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. 2019 Apr 15;15(4):e1007706. doi: 10.1371/journal.ppat.1007706

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© 2019 Filomatori et al

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Fig 1 — (A) Schematic representation (top) and nucleotide conservation plot (bottom) of the CHIKV complete genome and of the 3’UTR from the original ECSA and Asian strains (right). Direct Repeats (DRs) are represented with rectangular colored blocks and the Conserved Sequence Element (CSE) is shown in black. (B) Sequence alignment of re-emergent CHIKV. Alignment of ECSA- and Asian-derived re-emergent CHIKVs from 17 natural isolates, showing genetic variability in the number of DRs. Sequences are grouped by lineages. GeneBank accession numbers according to references are: HM045811.1 (ECSA), KY575567.1 (USA16), AM258994.1 (LR06), KY704954l (BRA16.1), KY704955 (BRA16.2), KY055011.1 (BRA16.3), MG000876.1 (HAI16), KT308163 (Asian), LN898111.1, (Cbn14), KY704000.17 (NIC15), KT327163.2 (MEX14.1), KP164571 (BRA14), KP851710.1 (MEX14.2), KP851709.1 (MEX14.3), KR559491 (COL14), KR55949 (SBA14), KY435464.1 (BAR14), KR264949.1 (PUE14), KY704001.17 (NIC15). Direct repeats are represented with colored lines and the absence of the respective sequences is shown with light grey lines. The 177-nt extra copy indicated between blue arrows in Cbn-CHIKV corresponds to the duplication of the sequence contained within orange arrows. (C) Base-pair probabilities, consensus sequences, and nucleotide conservation plots for DR1 (top), DR2 (middle) and SLY (bottom) at CHIKV 3’UTR. Sequence alignments were generated and analyzed using MAFFT and RNAalifold software, respectively. For ECSA-derived strains, DR1 corresponds to nucleotide positions 18–70 and 149–193; DR2 corresponds to 71–148, 194–265 and 281–349; and SLY corresponds to 364–442 in LR06 sequence. For Asian-derived strains DR1 corresponds to nucleotide positions 18–70, 168–223 and 345–400; DR2 corresponds to 81–160, 224–297, 401–486, 487–555 and 674–739; and SLY corresponds to 570–648 and 755–832 in Cbn14 sequence. (D) Predicted secondary RNA structure for SLY.