Table 1.
Analysis of mutations associated with epidemic trajectory and microcephaly.
| Nt | Residue | Gene | Residue2 | Epi Mut | Prev AA | Exposed | %(2006–17) | #(2006–17) | #2013 | #2014 | #2015 | #2016 | #2017 | Mutant Analysis |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 473 | 123 | Pr | 1 | A | V | yes | 98.2 | 397 | 12 | 13 | 67 | 295 | 10 | Analyzed, this study |
| 521 | 139 | Pr | 17 | N | S | yes | 95.4 | 379 | 9 | 11 | 66 | 284 | 9 | Yuan et al. 2017 [30]; Jaeger et al., 2019 [31] |
| 2393 | 763 | E | 473 | M | V | yes | 98.4 | 387 | 12 | 13 | 67 | 286 | 9 | Shan et al., 2020 [32] |
| 2786 | 894 | NS1 | 100 | A | G | yes | 25.0 | 99 | 6 | 88 | 5 | Analyzed, this study | ||
| 3050 | 982 | NS1 | 188 | V | A | yes | 97.4 | 385 | 12 | 12 | 67 | 285 | 9 | Liu et al., 2017 [33] |
| 3533 | 1143 | NS1 | 349 | V | M | yes | 25.3 | 100 | 6 | 5 | 85 | 4 | Attempted, this study | |
| 6326 | 2074 | NS3 | 572 | L | M | yes | 26.3 | 104 | 6 | 94 | 4 | Analyzed, this study | ||
| 6362 | 2086 | NS3 | 584 | H | Y | yes | 96.1 | 376 | 9 | 12 | 66 | 280 | 9 | Analyzed, this study |
| 8006 | 2634 | NS5 | 114 | V | T | yes | 89.1 | 335 | 7 | 65 | 256 | 7 | Attempted, this study | |
| 8630 | 2842 | NS5 | 322 | V | I | yes | 24.2 | 93 | 6 | 2 | 83 | 2 | No data | |
| 9239 | 3045 | NS5 | 525 | C | R | yes | 27.0 | 105 | 6 | 94 | 5 | No data | ||
| 10,298 | 3398 | NS5 | 878 | E | D | yes | 22.7 | 90 | 6 | 80 | 4 | Attempted, this study |
The 544 mutations previously identified as associated with the Zika epidemic (Borucki et al., 2019 [16]) were down selected to those occurring in greater than 10% of ZIKV genomes (Asian Lineage) between 2013–2017, persisting until 2017, with at least 25 cases occurring in 2016. Interestingly, the mutations that fit these criteria are all also predicted to occur on exposed regions of the protein and are present in the whole genome sequence of at least one known microcephaly cases associated with the epidemic (data analyzed through July 2017). Mutations which are in red text in the “Epi Mut” column are present in whole ZIKV genome sequences of all known microcephaly cases associated with the epidemic. The percentage of mutations during the epidemic is shown in column “% (2006–17)”. The mutant analysis column indicates if the mutation has been phenotyped using reverse genetic studies and provides references; “No Data” indicates that no published studies were found for the phenotype associated with the mutation. Mutant M1404I, although included in this study, is not shown in the table because it was not present in the genome consensus sequence data for greater than 10% of ZIKV genomes.