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Nat Microbiol. 2019 Mar 18. doi: 10.1038/s41564-019-0399-4. [Epub ahead of print]

Determinants of Zika virus host tropism uncovered by deep mutational scanning.

Author information

1
Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia. y.setoh@uq.edu.au.
2
Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia.
3
Australian Institute for Bioengineering and Nanotechnology, UQ stemCARE, University of Queensland, St Lucia, Queensland, Australia.
4
Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
5
Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan.
6
Department of Applied Biological Chemistry, School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan.
7
Inflammation Biology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
8
Research Computing Centre, University of Queensland, St Lucia, Queensland, Australia.
9
Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
10
Howard Hughes Medical Institute, Seattle WA, USA.
11
Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia. alexander.khromykh@uq.edu.au.

Abstract

Arboviruses cycle between, and replicate in, both invertebrate and vertebrate hosts, which for Zika virus (ZIKV) involves Aedes mosquitoes and primates1. The viral determinants required for replication in such obligate hosts are under strong purifying selection during natural virus evolution, making it challenging to resolve which determinants are optimal for viral fitness in each host. Herein we describe a deep mutational scanning (DMS) strategy2-5 whereby a viral cDNA library was constructed containing all codon substitutions in the C-terminal 204‚ÄČamino acids of ZIKV envelope protein (E). The cDNA library was transfected into C6/36 (Aedes) and Vero (primate) cells, with subsequent deep sequencing and computational analyses of recovered viruses showing that substitutions K316Q and S461G, or Q350L and T397S, conferred substantial replicative advantages in mosquito and primate cells, respectively. A 316Q/461G virus was constructed and shown to be replication-defective in mammalian cells due to severely compromised virus particle formation and secretion. The 316Q/461G virus was also highly attenuated in human brain organoids, and illustrated utility as a vaccine in mice. This approach can thus imitate evolutionary selection in a matter of days and identify amino acids key to the regulation of virus replication in specific host environments.

PMID:
30886357
DOI:
10.1038/s41564-019-0399-4

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