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Zika virus (ZIKV) has evolved into a global health threat because of its unexpected causal link to microcephaly. Phylogenetic analysis reveals that contemporary epidemic strains have accumulated multiple substitutions from their Asian ancestor. Here we show that a single serine-to-asparagine substitution [Ser139→Asn139 (S139N)] in the viral polyprotein substantially increased ZIKV infectivity in both human and mouse neural progenitor cells (NPCs) and led to more severe microcephaly in the mouse fetus, as well as higher mortality rates in neonatal mice. Evolutionary analysis indicates that the S139N substitution arose before the 2013 outbreak in French Polynesia and has been stably maintained during subsequent spread to the Americas. This functional adaption makes ZIKV more virulent to human NPCs, thus contributing to the increased incidence of microcephaly in recent ZIKV epidemics.

The newly identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global health emergency because of its rapid spread and high mortality. The molecular mechanism of interaction between host and viral genomic RNA is yet unclear. We demonstrate herein that SARS-CoV-2 genomic RNA, as well as the negative-sense RNA, is dynamically N6-methyladenosine (m6A)-modified in human and monkey cells. Combined RIP-seq and miCLIP analyses identified a total of 8 m6A sites at single-base resolution in the genome. Especially, epidemic strains with mutations at these identified m6A sites have emerged worldwide, and formed a unique cluster in the US as indicated by phylogenetic analysis. Further functional experiments showed that m6A methylation negatively regulates SARS-CoV-2 infection. SARS-CoV-2 infection also triggered a global increase in host m6A methylome, exhibiting altered localization and motifs of m6A methylation in mRNAs. Altogether, our results identify m6A as a dynamic epitranscriptomic mark mediating the virus–host interaction.

The re-emergence of Zika virus (ZIKV) in the Western Hemisphere has resulted in global public health crisis since 2015. ZIKV preferentially infects and targets human neural progenitor cells (hNPCs) and causes fetal microcephaly upon maternal infection. hNPCs not only play critical roles during fetal brain development, but also persist in adult brain throughout life. Yet the mechanism of innate antiviral immunity in hNPCs remains largely unknown. Here, we show that ZIKV infection triggers the abundant production of virus-derived small interfering RNAs in hNPCs, but not in the more differentiated progenies or somatic cells. Ablation of key RNAi machinery components significantly enhances ZIKV replication in hNPCs. Furthermore, enoxacin, a broad-spectrum antibiotic that is known as an RNAi enhancer, exerts potent anti-ZIKV activity in hNPCs and other RNAi-competent cells. Strikingly, enoxacin treatment completely prevents ZIKV infection and circumvents ZIKV-induced microcephalic phenotypes in brain organoid models that recapitulate human fetal brain development. Our findings highlight the physiological importance of RNAi-mediated antiviral immunity during the early stage of human brain development, uncovering a novel strategy to combat human congenital viral infections through enhancing RNAi.

Structural principles underlying the composition and synergistic mechanisms of protective monoclonal antibody cocktails are poorly defined. Here, we exploited antibody cooperativity to develop a therapeutic antibody cocktail against SARS-CoV-2. On the basis of our previously identified humanized cross-neutralizing antibody H014, we systematically analyzed a fully human naive antibody library and rationally identified a potent neutralizing antibody partner, P17, which confers effective protection in animal model. Cryo-EM studies dissected the nature of the P17 epitope, which is SARS-CoV-2 specific and distinctly different from that of H014. High-resolution structure of the SARS-CoV-2 spike in complex with H014 and P17, together with functional investigations revealed that in a two-antibody cocktail, synergistic neutralization was achieved by S1 shielding and conformational locking, thereby blocking receptor attachment and viral membrane fusion, conferring high potency as well as robustness against viral mutation escape. Furthermore, cluster analysis identified a hypothetical 3rd antibody partner for further reinforcing the cocktail as pan-SARS-CoVs therapeutics.

Dengue virus (DENV) poses a major global health threat, affecting an estimated 100 to 400 million people annually. The infection and pathogenesis remain incompletely understood, and no antiviral drug is currently approved for DENV treatment. Here, we develop a human pluripotent stem cell (hPSC)-derived liver organoid (hPLO) model to characterize DENV infection and screen for antivirals. The hPLOs, containing various liver cell types, are highly susceptible to DENV-2 infection, resulting in severe cell death and morphological changes that mimic the pathology observed in severe dengue cases. Single-cell RNA sequencing (scRNA-seq) of DENV-2 infected hPLOs reveals that proliferating hepatocyte-like cells are the primary target cells of DENV-2, with significant mitochondrial damage and alterations in cell-type composition. Further drug screening in hPLOs identifies oxyresveratrol (Oresveratrol, ORES) and omaveloxolone (RTA 408) as potent anti-DENV candidates. These compounds enhance resistance to DENV-2 infection by activating the NRF2 pathway, reducing oxidative stress, and preserving mitochondrial function. The efficacy of ORES and RTA 408 is further validated in the established AG6 mouse model. Our study not only establishes hPLOs as a valuable platform for studying DENV infection and pathogenesis, but also highlights the vital role of NRF2-mediated mitochondrial function for antiviral development. Here, Li et al. develop a human liver organoid model to elucidate Dengue virus infection dynamics and identify oxyresveratrol as a potential antiviral candidate, highlighting the NRF2 pathway’s crucial role in mitigating mitochondrial damage and enhancing cellular resistance.

Biomimetic viral mineralization improves viral vaccine stability and immunogenicity using inorganic metals such as Ca, Al, or Fe. Mn is a metal found in high concentrations in mammalian tissues; however, under natural or laboratory conditions, Mn mineralization by medical viruses has yet to be established. Herein, a single IAV particle is successfully encapsulated with manganese phosphate (MnP) under specific conditions using the human influenza A virus (IAV). MnP‐mineralized IAVs (IAV@Mn) exhibited physiochemical and in vitro properties similar to Ca‐mineralized IAVs. In animal models, IAV@Mn shows limited replication in immune‐competent cells and a significant attenuation compared to naïve cells. Moreover, a single‐dose vaccination with IAV@Mn induced robust humoral and cellular immune responses and conferred significant protection against a wild‐type IAV challenge in mice. Thus, Mn mineralization in pathogenic viruses provides a rapid and universal strategy for generating an emergency vaccine in response to emerging viruses. Mn mineralization of pathogenic viruses accomplishes a rapid and universal strategy to generates an emergency vaccine in response to the emerging viruses. As the model, IAV@Mn showed limited replication and significant attenuation phenotype in vitro and vivo. A single‐dose vaccination of IAV@Mn induced robust humoral and cellular immune response and confer significant protection against wild type IAV challenge in mice.

Biomineralization is a universal biological phenomenon in which organisms use inorganic minerals to form their own structures. Inspired by the discovery of mineralized phages in nature, the concept of artificial biomimetic viral mineralization is proposed and it is validated using a large panel of viruses. Different viruses can be mineralized under different conditions, and the same virus can be completely mineralized using different inorganic minerals. The biomineralized viruses with unique physical and chemical properties display biological phenotypes distinct from those of their native counterparts during the subsequent infection process. These new features are largely due to the inorganic minerals chosen. Calcium is the most frequently used material for viral mineralization, and other inorganic ions, including silicon, aluminum, and ferrum, have also been utilized. In this review, recent advances in the artificial biomimetic mineralization of viruses are summarized while highlighting the potential applications and challenges in biomedicine. Artificial biomimetic mineralization has been proposed and well explored in the field of viruses. Viruses can be mineralized by different inorganic minerals including but not limited to calcium. The resulting biomineralized viruses are endowed with unique physical and chemical properties, thus displaying different phenotypes during the subsequent infection process. These artificial mineralized viruses have shown promising application in biomedicine field.

Zika virus (ZIKV) has elicited global concern due to its unique biological features, unusual transmission routes, and unexpected clinical outcomes. Although ZIKV transmission through anal intercourse has been reported in humans, it remains unclear if ZIKV is detectable in the stool, if it can infect the host through the anal canal mucosa, and what the pathogenesis of such a route of infection might be in the mouse model. Herein, we demonstrate that ZIKV RNA can be recovered from stools in multiple mouse models, as well as from the stool of a ZIKV patient. Remarkably, intra-anal (i.a.) inoculation with ZIKV leads to efficient infection in both Ifnar1 −/− and immunocompetent mice, characterized by extensive viral replication in the blood and multiple organs, including the brain, small intestine, testes, and rectum, as well as robust humoral and innate immune responses. Moreover, i.a. inoculation of ZIKV in pregnant mice resulted in transplacental infection and delayed fetal development. Overall, our results identify the anorectal mucosa as a potential site of ZIKV infection in mice, reveal the associated pathogenesis of i.a. infection, and highlight the complexity of ZIKV transmission through anal intercourse.

The newly identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global health emergency because of its rapid spread and high mortality. The molecular mechanism of interaction between host and viral genomic RNA is yet unclear. We demonstrate herein that SARS-CoV-2 genomic RNA, as well as the negative-sense RNA, is dynamically N 6 -methyladenosine (m 6 A)-modified in human and monkey cells. Combined RIP-seq and miCLIP analyses identified a total of 8 m 6 A sites at single-base resolution in the genome. Especially, epidemic strains with mutations at these identified m 6 A sites have emerged worldwide, and formed a unique cluster in the US as indicated by phylogenetic analysis. Further functional experiments showed that m 6 A methylation negatively regulates SARS-CoV-2 infection. SARS-CoV-2 infection also triggered a global increase in host m 6 A methylome, exhibiting altered localization and motifs of m 6 A methylation in mRNAs. Altogether, our results identify m 6 A as a dynamic epitranscriptomic mark mediating the virus–host interaction.