Intrasegmental recombination as an evolutionary force of Lassa fever virus

Lassa fever (LF), caused by Lassa virus (LASV), is one of the most dangerous diseases to public health. Homologous recombination (HR) is a basic genetic power driving biological evolution. However, as a negative-stranded RNA virus, it is unknown whether HR occurs between LASVs and its influence on the outbreak of LF. In this study, after analyzing 575 S and 433 L segments of LASV collected in Africa, we found that LASV can achieve HR in both of its segments. Interestingly, although the length of S segment is less than half of the L segment, the proportion of LASVs with S recombinants is significantly higher than that with L recombinants. These results suggest that HR may be a feature of LASV, which can be set by natural selection to produce beneficial or eliminate harmful mutations for the virus, so it plays a role in LASV evolution during the outbreak of LF.


Fig. S2 .
Fig. S2.The evidence for recombination in the S segment of IRR 030 (A) Sequence similarity comparison of S segments of the recombinant IRR 030 and its putative parents IRR 027 and LASV 0167.IRR 030 is used as the query of the comparison.The y-axis indicates the percentage of similarity between IRR 030 and its two putative parents.The vertical lines indicate the recombination breakpoints.Different colors on the bold line represent the different genes in the S segment.Blue, GPC; Yellow, interval; Red, NP. (B) Bootscan plot of S segment sequences of IRR 030 and its putative parents.The y-axis gives the percentage of permutated trees of information sites.(C) and (D) are the phylogenic trees inferred from different regions of S segment.(C) The phylogenic tree inferred from the regions 93-556 + 1020-1218 +2877-3004.(D) The phylogenic tree inferred from the region 1218-2877.Only bootstrap values > 70% are displayed.The Recombinant isolates are marked with "■".

Fig. S3 .
Fig. S3.The evidence for recombination in the S segment of IRR 003 (A) Sequence similarity of S segments of the recombinant IRR 003 and its putative parents ISTH 0621 and IRR 005.IRR 003 is used as the query.The y-axis indicates the percentage of similarity between IRR 003 and its two putative parents.Different colors on the bold line represent the different genes in the S segment.Blue, GPC; Yellow, interval; Red, NP. (B) Bootscan plot of S segment sequences of IRR 003 and its putative parents.The y-axis gives the percentage of permutated trees of information sites.The vertical lines indicate the recombination breakpoints.(C) and (D) are the phylogenic trees inferred from different regions of S segment.(C) The phylogenic tree inferred from the regions 1-1412 +1581-3158.(D) The phylogenic tree inferred from the region 1412-1581.Only bootstrap values > 70% are displayed.

Fig. S4 .
Fig. S4.The evidence for recombination in the S segment of IRR 004 (A) Sequence similarity of S segments of the recombinant IRR 004 and its putative parents ISTH 0543 and IRR 002.IRR 004 is used as the query of the comparison.The y-axis indicates the percentage of similarity between IRR 004 and its two putative parents.(B) Bootscan plot of S segment sequences of IRR 004 and its putative parents.The y-axis gives the percentage of permutated trees of information sites.The vertical lines indicate the recombination breakpoints.(C) and (D) are the phylogenic trees inferred from different regions of S segment.(C) The phylogenic tree inferred from the region 1-3018.(D) The phylogenic tree inferred from the region 3018-3248.Only bootstrap values > 70% are displayed in the trees.

Fig. S5 .
Fig. S5.The evidence for recombination in the S segment of ISTH 1150 (A) Sequence similarity comparison of S segments of the recombinant ISTH 1150 and its putative parents ISTH 1250 and ISTH 0543.ISTH 1150 is used as the query of the comparison.The y-axis indicates the percentage of similarity between ISTH 1150 and its putative parents.(B) Bootscan plot of S segment sequences of ISTH 1150 and its putative parents.The y-axis gives the percentage of permutated trees.The vertical line indicates the recombination breakpoint.(C) and (D) are the phylogenic trees inferred from different regions of S segment.(C) The phylogenic tree inferred from the region 1-2907.(D) The phylogenic tree inferred from the regions 2908-3258.Only bootstrap values > 70% are displayed in the trees.

Fig. S6 .
Fig. S6.The evidence for recombination in the S segment of LASV 0169 (A) Sequence similarity comparison of S segments of the recombinant LASV 0169 and its putative parents LASV 0038 and LASV 0106.LASV 0169 is used as the query of the comparison.The y-axis indicates the percentage of similarity between LASV 0169 and its putative parents.(B) Bootscan plot of S segment sequences of LASV 0169 and its putative parents.The y-axis gives the percentage of permutated trees of the information sites.The vertical lines indicate the recombination breakpoints.(C) and (D) are the phylogenic trees inferred from different regions of S segment.(C) The phylogenic tree inferred from the region 1-2151.(D) The phylogenic tree inferred from the regions 2151-2401 + 3067-3258.Only bootstrap values > 70% are displayed in the trees.

Fig. S7 .
Fig. S7.The evidence for recombination in the S segment of IRR 073 and its sisters (A) Sequence similarity comparison of S segments of IRR 073 and its putative parents ISTH 2271 and LASV 0133.IRR 073 is used as the query of the comparison.The yaxis indicates the percentage of similarity between IRR 073 and its putative parents.Different colors on the bold line represent the different genes in the S segment.Blue, GPC; Yellow, interval; Red, NP. (B) Bootscan plot of S segment sequences of IRR 073 and its putative parents.The y-axis gives the percentage of permutated trees of the information sites.The vertical lines indicate the recombination breakpoints.(C) and (D) are the phylogenic trees inferred from different regions of S segment.(C) The phylogenic tree inferred from the regions 1-230 + 3001-3262.(D) The phylogenic tree inferred from the region 231-3000.Bootstrap values < 70% are hidden in the trees.