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 compared to K3L.
Figure S6. (A) Table of divergence value ranges of TR A to F. The value of TR B is not available because its sequence is AT only. (B) Each box (TR A, C, D, E, F) contains individual TRNs with different colors associated with the parental viral sequences: IRBA22-14 (I, ON755040), MUW1527495 (M, ON019276) or USA_2022_CA002 (U, ON954773) as Figure 1F. TRs and TRNs were validated by the TRAL algorithm with p-value < 10-4.

补充文件1：MPXV序列数据集的新ick树。补充文件2：2022年大流行期间MPXV基因组的根树系进化树。病毒序列的对齐采用MAFFT工具生成，进化树通过FigTree进行可视化。根节点通过引入骆驼痘病毒序列（MZ300860）作为外群病毒进行确定。MPXV基因组的U、M和I组分别用绿色、蓝色和红色标注。基于TR分析得到的重组MPXV分离株用橙色标注。补充文件3：本研究中2022年1月1日至7月20日（N=415）MPXV（B.1谱系）基因组的基因组序列。骆驼痘病毒序列（MZ300860）包含在补充文件2中的系统发育分析中。补充文件4：对补充文件3中MPXV基因组序列和图S6中注释的TRs进行的TRAL分析。补充表1：本研究中MPXV基因组序列信息摘要。图S1：包含具有强连锁不平衡的SNP对序列，其中D'的上限95%置信区间大于0.98，下限大于0.7。图S2：猴痘A47R和A49R基因间的TR C。图S3：猴痘A41L和A42R基因间的TR B。图S4：猴痘B18R和B19R基因间的TR D。图S5：痘苗K3L和猴痘C3L序列的比较。在bp 130-132引入了终止密码子，导致C3L与K3L相比为截断蛋白。图S6：(A) TR A至F的分歧值范围表。由于其序列为AT，因此TR B的值不可用。(B) 每个框（TR A、C、D、E、F）包含与亲本病毒序列相关联的不同颜色的单个TRNs：IRBA22-14（I，ON755040）、MUW1527495（M，ON019276）或USA_2022_CA002（U，ON954773）如图1F所示。TRs和TRNs通过TRAL算法进行验证，p值小于10^-4。