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Sabir AJ, Singh PP, Trus I, Le NPK, Karniychuk U. Asian Zika virus can acquire generic African-lineage mutations during in utero infection. Emerg Microbes Infect 2023; 12:2263592. [PMID: 37747060 PMCID: PMC10561574 DOI: 10.1080/22221751.2023.2263592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
The Zika virus 2015 epidemic showed an unusual phenotype for human flaviviruses, specifically fetal infection. We previously showed that in utero inoculation with the Asian Zika virus isolated from the human sample causes persistent infection in porcine fetuses. Here, we characterized the evolution of the Asian Zika virus in the fetal brain and placenta. Interestingly, the Asian Zika virus acquired generic African lineage K101R (A408G) and R1609 K (G4932A) mutations during in utero infection. Both African mutations were nonsynonymous and had a high frequency of nearly 100% in the fetal brain. Then, we synthetically generated the wild-type Asian variant and fetal brain-specific variant with generic African-lineage K101R and R1609 K mutations. In mosquito C6/36 cells, but not in human and pig cells, the fetal brain-specific variant showed higher virus loads compared to the Asian wild-type prototype. While in utero infection with both variants caused comparable virus loads in the placenta and amniotic fluids, fetuses injected with the fetal brain-specific variant had the trend to higher virus loads in lymph nodes. Also, introduced K101R and R1609 K mutations were stable and had high nearly 100% frequency at 28 days after in utero inoculation in both directly injected and trans-infected fetuses. These findings evoke concerns because Zika persists in pig herds and mosquitoes on farms in Mexico. It will be essential to identify how persistent in utero infection affects virus evolution and whether in utero-emerged Zika variants have the potential for shedding into the environment, more efficient transmission, and more aggressive infection phenotypes.
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Affiliation(s)
- Ahmad Jawad Sabir
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Canada
| | - Prince Pal Singh
- School of Public Health, University of Saskatchewan, Saskatoon, Canada
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Ivan Trus
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Nguyen Phuong Khanh Le
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Uladzimir Karniychuk
- School of Public Health, University of Saskatchewan, Saskatoon, Canada
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
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Evans AB, Winkler CW, Anzick SL, Ricklefs SM, Sturdevant DE, Peterson KE. Zika virus diversity in mice is maintained during early vertical transmission from placenta to fetus, but reduced in fetal bodies and brains at late stages of infection. PLoS Negl Trop Dis 2023; 17:e0011657. [PMID: 37796973 PMCID: PMC10581492 DOI: 10.1371/journal.pntd.0011657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/17/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023] Open
Abstract
Since emerging in French Polynesia and Brazil in the 2010s, Zika virus (ZIKV) has been associated with fetal congenital disease. Previous studies have compared ancestral and epidemic ZIKV strains to identify strain differences that may contribute to vertical transmission and fetal disease. However, within-host diversity in ZIKV populations during vertical transmission has not been well studied. Here, we used the established anti-interferon treated Rag1-/- mouse model of ZIKV vertical transmission to compare genomic variation within ZIKV populations in matched placentas, fetal bodies, and fetal brains via RNASeq. At early stages of vertical transmission, the ZIKV populations in the matched placentas and fetal bodies were similar. Most ZIKV single nucleotide variants were present in both tissues, indicating little to no restriction in transmission of ZIKV variants from placenta to fetus. In contrast, at later stages of fetal infection there was a sharp reduction in ZIKV diversity in fetal bodies and fetal brains. All fetal brain ZIKV populations were comprised of one of two haplotypes, containing either a single variant or three variants together, as largely homogenous populations. In most cases, the dominant haplotype present in the fetal brain was also the dominant haplotype present in the matched fetal body. However, in two of ten fetal brains the dominant ZIKV haplotype was undetectable or present at low frequencies in the matched placenta and fetal body ZIKV populations, suggesting evidence of a strict selective bottleneck and possible selection for certain variants during neuroinvasion of ZIKV into fetal brains.
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Affiliation(s)
- Alyssa B. Evans
- Laboratory of Neurological Infections and Immunity, Neuroimmunology Section; Rocky Mountain Laboratories; National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH); Hamilton, Montana, United States of America
| | - Clayton W. Winkler
- Laboratory of Neurological Infections and Immunity, Neuroimmunology Section; Rocky Mountain Laboratories; National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH); Hamilton, Montana, United States of America
| | - Sarah L. Anzick
- Genomics Research Section, Research Technologies Branch; Rocky Mountain Laboratories; National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH); Hamilton, Montana, United States of America
| | - Stacy M. Ricklefs
- Genomics Research Section, Research Technologies Branch; Rocky Mountain Laboratories; National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH); Hamilton, Montana, United States of America
| | - Dan E. Sturdevant
- Genomics Research Section, Research Technologies Branch; Rocky Mountain Laboratories; National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH); Hamilton, Montana, United States of America
| | - Karin E. Peterson
- Laboratory of Neurological Infections and Immunity, Neuroimmunology Section; Rocky Mountain Laboratories; National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH); Hamilton, Montana, United States of America
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Chan KWK, Bifani AM, Watanabe S, Choy MM, Ooi EE, Vasudevan SG. Tissue-specific expansion of Zika virus isogenic variants drive disease pathogenesis. EBioMedicine 2023; 91:104570. [PMID: 37068347 PMCID: PMC10130475 DOI: 10.1016/j.ebiom.2023.104570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/09/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The Asian lineage Zika virus (ZIKV) emerged as a public health emergency in 2016 causing severe neurological pathologies with no apparent historical correlate to the mild, disease-causing innocuous member of the mosquito-borne flavivirus genus that was discovered in Africa in 1947. Replication error rate of RNA viruses combined with viral protein/RNA structural plasticity can lead to evolution of virus-induced pathogenicity that is critical to identify and validate. METHODS Infection studies in cells and A129 interferon alpha/beta receptor deficient mice with ZIKV French Polynesian H/PF/2013 clinical isolate, plaque-purified isogenic clone derivatives as well as infectious cDNA clone derived wild-type and site-specific mutant viruses, were employed together with Next-Generation Sequencing (NGS) to pin-point the contributions of specific viral variants in neurovirulence recapitulated in our ZIKV mouse model. FINDINGS NGS analysis of the low-passage inoculum virus as well as mouse serum, brain and testis derived virus, revealed specific enrichment in the mouse brain that were not found in the other tissues. Specifically, non-structural (NS) protein 2A variant at position 117 along with changes in NS1 and NS4B were uniquely associated with the mouse brain isolate. Mutational analysis of these variants in cDNA infectious clones identified the NS2A A117V as the lethal pathogenic determinant with potential epistatic contribution of NS1 and NS4B variants in ZIKV brain penetrance. INTERPRETATION Our findings confirm that viral subpopulations drive ZIKV neuropathogenicity and identify specific sequence variants that expand in the mouse brain that associates with this phenotype which can serve as predictors of severe epidemics. FUNDING Duke-NUS Khoo Post-doctoral Fellowship Award 2020 (KWKC) and National Medical Research Council of Singapore grants MOH-000524 (OFIRG) (SW) and MOH-OFIRG20nov-0002 (SGV).
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Affiliation(s)
- Kitti Wing Ki Chan
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Amanda Makha Bifani
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Satoru Watanabe
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Milly M Choy
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore; Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, 117545, Singapore.
| | - Subhash G Vasudevan
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore; Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, 117545, Singapore; Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, 4222, Australia.
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Regla-Nava JA, Wang YT, Fontes-Garfias CR, Liu Y, Syed T, Susantono M, Gonzalez A, Viramontes KM, Verma SK, Kim K, Landeras-Bueno S, Huang CT, Prigozhin DM, Gleeson JG, Terskikh AV, Shi PY, Shresta S. A Zika virus mutation enhances transmission potential and confers escape from protective dengue virus immunity. Cell Rep 2022; 39:110655. [PMID: 35417697 PMCID: PMC9093040 DOI: 10.1016/j.celrep.2022.110655] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/08/2022] [Accepted: 03/18/2022] [Indexed: 12/14/2022] Open
Abstract
Zika virus (ZIKV) and dengue virus (DENV) are arthropod-borne pathogenic flaviviruses that co-circulate in many countries. To understand some of the pressures that influence ZIKV evolution, we mimic the natural transmission cycle by repeating serial passaging of ZIKV through cultured mosquito cells and either DENV-naive or DENV-immune mice. Compared with wild-type ZIKV, the strains passaged under both conditions exhibit increased pathogenesis in DENV-immune mice. Application of reverse genetics identifies an isoleucine-to-valine mutation (I39V) in the NS2B proteins of both passaged strains that confers enhanced fitness and escape from pre-existing DENV immunity. Introduction of I39V or I39T, a naturally occurring homologous mutation detected in recent ZIKV isolates, increases the replication of wild-type ZIKV in human neuronal precursor cells and laboratory-raised mosquitoes. Our data indicate that ZIKV strains with enhanced transmissibility and pathogenicity can emerge in DENV-naive or -immune settings, and that NS2B-I39 mutants may represent ZIKV variants of interest.
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Affiliation(s)
- Jose Angel Regla-Nava
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Ying-Ting Wang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Camila R Fontes-Garfias
- Department of Biochemistry and Molecular Biology, Sealy Institute for Drug Discovery, Department of Pharmacology and Toxicology and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, Sealy Institute for Drug Discovery, Department of Pharmacology and Toxicology and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Thasneem Syed
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Mercylia Susantono
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Andrew Gonzalez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Karla M Viramontes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Shailendra Kumar Verma
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kenneth Kim
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Sara Landeras-Bueno
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Chun-Teng Huang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, Rady Children's Institute of Genomic Medicine, Department of Neurosciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Alexey V Terskikh
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, Sealy Institute for Drug Discovery, Department of Pharmacology and Toxicology and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
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Structurally conserved domains between flavivirus and alphavirus fusion glycoproteins contribute to replication and infectious virion production. J Virol 2021; 96:e0177421. [PMID: 34757841 DOI: 10.1128/jvi.01774-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Alphaviruses and flaviviruses have class II fusion glycoproteins that are essential for virion assembly and infectivity. Importantly, the tip of domain II is structurally conserved between the alphavirus and flavivirus fusion proteins, yet whether these structural similarities between virus families translate to functional similarities is unclear. Using in vivo evolution of Zika virus (ZIKV), we identified several novel emerging variants including an envelope glycoprotein variant in β-strand c (V114M) of domain II. We have previously shown that the analogous β-strand c and the ij loop, located in the tip of domain II of the alphavirus E1 glycoprotein, are important for infectivity. This led us to hypothesize that flavivirus E β-strand c also contributes to flavivirus infection. We generated this ZIKV glycoprotein variant and found that while it had little impact on infection in mosquitoes, it reduced replication in human cells and mice, and increased virus sensitivity to ammonium chloride, as seen for alphaviruses. In light of these results and given our alphavirus ij loop studies, we mutated a conserved alanine at the tip of the flavivirus ij loop to valine to test its effect on ZIKV infectivity. Interestingly, this mutation inhibited infectious virion production of ZIKV and yellow fever virus, but not West Nile virus. Together, these studies show that shared domains of the alphavirus and flavivirus class II fusion glycoproteins harbor structurally analogous residues that are functionally important and contribute to virus infection in vivo. Importance Arboviruses are a significant global public health threat, yet there are no antivirals targeting these viruses. This problem is in part due to our lack of knowledge on the molecular mechanisms involved in the arbovirus life cycle. In particular, virus entry and assembly are essential processes in the virus life cycle and steps that can be targeted for the development of antiviral therapies. Therefore, understanding common, fundamental mechanisms used by different arboviruses for entry and assembly is essential. In this study, we show that flavivirus and alphavirus residues located in structurally conserved and analogous regions of the class II fusion proteins contribute to common mechanisms of entry, dissemination, and infectious virion production. These studies highlight how class II fusion proteins function and provide novel targets for development of antivirals.
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Udenze D, Trus I, Munyanduki H, Berube N, Karniychuk U. The Isolated in Utero Environment Is Conducive to the Emergence of RNA and DNA Virus Variants. Viruses 2021; 13:v13091827. [PMID: 34578408 PMCID: PMC8473323 DOI: 10.3390/v13091827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/06/2021] [Accepted: 09/11/2021] [Indexed: 01/04/2023] Open
Abstract
The host’s immune status may affect virus evolution. Little is known about how developing fetal and placental immune milieus affect virus heterogeneity. This knowledge will help us better understand intra-host virus evolution and how new virus variants emerge. The goal of our study was to find out whether the isolated in utero environment—an environment with specialized placental immunity and developing fetal immunity—supports the emergence of RNA and DNA virus variants. We used well-established porcine models for isolated Zika virus (RNA virus) and porcine circovirus 2 (DNA virus) fetal infections. We found that the isolated in utero environment was conducive to the emergence of RNA and DNA virus variants. Next-generation sequencing of nearly whole virus genomes and validated bioinformatics pipelines identified both unique and convergent single nucleotide variations in virus genomes isolated from different fetuses. Zika virus and PCV2 in utero evolution also resulted in single nucleotide variations previously reported in the human and porcine field samples. These findings should encourage further studies on virus evolution in placenta and fetuses, to better understand how virus variants emerge and how in utero viral evolution affects congenital virus transmission and pathogenicity.
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Affiliation(s)
- Daniel Udenze
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (D.U.); (I.T.); (H.M.); (N.B.)
- School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 2Z4, Canada
| | - Ivan Trus
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (D.U.); (I.T.); (H.M.); (N.B.)
| | - Henry Munyanduki
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (D.U.); (I.T.); (H.M.); (N.B.)
| | - Nathalie Berube
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (D.U.); (I.T.); (H.M.); (N.B.)
| | - Uladzimir Karniychuk
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (D.U.); (I.T.); (H.M.); (N.B.)
- School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 2Z4, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Correspondence: ; Tel.: +1-306-966-5510
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