1
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Marano JM, Weger-Lucarelli J. Preexisting inter-serotype immunity drives antigenic evolution of dengue virus serotype 2. Virology 2024; 590:109951. [PMID: 38096749 PMCID: PMC10855010 DOI: 10.1016/j.virol.2023.109951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/10/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
Dengue virus (DENV) infects roughly 400 million people annually, causing febrile and hemorrhagic disease. While preexisting inter-serotype immunity (PISI) provides transient protection, it may drive severe disease over time. PISI's impact on virus evolution, however, is less understood. Retrospective epidemiological analyses suggest that PISI may drive DENV evolution. Using in vitro directed evolution, we explored how DENV2 evolves in the presence of DENV3/4 convalescent serum. Two post-passaging mutations (E-I6M and E-N203D) were then studied for fitness effects in mammalian and insect hosts and immune escape. E-I6M resisted neutralization, altered fitness in mammalian cell culture models, and had no effect in Aedes albopictus mosquitoes. E-N203D showed no change in neutralization sensitivity, reduced fitness in a DENV-naïve epithelial model, and no effects in the other models. These results align with surveillance data, where E-I6M emerged and disappeared, while E-203D and E-203 N cocirculate, thus suggesting that PISI can drive DENV evolution.
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Affiliation(s)
- Jeffrey M Marano
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, United States; Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States.
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2
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Xia H, Yeung J, Kalveram B, Bills CJ, Chen JYC, Kurhade C, Zou J, Widen SG, Mann BR, Kondor R, Davis CT, Zhou B, Wentworth DE, Xie X, Shi PY. Cross-neutralization and viral fitness of SARS-CoV-2 Omicron sublineages. Emerg Microbes Infect 2023; 12:e2161422. [PMID: 36594261 PMCID: PMC9848280 DOI: 10.1080/22221751.2022.2161422] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The rapid evolution of SARS-CoV-2 Omicron sublineages mandates a better understanding of viral replication and cross-neutralization among these sublineages. Here we used K18-hACE2 mice and primary human airway cultures to examine the viral fitness and antigenic relationship among Omicron sublineages. In both K18-hACE2 mice and human airway cultures, Omicron sublineages exhibited a replication order of BA.5 ≥ BA.2 ≥ BA.2.12.1 > BA.1; no difference in body weight loss was observed among different sublineage-infected mice. The BA.1-, BA.2-, BA.2.12.1-, and BA.5-infected mice developed distinguishable cross-neutralizations against Omicron sublineages, but exhibited little neutralization against the index virus (i.e. USA-WA1/2020) or the Delta variant. Surprisingly, the BA.5-infected mice developed higher neutralization activity against heterologous BA.2 and BA.2.12.1 than that against homologous BA.5; serum neutralizing titres did not always correlate with viral replication levels in infected animals. Our results revealed a distinct antigenic cartography of Omicron sublineages and support the bivalent vaccine approach.
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Affiliation(s)
- Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jason Yeung
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Birte Kalveram
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Cody J. Bills
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - John Yun-Chung Chen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Steven G. Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Brian R. Mann
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rebecca Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - C. Todd Davis
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bin Zhou
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - David E. Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA, Xuping Xie ; Pei-Yong Shi
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA,Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA,Sealy, Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA,Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA,Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA,Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
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3
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Liu LB, Yang W, Chang JT, Fan DY, Wu YH, Wang PG, An J. Zika virus infection leads to hormone deficiencies of the hypothalamic-pituitary-gonadal axis and diminished fertility in mice. J Virol 2023; 97:e0100623. [PMID: 37732785 PMCID: PMC10617514 DOI: 10.1128/jvi.01006-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/03/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Zika virus (ZIKV) infection in pregnant women during the third trimester can cause neurodevelopmental delays and cryptorchidism in children without microcephaly. However, the consequences of congenital ZIKV infection on fertility in these children remain unclear. Here, using an immunocompetent mouse model, we reveal that congenital ZIKV infection can cause hormonal disorders of the hypothalamic-pituitary-gonadal axis, leading to reduced fertility and decreased sexual preference. Our study has for the first time linked the hypothalamus to the reproductive system and social behaviors after ZIKV infection. Although the extent to which these observations in mice translate to humans remains unclear, these findings did suggest that the reproductive health and hormone levels of ZIKV-exposed children should receive more attention to improve their living quality.
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Affiliation(s)
- Li-Bo Liu
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Wei Yang
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
- Department of Neurosurgery, Capital Medical University Sanbo Brain Hospital, Beijing, China
| | - Jia-Tong Chang
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Dong-Ying Fan
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yan-Hua Wu
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Pei-Gang Wang
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jing An
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
- Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing, China
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4
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Campos RK, Rossi SL, Tesh RB, Weaver SC. Zoonotic mosquito-borne arboviruses: Spillover, spillback, and realistic mitigation strategies. Sci Transl Med 2023; 15:eadj2166. [PMID: 37851824 PMCID: PMC10807030 DOI: 10.1126/scitranslmed.adj2166] [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] [Indexed: 10/20/2023]
Abstract
Emerging zoonotic mosquito-borne viruses pose increasing health threats because of growing mosquito population, geographic expansions, and control challenges. We emphasize the need for global preparedness to effectively mitigate the health, societal, and economic impacts of spillover by these viruses through proactive measures of prediction, surveillance, prevention, and treatment.
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Affiliation(s)
- Rafael K. Campos
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shannan L. Rossi
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | - Robert B. Tesh
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, USA
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5
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Bayandin RB, Makenov MT, Boumbaly S, Stukolova OA, Gladysheva AV, Shipovalov AV, Skarnovich MO, Camara O, Toure AH, Svyatchenko VA, Shvalov AN, Ternovoi VA, Boiro MY, Agafonov AP, Karan LS. The First Case of Zika Virus Disease in Guinea: Description, Virus Isolation, Sequencing, and Seroprevalence in Local Population. Viruses 2023; 15:1620. [PMID: 37631963 PMCID: PMC10459603 DOI: 10.3390/v15081620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
The Zika virus (ZIKV) is a widespread mosquito-borne pathogen. Phylogenetically, two lineages of ZIKV are distinguished: African and Asian-American. The latter became the cause of the 2015-2016 pandemic, with severe consequences for newborns. In West African countries, the African lineage was found, but there is evidence of the emergence of the Asian-American lineage in Cape Verde and Angola. This highlights the need to not only monitor ZIKV but also sequence the isolates. In this article, we present a case report of Zika fever in a pregnant woman from Guinea identified in 2018. Viral RNA was detected through qRT-PCR in a serum sample. In addition, the seroconversion of anti-Zika IgM and IgG antibodies was detected in repeated blood samples. Subsequently, the virus was isolated from the C6/36 cell line. The detected ZIKV belonged to the African lineage, the Nigerian sublineage. The strains with the closest sequences were isolated from mosquitoes in Senegal in 2011 and 2015. In addition, we conducted the serological screening of 116 blood samples collected from patients presenting to the hospital of Faranah with fevers during the period 2018-2021. As a result, it was found that IgM-positive patients were identified each year and that the seroprevalence varied between 5.6% and 17.1%.
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Affiliation(s)
- Roman B. Bayandin
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Novosibirsk Oblast, Russia (M.O.S.)
| | - Marat T. Makenov
- Central Research Institute of Epidemiology, Novogireevskaya St. 3A, 111123 Moscow, Russia
| | - Sanaba Boumbaly
- Virology Research Center/Laboratory of Viral Hemorrhagic Fevers, Conakry, Guinea
| | - Olga A. Stukolova
- Central Research Institute of Epidemiology, Novogireevskaya St. 3A, 111123 Moscow, Russia
| | - Anastasia V. Gladysheva
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Novosibirsk Oblast, Russia (M.O.S.)
| | - Andrey V. Shipovalov
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Novosibirsk Oblast, Russia (M.O.S.)
| | - Maksim O. Skarnovich
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Novosibirsk Oblast, Russia (M.O.S.)
| | | | - Aboubacar Hady Toure
- Research Institute of Applied Biology of Guinea, Pastoria, CREMS, Kindia, Guinea
| | - Victor A. Svyatchenko
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Novosibirsk Oblast, Russia (M.O.S.)
| | - Alexander N. Shvalov
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Novosibirsk Oblast, Russia (M.O.S.)
| | - Vladimir A. Ternovoi
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Novosibirsk Oblast, Russia (M.O.S.)
| | - Mamadou Y. Boiro
- Research Institute of Applied Biology of Guinea, Pastoria, CREMS, Kindia, Guinea
| | - Alexander P. Agafonov
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Novosibirsk Oblast, Russia (M.O.S.)
| | - Lyudmila S. Karan
- Central Research Institute of Epidemiology, Novogireevskaya St. 3A, 111123 Moscow, Russia
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6
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Lu AY, Gustin A, Newhouse D, Gale M. Viral Protein Accumulation of Zika Virus Variants Links with Regulation of Innate Immunity for Differential Control of Viral Replication, Spread, and Response to Interferon. J Virol 2023; 97:e0198222. [PMID: 37162358 PMCID: PMC10231147 DOI: 10.1128/jvi.01982-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/13/2023] [Indexed: 05/11/2023] Open
Abstract
Asian lineage Zika virus (ZIKV) strains emerged globally, causing outbreaks linked with critical clinical disease outcomes unless the virus is effectively restricted by host immunity. We have previously shown that retinoic acid-inducible gene-I (RIG-I) senses ZIKV to trigger innate immunity to direct interferon (IFN) production and antiviral responses that can control ZIKV infection. However, ZIKV proteins have been demonstrated to antagonize IFN. Here, we conducted in vitro analyses to assess how divergent prototypic ZIKV variants differ in virologic properties, innate immune regulation, and infection outcome. We comparatively assessed African lineage ZIKV/Dakar/1984/ArD41519 (ZIKV/Dakar) and Asian lineage ZIKV/Malaysia/1966/P6740 (ZIKV/Malaysia) in a human epithelial cell infection model. De novo viral sequence determination identified amino acid changes within the ZIKV/Dakar genome compared to ZIKV/Malaysia. Viral growth analyses revealed that ZIKV/Malaysia accumulated viral proteins and genome copies earlier and to higher levels than ZIKV/Dakar. Both ZIKV strains activated RIG-I/IFN regulatory factor (IRF3) and NF-κB pathways to induce inflammatory cytokine expression and types I and III IFNs. However, ZIKV/Malaysia, but not ZIKV/Dakar, potently blocked downstream IFN signaling. Remarkably, ZIKV/Dakar protein accumulation and genome replication were rescued in RIG-I knockout (KO) cells late in acute infection, resulting in ZIKV/Dakar-mediated blockade of IFN signaling. We found that RIG-I signaling specifically restricts viral protein accumulation late in acute infection where early accumulation of viral proteins in infected cells confers enhanced ability to limit IFN signaling, promoting viral replication and spread. Our results demonstrate that RIG-I-mediated innate immune signaling imparts restriction of ZIKV protein accumulation, which permits IFN signaling and antiviral actions controlling ZIKV infection. IMPORTANCE ZIKV isolates are classified under African or Asian lineages. Infection with emerging Asian lineage-derived ZIKV strains is associated with increased incidence of neurological symptoms that were not previously reported during infection with African or preemergent Asian lineage viruses. In this study, we utilized in vitro models to compare the virologic properties of and innate immune responses to two prototypic ZIKV strains from distinct lineages: African lineage ZIKV/Dakar and Asian lineage ZIKV/Malaysia. Compared to ZIKV/Dakar, ZIKV/Malaysia accumulates viral proteins earlier, replicates to higher levels, and robustly blocks IFN signaling during acute infection. Early accumulation of ZIKV/Malaysia NS5 protein confers enhanced ability to antagonize IFN signaling, dampening innate immune responses to promote viral spread. Our data identify the kinetics of viral protein accumulation as a major regulator of host innate immunity, influencing host-mediated control of ZIKV replication and spread. Importantly, these findings provide a novel framework for evaluating the virulence of emerging variants.
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Affiliation(s)
- Amy Y. Lu
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Andrew Gustin
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Daniel Newhouse
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
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7
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Bills CJ, Xia H, Chen JYC, Yeung J, Kalveram B, Walker D, Xie X, Shi PY. Mutations in SARS-CoV-2 variant nsp6 enhance type-I interferon antagonism. Emerg Microbes Infect 2023; 12:2209208. [PMID: 37114433 PMCID: PMC10184609 DOI: 10.1080/22221751.2023.2209208] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve after its emergence. Given its importance in viral infection and vaccine development, mutations in the viral Spike gene have been studied extensively; however, the impact of mutations outside the Spike gene are poorly understood. Here, we report that a triple deletion (ΔSGF or ΔLSG) in nonstructural protein 6 (nsp6) independently acquired in Alpha and Omicron sublineages of SARS-CoV-2 augments nsp6-mediated antagonism of type-I interferon (IFN-I) signaling. Specifically, these triple deletions enhance the ability of mutant nsp6 to suppress phosphorylation of STAT1 and STAT2. A parental SARS-CoV-2 USA-WA1/2020 strain containing the nsp6 ΔSGF deletion (ΔSGF-WA1) shows reduced susceptibility to IFN-I treatment in vitro, outcompetes the parental strain in human primary airway cultures, and increases virulence in mice; however, the ΔSGF-WA1 virus is less virulent than the Alpha variant (which has the nsp6 ΔSGF deletion and additional mutations in other genes). Analyses of host responses from ΔSGF-WA1-infected mice and primary airway cultures reveal activation of pathways indicative of a cytokine storm. These results provide evidence that mutations outside the Spike protein affect virus-host interactions and may alter pathogenesis of SARS-CoV-2 variants in humans.
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Affiliation(s)
- Cody J Bills
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - John Yun-Chung Chen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jason Yeung
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Birte Kalveram
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - David Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
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8
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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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9
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Marano JM, Weger-Lucarelli J. Replication in the presence of dengue convalescent serum impacts Zika virus neutralization sensitivity and fitness. Front Cell Infect Microbiol 2023; 13:1130749. [PMID: 36968111 PMCID: PMC10034770 DOI: 10.3389/fcimb.2023.1130749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
Introduction Flaviviruses like dengue virus (DENV) and Zika virus (ZIKV) are mosquito-borne viruses that cause febrile, hemorrhagic, and neurological diseases in humans, resulting in 400 million infections annually. Due to their co-circulation in many parts of the world, flaviviruses must replicate in the presence of pre-existing adaptive immune responses targeted at serologically closely related pathogens, which can provide protection or enhance disease. However, the impact of pre-existing cross-reactive immunity as a driver of flavivirus evolution, and subsequently the implications on the emergence of immune escape variants, is poorly understood. Therefore, we investigated how replication in the presence of convalescent dengue serum drives ZIKV evolution. Methods We used an in vitro directed evolution system, passaging ZIKV in the presence of serum from humans previously infected with DENV (anti-DENV) or serum from DENV-naïve patients (control serum). Following five passages in the presence of serum, we performed next-generation sequencing to identify mutations that arose during passaging. We studied two non-synonymous mutations found in the anti-DENV passaged population (E-V355I and NS1-T139A) by generating individual ZIKV mutants and assessing fitness in mammalian cells and live mosquitoes, as well as their sensitivity to antibody neutralization. Results and discussion Both viruses had increased fitness in Vero cells with and without the addition of anti-DENV serum and in human lung epithelial and monocyte cells. In Aedes aegypti mosquitoes-using blood meals with and without anti-DENV serum-the mutant viruses had significantly reduced fitness compared to wild-type ZIKV. These results align with the trade-off hypothesis of constrained mosquito-borne virus evolution. Notably, only the NS1-T139A mutation escaped neutralization, while E-V335I demonstrated enhanced neutralization sensitivity to neutralization by anti-DENV serum, indicating that neutralization escape is not necessary for viruses passaged under cross-reactive immune pressures. Future studies are needed to assess cross-reactive immune selection in humans and relevant animal models or with different flaviviruses.
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Affiliation(s)
- Jeffrey M. Marano
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, United States
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
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10
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Li QH, Kim K, Shresta S. Mouse models of Zika virus transplacental transmission. Antiviral Res 2023; 210:105500. [PMID: 36567026 PMCID: PMC9852097 DOI: 10.1016/j.antiviral.2022.105500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Seven years after the onset of the Zika virus (ZIKV) epidemic in the Americas, longitudinal studies are beginning to demonstrate that children infected in utero and born without severe birth defects exhibit motor skill deficits at up to 3 years of age. Long term health and socioeconomic impacts of fetal ZIKV infection appear imminent. ZIKV continues to circulate in low levels much as the virus did for decades prior to the 2015 epidemic, and the timing of the ZIKV outbreak is unknown. Thus, in the continued absence of ZIKV vaccines or antivirals, small animal models of ZIKV transplacental transmission have never been more necessary to test antiviral strategies for both mother and fetuses, and to elucidate mechanisms of immunity at the maternal-fetal interface. Here we review the state of ZIKV transplacental transmission models, highlight key unanswered questions, and set goals for the next generation of mouse models.
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Affiliation(s)
- Qin Hui Li
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Kenneth Kim
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
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11
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Zhang Y, Jiang N, Qi W, Li T, Zhang Y, Wu J, Zhang H, Zhou M, Cui P, Yu T, Fu Z, Zhou Y, Lin K, Wang H, Wei T, Zhu Z, Ai J, Qiu C, Zhang W. SARS-CoV-2 intra-host single-nucleotide variants associated with disease severity. Virus Evol 2022; 8:veac106. [PMID: 36505092 PMCID: PMC9728387 DOI: 10.1093/ve/veac106] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 10/24/2022] [Accepted: 11/26/2022] [Indexed: 11/30/2022] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 frequently arise within infected individuals. Here, we explored the level and pattern of intra-host viral diversity in association with disease severity. Then, we analyzed information underlying these nucleotide changes to infer the impetus including mutational signatures and immune selection from neutralizing antibody or T-cell recognition. From 23 January to 31 March 2020, a set of cross-sectional samples were collected from individuals with homogeneous founder virus regardless of disease severity. Intra-host single-nucleotide variants (iSNVs) were enumerated using deep sequencing. Human leukocyte antigen (HLA) alleles were genotyped by Sanger sequencing. Medical records were collected and reviewed by attending physicians. A total of 836 iSNVs (3-106 per sample) were identified and distributed in a highly individualized pattern. The number of iSNVs paced with infection duration peaked within days and declined thereafter. These iSNVs did not stochastically arise due to a strong bias toward C > U/G > A and U > C/A > G substitutions in reciprocal proportion with escalating disease severity. Eight nonsynonymous iSNVs in the receptor-binding domain could escape from neutralization, and eighteen iSNVs were significantly associated with specific HLA alleles. The level and pattern of iSNVs reflect the in vivo viral-host interaction and the disease pathogenesis.
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Affiliation(s)
| | | | | | | | - Yumeng Zhang
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jing Wu
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Haocheng Zhang
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Mingzhe Zhou
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Peng Cui
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Tong Yu
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhangfan Fu
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Yang Zhou
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Ke Lin
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Hongyu Wang
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Tongqing Wei
- State Key Laboratory of Genetic Engineering and Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
| | | | | | - Chao Qiu
- *Corresponding authors: E-mail: ; ; ;
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12
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Rochman ND, Wolf YI, Koonin EV. Molecular adaptations during viral epidemics. EMBO Rep 2022; 23:e55393. [PMID: 35848484 PMCID: PMC9346483 DOI: 10.15252/embr.202255393] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 07/20/2023] Open
Abstract
In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Yuri I Wolf
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Eugene V Koonin
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
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13
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Liu Y, Liu J, Johnson BA, Xia H, Ku Z, Schindewolf C, Widen SG, An Z, Weaver SC, Menachery VD, Xie X, Shi PY. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Cell Rep 2022; 39:110829. [PMID: 35550680 PMCID: PMC9050581 DOI: 10.1016/j.celrep.2022.110829] [Citation(s) in RCA: 149] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/28/2022] [Accepted: 04/26/2022] [Indexed: 01/28/2023] Open
Abstract
We report that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta spike mutation P681R plays a key role in the Alpha-to-Delta variant replacement during the coronavirus disease 2019 (COVID-19) pandemic. Delta SARS-CoV-2 efficiently outcompetes the Alpha variant in human lung epithelial cells and primary human airway tissues. The Delta spike mutation P681R is located at a furin cleavage site that separates the spike 1 (S1) and S2 subunits. Reverting the P681R mutation to wild-type P681 significantly reduces the replication of the Delta variant to a level lower than the Alpha variant. Mechanistically, the Delta P681R mutation enhances the cleavage of the full-length spike to S1 and S2, which could improve cell-surface-mediated virus entry. In contrast, the Alpha spike also has a mutation at the same amino acid (P681H), but the cleavage of the Alpha spike is reduced compared with the Delta spike. Our results suggest P681R as a key mutation in enhancing Delta-variant replication via increased S1/S2 cleavage.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Craig Schindewolf
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
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14
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Liu Y, Liu J, Johnson BA, Xia H, Ku Z, Schindewolf C, Widen SG, An Z, Weaver SC, Menachery VD, Xie X, Shi PY. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Cell Rep 2022. [PMID: 35550680 DOI: 10.1101/2021.08.12.456173v3.full] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
We report that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta spike mutation P681R plays a key role in the Alpha-to-Delta variant replacement during the coronavirus disease 2019 (COVID-19) pandemic. Delta SARS-CoV-2 efficiently outcompetes the Alpha variant in human lung epithelial cells and primary human airway tissues. The Delta spike mutation P681R is located at a furin cleavage site that separates the spike 1 (S1) and S2 subunits. Reverting the P681R mutation to wild-type P681 significantly reduces the replication of the Delta variant to a level lower than the Alpha variant. Mechanistically, the Delta P681R mutation enhances the cleavage of the full-length spike to S1 and S2, which could improve cell-surface-mediated virus entry. In contrast, the Alpha spike also has a mutation at the same amino acid (P681H), but the cleavage of the Alpha spike is reduced compared with the Delta spike. Our results suggest P681R as a key mutation in enhancing Delta-variant replication via increased S1/S2 cleavage.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Craig Schindewolf
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
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15
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Peng NYG, Amarilla AA, Hugo LE, Modhiran N, Sng JDJ, Slonchak A, Watterson D, Setoh YX, Khromykh AA. The distinguishing NS5-M114V mutation in American Zika virus isolates has negligible impacts on virus replication and transmission potential. PLoS Negl Trop Dis 2022; 16:e0010426. [PMID: 35536870 PMCID: PMC9122223 DOI: 10.1371/journal.pntd.0010426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 05/20/2022] [Accepted: 04/18/2022] [Indexed: 11/18/2022] Open
Abstract
During 2015–2016, outbreaks of Zika virus (ZIKV) occurred in Southeast Asia and the Americas. Most ZIKV infections in humans are asymptomatic, while clinical manifestation is usually a self-limiting febrile disease with maculopapular rash. However, ZIKV is capable of inducing a range of severe neurological complications collectively described as congenital Zika syndrome (CZS). Notably, the scale and magnitude of outbreaks in Southeast Asia were significantly smaller compared to those in the Americas. Sequence comparison between epidemic-associated ZIKV strains from Southeast Asia with those from the Americas revealed a methionine to valine substitution at residue position 114 of the NS5 protein (NS5-M114V) in all the American isolates. Using an American isolate of ZIKV (Natal), we investigated the impact of NS5-M114V mutation on virus replication in cells, virulence in interferon (IFN) α/β receptor knockout (Ifnar-/-) mice, as well as replication and transmission potential in Aedes aegypti mosquitoes. We demonstrated that NS5-M114V mutation had insignificant effect on ZIKV replication efficiency in cells, its ability to degrade STAT2, and virulence in vivo, albeit viremia was slightly prolonged in mice. Furthermore, NS5-M114V mutation decreased mosquito infection and dissemination rates but had no effect on virus secretion into the saliva. Taken together, our findings support the notion that NS5-M114V mutation is unlikely to be a major determinant for virus replication and transmission potential. Zika virus (ZIKV) emerged to cause outbreaks in Southeast Asia and the Americas during 2015–2016. However, the scale of outbreaks in Southeast Asia were significantly smaller compared to epidemic in the Americas. A methionine to valine amino acid mutation at residue position 114 of the NS5 protein (NS5-M114V) is hypothesized to influence the epidemic outcomes of ZIKV, which led to the large-scale epidemic that occurred in the Americas. By analyzing infection of mammalian and mosquito cells, IFNα/β receptor knockout (Ifnar-/-) mice and Aedes aegypti mosquitoes with engineered ZIKV isolates containing either methionine or valine at residue position 114 of the NS5 protein, we demonstrated that the NS5-M114V mutation did not affect virus replication efficiency and STAT2 degradation in cells, virulence in mice, or virus secretion into the mosquito saliva. The NS5-M114V mutation slightly prolonged viremia in Ifnar-/- mice and reduced mosquito infection rate. Collectively, our findings suggest that the NS5-M114V mutation is unlikely to have significantly influenced the ZIKV epidemic in the Americas.
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Affiliation(s)
- Nias Y. G. Peng
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Leon E. Hugo
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Queensland, Brisbane, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Julian D. J. Sng
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Andrii Slonchak
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Queensland, Brisbane, Australia
- * E-mail: (DW); (YXS); (AAK)
| | - Yin Xiang Setoh
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
- * E-mail: (DW); (YXS); (AAK)
| | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Queensland, Brisbane, Australia
- * E-mail: (DW); (YXS); (AAK)
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16
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Azarm A, Nasrabadi M, Shahidi F, Dehghan A, Nikpoor F, Zahraie-Ramazani A, Molaeezadeh SM, Bozorgomid F, Tashakori G, Vatandoost H. Insecticide Resistance in the West Nile Encephalitis, Japanese Encephalitis, Avian Malaria and Lymphatic Elephantiasis Vector, Culex pipiens complex (Diptera: Culicidae) in Iran. J Arthropod Borne Dis 2021; 15:349-357. [PMID: 36644301 PMCID: PMC9810576 DOI: 10.18502/jad.v15i4.10499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/22/2021] [Indexed: 01/18/2023] Open
Abstract
Background Culex pipiens complex is considered as a vector of some important diseases such as West Nile fever, equine encephalitis, Rift valley fever, St. Louis encephalitis, Elephanthiasis and avian malaria in the world. The main measure for vector control is using insecticides. High use of insecticides caused resistance in the populations. The aim of this study was to review the status of insecticide resistance in the vector. Methods Insecticide resistance in this species was found by the available papers and map of the data for carbamates, organochlorine, organophosphates, pyrethroids, microbial and insect growth regulator insecticides were done. An intensive search of scientific literature was done in "PubMed", "Web of Knowledge", "Scopus", "Google Scholar", "SID", and related resources. Results Results showed that a wide variety of resistance to different insecticides in the country. Due to importance of this species in transmission of diseases. Discussion resistance management strategies should be further considered to prevent from in secticide resistance and replacement of novel approach for vector control.
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Affiliation(s)
- Amrollah Azarm
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Nasrabadi
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Shahidi
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Awat Dehghan
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Fateme Nikpoor
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Zahraie-Ramazani
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyede Maryam Molaeezadeh
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Faramarz Bozorgomid
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghazal Tashakori
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Vatandoost
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran,Department of Environmental Chemical Pollutants and Pesticides, Institute for Environmental Research, Tehran University of Medical Sciences, Tehran, Iran,Corresponding author: Hassan Vatandoost, E-mail: ,
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17
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Lineage Divergence and Vector-Specific Adaptation Have Driven Chikungunya Virus onto Multiple Adaptive Landscapes. mBio 2021; 12:e0273821. [PMID: 34749526 PMCID: PMC8576524 DOI: 10.1128/mbio.02738-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have shown that the adaptation of Indian Ocean lineage (IOL) chikungunya virus (CHIKV) strains for Aedes albopictus transmission was mediated by an E1-A226V substitution, followed by either a single substitution in E2 or synergistic substitutions in the E2 and E3 envelope glycoproteins. Here, we examined whether Asian lineage strains, including those that descended from the 2014 Caribbean introduction, are likely to acquire these A. albopictus-adaptive E2 substitutions. Because Asian lineage strains cannot adapt through the E1-A226V substitution due to an epistatic constraint, we first determined that the beneficial effect of these E2 mutations in IOL strains is independent of E1-A226V. We then introduced each of these E2 adaptive mutations into the Asian lineage backbone to determine if they improve infectivity for A. albopictus. Surprisingly, our results indicated that in the Asian lineage backbone, these E2 mutations significantly decreased CHIKV fitness in A. albopictus. Furthermore, we tested the effects of these mutations in Aedes aegypti and observed different results from those in A. albopictus, suggesting that mosquito species-specific factors that interact with the envelope proteins are involved in vector infection efficiency. Overall, our results indicate that the divergence between Asian lineage and IOL CHIKVs has led them onto different adaptive landscapes with differing potentials to expand their vector host range. IMPORTANCE Since its introduction into the Caribbean in October 2013, CHIKV has rapidly spread to almost the entire neotropical region. However, its potential to further spread globally, including into more temperate climates, depends in part on its ability to be transmitted efficiently by Aedes albopictus, which can survive colder winters than A. aegypti. We examined in an Asian lineage backbone A. albopictus-adaptive mutations that arose from 2005 to 2009 in Indian Ocean lineage (IOL) strains. Our results predict that the Asian CHIKV lineage now in the Americas will not readily adapt for enhanced A. albopictus transmission via the same mechanisms or adaptive mutations used previously by IOL strains. The vector species- and CHIKV lineage-specific effects caused by adaptive CHIKV envelope glycoprotein substitutions may elucidate our understanding of the mechanisms of mosquito infection and spread.
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18
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The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Nature 2021; 602:294-299. [PMID: 34818667 DOI: 10.1038/s41586-021-04245-0] [Citation(s) in RCA: 256] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]
Abstract
Beginning in the summer of 2020, a variant of SARS-CoV-2, the cause of the COVID-19 pandemic, emerged in the United Kingdom. This B.1.1.7 variant, also known as Alpha, increased rapidly in prevalence, attributed to an increase in infection and/or transmission efficiency1. The Alpha variant has 19 nonsynonymous mutations across its viral genome, including 8 substitutions or deletions in the spike protein, which interacts with cellular receptors to mediate infection and tropism. Here, using a reverse genetics approach, we show that, of the 8 individual spike protein substitutions, only N501Y exhibited consistent fitness gains for replication in the upper airway in the hamster model as well as primary human airway epithelial cells. The N501Y substitution recapitulated the phenotype of enhanced viral transmission seen with the combined 8 Alpha spike mutations, suggesting it is a major determinant of increased transmission of this variant. Mechanistically, the N501Y substitution improved the affinity of the viral spike protein for cellular receptors. As suggested by its convergent evolution in Brazil, South Africa, and elsewhere2,3, our results indicate that N501Y substitution is a major adaptive spike mutation of major concern.
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19
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Yu X, Shan C, Zhu Y, Ma E, Wang J, Wang P, Shi PY, Cheng G. A mutation-mediated evolutionary adaptation of Zika virus in mosquito and mammalian host. Proc Natl Acad Sci U S A 2021; 118:e2113015118. [PMID: 34620704 PMCID: PMC8545446 DOI: 10.1073/pnas.2113015118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2021] [Indexed: 01/18/2023] Open
Abstract
Zika virus (ZIKV) caused millions of infections during its rapid and expansive spread from Asia to the Americas from 2015 to 2017. Here, we compared the infectivity of ZIKV mutants with individual stable substitutions which emerged throughout the Asian ZIKV lineage and were responsible for the explosive outbreaks in the Americas. A threonine (T) to alanine (A) mutation at the 106th residue of the ZIKV capsid (C) protein facilitated the transmission by its mosquito vector, as well as infection in both human cells and immunodeficient mice. A mechanistic study showed that the T106A substitution rendered the C a preferred substrate for the NS2B-NS3 protease, thereby facilitating the maturation of structural proteins and the formation of infectious viral particles. Over a complete "mosquito-mouse-mosquito" cycle, the ZIKV C-T106A mutant showed a higher prevalence of mosquito infection than did the preepidemic strain, thus promoting ZIKV dissemination. Our results support the contribution of this evolutionary adaptation to the occasional widespread reemergence of ZIKV in nature.
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Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
- Shenzhen Center for Disease Control and Prevention, Institute of Pathogenic Organisms, Shenzhen 518055, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chao Shan
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
| | - Yibin Zhu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
- Shenzhen Center for Disease Control and Prevention, Institute of Pathogenic Organisms, Shenzhen 518055, China
| | - Enhao Ma
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jinglin Wang
- Yunnan Tropical and Subtropical Animal Viral Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming 650224, China
| | - Penghua Wang
- Department of Immunology, School of Medicine, the University of Connecticut Health Center, Farmington, CT 06030
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China;
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
- Shenzhen Center for Disease Control and Prevention, Institute of Pathogenic Organisms, Shenzhen 518055, China
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20
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Liu Y, Liu J, Johnson BA, Xia H, Ku Z, Schindewolf C, Widen SG, An Z, Weaver SC, Menachery VD, Xie X, Shi PY. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.12.456173. [PMID: 34462752 PMCID: PMC8404900 DOI: 10.1101/2021.08.12.456173] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
SARS-CoV-2 Delta variant has rapidly replaced the Alpha variant around the world. The mechanism that drives this global replacement has not been defined. Here we report that Delta spike mutation P681R plays a key role in the Alpha-to-Delta variant replacement. In a replication competition assay, Delta SARS-CoV-2 efficiently outcompeted the Alpha variant in human lung epithelial cells and primary human airway tissues. Delta SARS-CoV-2 bearing the Alpha-spike glycoprotein replicated less efficiently than the wild-type Delta variant, suggesting the importance of Delta spike in enhancing viral replication. The Delta spike has accumulated mutation P681R located at a furin cleavage site that separates the spike 1 (S1) and S2 subunits. Reverting the P681R mutation to wild-type P681 significantly reduced the replication of Delta variant, to a level lower than the Alpha variant. Mechanistically, the Delta P681R mutation enhanced the cleavage of the full-length spike to S1 and S2, leading to increased infection via cell surface entry. In contrast, the Alpha spike also has a mutation at the same amino acid (P681H), but the spike cleavage from purified Alpha virions was reduced compared to the Delta spike. Collectively, our results indicate P681R as a key mutation in enhancing Delta variant replication via increased S1/S2 cleavage. Spike mutations that potentially affect furin cleavage efficiency must be closely monitored for future variant surveillance.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Jianying Liu
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Craig Schindewolf
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Steven G. Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Scott C. Weaver
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Vineet D. Menachery
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
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21
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de Matos SMS, Hennigen AF, Wachholz GE, Rengel BD, Schuler-Faccini L, Roehe PM, Varela APM, Fraga LR. Possible Emergence of Zika Virus of African Lineage in Brazil and the Risk for New Outbreaks. Front Cell Infect Microbiol 2021; 11:680025. [PMID: 34368011 PMCID: PMC8342935 DOI: 10.3389/fcimb.2021.680025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sophia Martins Simon de Matos
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - André Ferreira Hennigen
- Laboratory of Virology, Department of Microbiology, Immunology and Parasitology, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Gabriela Elis Wachholz
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Teratogen Information Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Bruna Duarte Rengel
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Teratogen Information Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Lavinia Schuler-Faccini
- Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Teratogen Information Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Paulo Michel Roehe
- Laboratory of Virology, Department of Microbiology, Immunology and Parasitology, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Paula Muterle Varela
- Postgraduate Program in Bioscience, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Teratogen Information Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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22
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Chen RM. Quantifying collective intelligence and behaviours of SARS-CoV-2 via environmental resources from virus' perspectives. ENVIRONMENTAL RESEARCH 2021; 198:111278. [PMID: 33989630 PMCID: PMC9188670 DOI: 10.1016/j.envres.2021.111278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 05/22/2023]
Abstract
Collective intelligence of viruses is witnessed in many research articles. Most of the researches focus on the qualitative properties or observations. In this research, we model the behaviours and collective intelligence of SARS-CoV-2 by minimal spanning trees (MSTs), which specify the underlying mechanisms of resource allocation in the viral colony. The vertices of the trees are 50 states, DC and NYC in the USA. The weights of the edges are assigned by the reciprocal of the sum of cases or deaths of COVID-19. The types of trees are decided by the chosen 18 factors. We sample 304 time-series data and compute their MST-based auto-correlations for stability analysis. Then we perform correlated analysis and comparative analysis on these stable factors. Our results show MST approach fits the collective intelligence modelling very well; the total cases and total deaths over areas are highly correlated in terms of MSTs; and these stable factors have little to do with the geographical distance. The results also indicate the colonisation of SARS-CoV-2 is pretty mature and organised. Based on the results, for environmental or health policies, we should also turn our attention to the transmission routes that are independent of or far away from human population or densities. The viruses' colonies might already exist in the wild in a large scale, not only in the populated or polluted cities. We shall build or conduct a monitoring system of their colonisation and survival techniques, in order to terminate, contain or live with their communities.
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Affiliation(s)
- Ray-Ming Chen
- School of Mathematics and Statistics, Baise University, 21, Zhongshan No.2 Road, Guangxi Province, China.
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23
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O'Connor O, Ou TP, Aubry F, Dabo S, Russet S, Girault D, In S, Minier M, Lequime S, Hoem T, Boyer S, Dussart P, Pocquet N, Burtet-Sarramegna V, Lambrechts L, Duong V, Dupont-Rouzeyrol M. Potential role of vector-mediated natural selection in dengue virus genotype/lineage replacements in two epidemiologically contrasted settings. Emerg Microbes Infect 2021; 10:1346-1357. [PMID: 34139961 PMCID: PMC8259877 DOI: 10.1080/22221751.2021.1944789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dengue virus (DENV) evolutionary dynamics are characterized by frequent DENV genotype/lineage replacements, potentially associated with changes in disease severity and human immunity. New Caledonia (NC) and Cambodia, two contrasted epidemiological settings, respectively experienced a DENV-1 genotype IV to I replacement in 2012 and a DENV-1 genotype I lineage 3–4 replacement in 2005–2007, both followed by a massive dengue outbreak. However, their underlying evolutionary drivers have not been elucidated. Here, we tested the hypothesis that these genotype/lineage switches reflected a higher transmission fitness of the replacing DENV genotype/lineage in the mosquito vector using in vivo competition experiments. For this purpose, field-derived Aedes aegypti from NC and Cambodia were orally challenged with epidemiologically relevant pairs of four DENV-1 genotype I and IV strains from NC or four DENV-1 genotype I lineage 3 and 4 strains from Cambodia, respectively. The relative transmission fitness of each DENV-1 genotype/lineage was measured by quantitative RT–PCR for infection, dissemination, and transmission rates. Results showed a clear transmission fitness advantage of the replacing DENV-1 genotype I from NC within the vector. A similar but more subtle pattern was observed for the DENV-1 lineage 4 replacement in Cambodia. Our results support the hypothesis that vector-driven selection contributed to the DENV-1 genotype/lineage replacements in these two contrasted epidemiological settings, and reinforce the idea that natural selection taking place within the mosquito vector plays an important role in DENV short-term evolutionary dynamics.
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Affiliation(s)
- Olivia O'Connor
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Tey Putita Ou
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Fabien Aubry
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Stéphanie Dabo
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Sylvie Russet
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Dominique Girault
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Saraden In
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Marine Minier
- Medical Entomology Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Sebastian Lequime
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Thavry Hoem
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Sébastien Boyer
- Medical Entomology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Nicolas Pocquet
- Medical Entomology Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Valérie Burtet-Sarramegna
- Institute For Exact and Applied Sciences, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Veasna Duong
- Medical Entomology Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Myrielle Dupont-Rouzeyrol
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
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24
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Hung SJ, Huang SW. Contributions of Genetic Evolution to Zika Virus Emergence. Front Microbiol 2021; 12:655065. [PMID: 34025610 PMCID: PMC8137341 DOI: 10.3389/fmicb.2021.655065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/12/2021] [Indexed: 12/15/2022] Open
Abstract
Mosquito-borne Zika virus (ZIKV) was considered an obscure virus causing only mild or self-limited symptoms until the explosive outbreaks in French Polynesia in 2013–2014 and in the Americas in 2015–2016, resulting in more than 700,000 cases of the disease, with occasional miscarriage and severe congenital birth defects, such as intrauterine growth restriction, fetal microcephaly, and other neurodevelopmental malformations. In this review, we summarized the evolution of ZIKV from a mundane virus to an epidemic virus. ZIKV has acquired a panel of amino acid substitutions during evolution when the virus spread from Africa, Asia, Pacific, through to the Americas. Robust occurrence of mutations in the evolution of ZIKV has increased its epidemic potential. Here we discussed the contributions of these evolutionary mutations to the enhancement of viral pathogenicity and host-mosquito transmission. We further explored the potential hypotheses for the increase in ZIKV activity in recent decades. Through this review, we also explored the hypotheses for the occurrence of the recent ZIKV epidemics and highlighted the potential roles of various factors including pathogen-, host-, vector-related, and environmental factors, which may have synergistically contributed to the ZIKV epidemics.
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Affiliation(s)
- Su-Jhen Hung
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
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25
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Liu Y, Liu J, Plante KS, Plante JA, Xie X, Zhang X, Ku Z, An Z, Scharton D, Schindewolf C, Menachery VD, Shi PY, Weaver SC. The N501Y spike substitution enhances SARS-CoV-2 transmission. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33758836 PMCID: PMC7986995 DOI: 10.1101/2021.03.08.434499] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Beginning in the summer of 2020, a variant of SARS-CoV-2, the cause of the COVID-19 pandemic, emerged in the United Kingdom (UK). This B.1.1.7 variant increased rapidly in prevalence among sequenced strains, attributed to an increase in infection and/or transmission efficiency. The UK variant has 19 nonsynonymous mutations across its viral genome including 8 substitutions or deletions in the spike protein, which interacts with cellular receptors to mediate infection and tropism. Here, using a reverse genetics approach, we show that, of the 8 individual spike protein substitutions, only N501Y exhibited consistent fitness gains for replication in the upper airway in the hamster model as well as primary human airway epithelial cells. The N501Y substitution recapitulated the phenotype of enhanced viral transmission seen with the combined 8 UK spike mutations, suggesting it is a major determinant responsible for increased transmission of this variant. Mechanistically, the N501Y substitution improved the affinity of the viral spike protein for cellular receptors. As suggested by its convergent evolution in Brazil and South Africa, our results indicate that N501Y substitution is a major adaptive spike mutation of major concern.
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26
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Weaver SC, Forrester NL, Liu J, Vasilakis N. Population bottlenecks and founder effects: implications for mosquito-borne arboviral emergence. Nat Rev Microbiol 2021; 19:184-195. [PMID: 33432235 PMCID: PMC7798019 DOI: 10.1038/s41579-020-00482-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2020] [Indexed: 01/31/2023]
Abstract
Transmission of arthropod-borne viruses (arboviruses) involves infection and replication in both arthropod vectors and vertebrate hosts. Nearly all arboviruses are RNA viruses with high mutation frequencies, which leaves them vulnerable to genetic drift and fitness losses owing to population bottlenecks during vector infection, dissemination from the midgut to the salivary glands and transmission to the vertebrate host. However, despite these bottlenecks, they seem to avoid fitness declines that can result from Muller's ratchet. In addition, founder effects that occur during the geographic introductions of human-amplified arboviruses, including chikungunya virus and Zika virus, can affect epidemic and endemic circulation, as well as virulence. In this Review, we discuss the role of genetic drift following population bottlenecks and founder effects in arboviral evolution and spread, and the emergence of human disease.
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Affiliation(s)
- Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
| | | | - Jianying Liu
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Nikos Vasilakis
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
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