From Mosquitos to Humans: Genetic evolution of Zika Virus

Transcription

1 Article: From Mosquitos to Humans: Genetic evolution of Zika Virus Renata Pellegrino, PhD Director, Sequencing lab Center for Applied Genomics The Children s Hospital of Philadelphia Journal Club

2

3 Clinical features comparisons

4 Mosquito: Aedes aegypti Nature Reviews Microbiology 5, (July 2007) and Kraemer et al. elife 2015;4:e08347

5

6 7 Germany x 1 Brazil

7 Zika activity: symptoms are not the worse scenario National information: ~44k European CDC :~440k 4783 cases of MICROCEPHALY in Brasil 20 times higher previous years 99.7 per 100,000 livebirths (1.02 per 10,000 births in UK) 1118 cases confirmed according to the new WHO Classification

8 Social impact

9 ZIKV is a flavivirus closely related to dengue virus (DENV). Its genome is a single-stranded positive-sense RNA molecule of approximately 10,800 base pairs. The virion RNA is infectious and serves as both the genome and the viral messenger RNA. The whole genome is translated in a polyprotein 3,419 aa long, which is processed co- and posttranslationally by host and viral proteases. Arch Virol (2007) 152: and Viruses 2015, 7,

10 Cell Host & Microbe 5, April 23, 2009

11

12

13 Rationale Despite circulating throughout Africa and Asia for the latter half of the 20th century, ZIKV infections were not associated with significant human pathology until now. It has been hypothesized that the virus may have recently evolved to become more neurotropic, to exhibit increased replicative capacity, and/or to become more transmissible to humans.

14 Methods Phylogenetic and genetic analyses, as well as targeted structural modeling, on all known full-length ORFs of ZIKV available to date (with an emphasis on the recent human strains). Nucleotide sequences from 41 strains were included in the analysis: 30 human isolates (including two newly reported here), ten mosquito isolates, and one monkey isolate.

15 HUMAN 2007 Malaysia outbreak MOSQUITO 2007 Micronesia outbreak 2012 French Polynesia 2014/2015 Brasil/ Caribbean / South America 2014/2015 Brasil/ Caribbean / South America

16

17 Phylogenetic tree constructed from nucleotide data from 41 viral complete ORF sequences of ZIKV strains by the maximum-likelihood-method logarithm in MEGA7 based on the Tamura-Nei model. Strains isolated from human, mosquito, and monkey (NIH reference strain) were labeled with blue, orange, and black circles, respectively. The two subtypes were labeled on the right side of the tree. The new strains Rio-U1 and Rio-S1 were highlighted using (*). All contemporary human isolates share a common ancestor with the P6-740 strain isolated from Aedes aegypti mosquito Common ancestor?

18 Fetal brain Amniotic Urine pregnant Saliva There were 15, 13, 16, and 15 nucleotide changes in Natal_RGN, ZKV2015, Rio-U1, and Rio-S1, respectively. NOT REALLY Graphical representation of unique nucleotide mutations (blue circle) in Natal_RGN, ZKV2015, Rio-U1, and Rio-S1 strains among all (29 total) current human strains within Asian lineage by using pairwise comparisons. Nucleotide alignments were made using MUSCLE from ViPR. Alignment comparisons were made using Jal view V2.9.

19

20 2007 Malaysia 2013 French Pol South America FSM (Micronesia 2007) (comp with P6-740) had over 400 variations at the nucleotide level and 26 unique substitutions at the protein level. FSM, H/PF/2013, and Brazilian strains: have acquired changes at an additional eight positions, for a total of 34 amino acid changes compared to P6-740 (Figure 2B). Furthermore, all isolates show identical amino acids at these positions, with the exception of position T2634M/V in the NS5 protein.

21 Results All contemporary human isolates share a common ancestor with the P6-740 strain isolated from Aedes aegypti mosquito Sequences (including FSM, H/PF/2013, and Brazilian strains): acquired changes at an additional eight positions, for a total of 34 amino acid changes compared to P Furthermore, all isolates show identical amino acids at these positions, with the exception of position T2634M/V in the NS5 protein. Specific aa substitutions: NOT SHOWN IN THE TABLES Natal_RGN: K940E; M1143V and T1027A in NS1, and T2509I in NS4B. ZKV2015: S550T in E, L1259F in NS2A, and E2831V in NS5. Rio-U1: K2039R in NS3. Rio-S1: T625A in E, A2122T in NS4A, and V2688A in NS5.

22 PrM protein of ZIKV shows significant structural alterations The N and C termini of the structures were labeled with letters. The differences between these two virus strains were shown in sticks % and 50.55% primary sequence identity with the ZIKV PrM proteins from Rio-U1 and ARB13565

23 Thoughts The pr region of prm protein had the highest percentage variability between the Asian human and the African mosquito subtypes. Six of the 59 (10%) amino acid variations between these subtypes, namely I110V, K143E, A148P, V153M, H157Y, and V158I, were in the pr region of prm. Structural predictions based on the DENV 1 pr protein (PDB: 4b03) showed significant differences between Rio-U1 and ARB A148P could possibly play a critical role in mediating a ten-amino-acid structural change from a loop into a continuous b sheet. This change was only present in human isolates from both lineages, which suggests a potential relevance in human infectivity.

24 Low-pH environment (maturation): viral surface proteins drastic conformational rearrangement due to dissociation of prm- E, formation of E homodimers, and exposure of the prm cleavage site to furin protease to the extracellular area. Immature viral particles translocate from the ER to the highly acidic environment of the trans-golgi network where they are packaged into exosomes Zhang, et al. (2012). J. Biol. Chem. 287, PrM forms a heterodimer with the main viral surface protein, E, in the neutral ph of the lumen of the endoplasmic reticulum (ER).

25 Isolation of virus in the fetus brain: placenta infection? CDC report showing evidence between birth defects and the virus infection

26

27 Science, April 2016 Number of airline passengers from specific countries arriving in Brazil per month versus number of suspected cases of ZIKV in French Polynesia. The blue curve (left y axis) shows a polynomial fitting of the number of travelers (blue points) from countries with recorded ZIKV outbreaks between 2012 and 2015 (French Polynesia, Thailand, Indonesia, Malaysia, Cambodia, and New Caledonia) (supplementary materials section 6), aggregated across 20 Brazilian national airports. The purple bars represent weekly numbers of suspected ZIKV cases (right y axis) in French Polynesia (FP) from 30 October 2013 to 14 February 2014.

28 Last 24 hours

29 NATURE Yesterday

30 Final message Thank you!