree. Rooting was done by introducing the camelpox virus sequence (MZ300860) as an outgroup virus. Group U, M, and I of MPXV genomes is labeled in green, blue, and red, respectively. Recombinant MPXV isolates based on TR analysis are labeled in orange. Supplemental File 3. Genomic sequences of MPXV (B.1 clade) from January 1 to July 20, 2022 (N=415) in this study. The camelpox virus sequence (MZ300860) is included for phylogenetic analysis in Supplemental File 2. Supplemental File 4. TRAL analysis of the annotated TRs in MPXV genomic sequences of Supplemental File 3 and Figure S6. Supplemental Table 1. Summary of MPXV genome sequence information in this study. Figure S1. Sequences that contain SNP pairs with strong linkage disequilibrium, which the upper 95% confidence bound of the D’ is above 0.98 and the lower bound is above 0.7. Figure S2. TR C in the intergenic region of monkeypox A47R and A49R. (A) The map of TR C, A47R, and A49R gene. Arrows indicate the gene direction. (B) The location of TR C at the 3’-untranslated region of A47R transcript. The 3’ termination UUUUUNU sequence for adding poly(A) tail is boxed in red. Reference MPXV sequence is OP19276. Figure S3. TR B in the intergenic region of monkeypox A41L and A42R. (A) The map of TR B, A41L, and A42R gene. Arrows indicate the gene direction. Sequence b and c are shown in (B) and (C). (B) Sequence of TR B insertion in monkeypox genome as in (A) compared to vaccinia sequence. (C) Alignment of monkeypox and vaccinia in A42R promoter. TAAAT and AAAAAA element are boxed in red. Reference MPXV sequence is OP19276. Figure S4. TR D in the intergenic region of monkeypox B18R and B19R. (A) (A) The map of TR D, B18R, and B19R gene. Arrows indicate the gene direction. Sequence b, c and d are shown in (B), (C) and (D). (B) Alignment of monkeypox sequence B with vaccinia B19R promoter, including TAAAT and AAAAAAA element only found in vaccinia. (C and D) Sequences of B19R promoter of monkeypox. Sequence of TR D insertion in monkeypox genome as in (A). Reference MPXV sequence is OP19276. Figure S5. Comparison of vaccinia K3L and monkeypox C3L sequence. The stop codon was introduced at bp 130-132, causing C3L a truncated protein c