We identified an emerging SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California, a state in the Western United States. Named B.1.427/B.1.429 to denote its 2 lineages, the variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6-24% increased transmissibility relative to wild-type circulating strains. The variant carries 3 mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation common to variants B.1.1.7, B.1.351, and P.1. Antibody neutralization assays revealed 4.0 to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California exhibiting decreased antibody neutralization warrants further investigation.

Emerging evidence points towards an intricate relationship between the pandemic of coronavirus disease 2019 (COVID-19) and diabetes. While pre-existing diabetes is associated with severe COVID-19 , it is unclear if COVID-19 severity is a cause or consequence of diabetes . To mechanistically link COVID-19 to diabetes, we tested whether insulin-producing pancreatic β-cells can be infected by SARS-CoV-2 and cause β-cell depletion. We found that the SARS-CoV-2 receptor, ACE2 and related entry factors (TMPRSS2, NRP1, TRFC) are expressed in β-cells, with selectively high expression of NRP1. We discovered that SARS-CoV-2 infects human pancreatic β-cells in patients who succumbed to COVID-19 and selectively infects human islet β-cells in vitro . We demonstrated SARS-CoV-2 infection attenuates pancreatic insulin levels and secretion, and induces β-cell apoptosis, each rescued by NRP1 inhibition. Phosphoproteomic pathway analysis of infected islets indicates apoptotic β-cell signaling, similar to that observed in Type 1 diabetes (T1D). In summary, our study shows SARS-CoV-2 can directly induce β-cell killing.

We identified a novel SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 remnant nasal/nasopharyngeal swab samples from 44 counties in California. Named B.1.427/B.1.429 or 20C/L452R, the variant emerged around May 2020 and increased from 0% to >50% of sequenced cases from September 1, 2020 to January 29, 2021, exhibiting an estimated 18.6-24% increase in transmissibility relative to wild-type circulating strains. This variant is characterized by three mutations in the spike protein, including a L452R substitution in the receptor-binding domain. Our analyses revealed 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation found in SARS-CoV-2 variants of concern (B.1.1.7, B.1.351, and P.1 lineages). Antibody neutralization assays showed 4.0 to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California associated with decreased antibody neutralization warrants further investigation.

Some picornaviruses, for example, poliovirus, increase bidirectional permeability of the nuclear envelope and suppress active nucleocytoplasmic transport. These activities require the viral protease 2Apro . Here, we studied nucleocytoplasmic traffic in cells infected with encephalomyocarditis virus (EMCV; a cardiovirus), which lacks the poliovirus 2A pro -related protein. EMCV similarly enhanced bidirectional nucleocytoplasmic traffic. By using the fluorescent "Timer" protein, which contains a nuclear localization signal, we showed that the cytoplasmic accumulation of nuclear proteins in infected cells was largely due to the nuclear efflux of "old" proteins rather than impaired active nuclear import of newly synthesized molecules. The nuclear envelope of digitonin-treated EMCV-infected cells permitted rapid efflux of a nuclear marker protein. Inhibitors of poliovirus 2A pro did not prevent the EMCV-induced efflux. Extracts from EMCV-infected cells and products of in vitro translation of viral RNAs contained an activity increasing permeability of the nuclear envelope of uninfected cells. This activity depended on the expression of the viral leader protein. Mutations disrupting the zinc finger motif of this protein abolished its efflux-inducing ability. Inactivation of the L protein phosphorylation site (Thr473Ala) resulted in a delayed efflux, while a phosphorylation-mimicking (Thr473Asp) replacement did not significantly impair the efflux-inducing ability. Such activity of extracts from EMCV-infected cells was suppressed by the protein kinase inhibitor staurosporine. As evidenced by electron microscopy, cardiovirus infection resulted in alteration of the nuclear pores, but it did not trigger degradation of the nucleoporins known to be degraded in the poliovirus-infected cells. Thus, two groups of picornaviruses, enteroviruses and cardioviruses, similarly alter the nucleocytoplasmic traffic but achieve this by strikingly different mechanisms.Picornaviruses, small nonenveloped icosahedral animal viruses with a single-stranded RNA genome of positive (mRNA) polarity, encompass the Enterovirus, Rhinoviruses, Cardiovirus, Aphthovirus, Parechovirus, and some other genera (64). All essential steps of their reproduction, such as translation, RNA synthesis, and encapsidation, take place in the cytoplasm of infected cells. The nonessential role of the nucleus for their reproduction follows from their ability to fulfill the complete infectious cycle in nuclei-free cytoplasts (31, 60) or cytoplasmic extracts (7,52,71). This fact, however, does not mean that the nuclei are not involved in the infectious process. Indeed, virusspecific proteins have been detected in the nuclei of poliovirusinfected (11, 29) and encephalomyocarditis virus (EMCV)-infected (5, 6) cells. Poliovirus proteases 2A and 3C are known to target a variety of nuclear transcription factors and histones (66,78,79,80). The EMCV 2A protein enters the nucleoli and interacts there with a ribosome precursor, contributing thereby to alterations in the translation c...

Poliovirus and some other picornaviruses trigger relocation of certain nuclear proteins into the cytoplasm. Here, by using a protein changing its fluorescence color with time and containing a nuclear localization signal (NLS), we demonstrate that the poliovirus-triggered relocation is largely due to the exit of presynthesized nuclear protein into the cytoplasm. The leakiness of the nuclear envelope was also documented by the inability of nuclei from digitonin-permeabilized, virus-infected (but not mock-infected) cells to retain an NLS-containing derivative of green fluorescent protein (GFP). The cytoplasm-to-nucleus traffic was also facilitated during infection, as evidenced by experiments with GAPDH (glyceraldehyde-3-phosphate dehydrogenase), cyclin B1, and an NLS-lacking derivative of GFP, which are predominantly cytoplasmic in uninfected cells. Electron microscopy demonstrated that a bar-like barrier structure in the channel of the nuclear pores, seen in unin- Picornaviruses (61) are cytoplasmic viruses. All essential steps of their reproduction, such as translation and replication of the viral RNA and maturation of virions, are confined to the cytoplasm. Not surprisingly, picornaviruses, such as poliovirus, echovirus, and encephalomyocarditis virus, are known to produce infectious progeny in nucleus-free cytoplasts (24, 54) or cytoplasmic extracts (5, 48, 66). This does not mean, however, that the nucleus or its components have no role in picornavirus reproduction. Indeed, the nucleus-free cytoplasts generated much less virus than did intact cells, and the former, in contrast to the latter, failed to support viral reproduction after infection with double-stranded replicative form RNA of poliovirus (14). Also, some cellular proteins known to have predominantly nuclear localization appear to relocate into the cytoplasm and to stimulate viral RNA translation (46, 37) or replication (45,71). On the other hand, the entry of virus-specific (and possibly of some cellular) cytoplasmic proteins into the nucleus of picornavirus-infected cell exerts important effects on the course of viral reproduction and the cell fate. Thus, viral proteases 2A and 3C were reported to target several transcription factors (56,73,(78)(79)(80) and histones (21). Accumulation of virus-specific proteins in the nuclei of poliovirus-infected (8, 22) and encephalomyocarditis virus-infected (3, 4) cells was directly observed. Nuclear alterations developing upon different forms of picornavirus-induced apoptosis (7,28,35,40,50,69) also require entry of certain proapoptotic host proteins (e.g., effector caspases and DNases) into the nuclei (cf., references 20 and 55).Nucleocytoplasmic protein exchange is a sophisticated, tightly regulated process ensuring accurate control of gene expression and other cellular functions (43,44,74). The nucleus is surrounded by an envelope (10, 58) consisting of the outer and inner protein-containing lipid membranes and an underlying meshwork-like proteinaceous lamina. The major gates for the nucleocytoplasmic exch...