Giant viruses inhibit superinfection by downregulating phagocytosis in Acanthamoeba.

In the context of the virosphere, viral particles can compete for host cells. In this scenario, some viruses block the entry of exogenous virions upon infecting a cell, a phenomenon known as superinfection inhibition. The molecular mechanisms associated with superinfection inhibition vary depending on the viral species and the host, but generally, blocking superinfection ensures the genetic supremacy of the virus's progeny that first infects the cell. Giant amoeba-infecting viruses have attracted the scientific community's attention due to the complexity of their particles and genomes. However, there are no studies on the occurrence of superinfection and its inhibition induced by giant viruses. This study shows that mimivirus, moumouvirus, and megavirus, exhibit different strategies related to the infection of Acanthamoeba. For the first time, we have reported that mimivirus and moumouvirus induce superinfection inhibition in amoebas. Interestingly, megaviruses do not exhibit this ability, allowing continuous entry of exogenous virions into infected amoebas. Our investigation into the mechanisms behind superinfection blockage reveals that mimivirus and moumouvirus inhibit amoebic phagocytosis, leading to significant changes in the morphology and activity of the host cells. In contrast, megavirus-infected amoebas continue incorporating newly formed virions, negatively affecting the available viral progeny. This effect, however, is reversible with chemical inhibition of phagocytosis. This work contributes to the understanding of superinfection and its inhibition in mimivirus, moumouvirus, and megavirus, demonstrating that despite their evolutionary relatedness, these viruses exhibit profound differences in their interactions with their hosts.IMPORTANCESome viruses block the entry of new virions upon infecting a cell, a phenomenon known as superinfection inhibition. Superinfection inhibition in giant viruses has yet to be studied. This study reveals that even closely related viruses, such as mimivirus, moumouvirus, and megavirus, have different infection strategies for Acanthamoeba. For the first time, we have reported that mimivirus and moumouvirus induce superinfection inhibition in amoebas. In contrast, megaviruses do not exhibit this ability, allowing continuous entry of exogenous virions into infected amoebas. Our investigation shows that mimivirus and moumouvirus inhibit amoebic phagocytosis, causing significant changes in host cell morphology and activity. Megavirus-infected amoebas, however, continue incorporating newly formed viruses, affecting viral progeny. This research enhances our understanding of superinfection inhibition in these viruses, highlighting their differences in host interactions.

How structural biology has changed our understanding of icosahedral viruses.

Cryo-electron microscopy and tomography have allowed us to unveil the remarkable structure of icosahedral viruses. However, in the past few years, the idea that these viruses must have perfectly symmetric virions, but in some cases, it might not be true. This has opened the door to challenging paradigms in structural virology and raised new questions about the biological implications of "unusual" or "defective" symmetries and structures. Also, the continual improvement of these technologies, coupled with more rigorous sample purification protocols, improvements in data processing, and the use of artificial intelligence, has allowed solving the structure of sub-viral particles in highly heterogeneous samples and finding novel symmetries or structural defects. In this review, I initially analyzed the case of the symmetry and composition of hepatitis B virus-produced spherical sub-viral particles. Then, I focused on Alphaviruses as an example of "imperfect" icosahedrons and analyzed how structural biology has changed our understanding of the Alphavirus assembly and some biological implications arising from these discoveries.

Extraction of Modified Adeno-Associated Virus-Like Particles Displaying Peptides on Their Surface.

Virus-like particles (VLPs) of the adeno-associated virus (AAV) can be produced using the baculovirus expression vector system. Insertion of small peptides on the surface of the AAV or AAV VLPs has been used to redirect the AAV to different target tissues and for vaccine development. Usually, the VLPs self-assemble intracellularly, and an extraction step must be performed before purification. Here, we describe the method we have used to extract AAV VLPs from insect cells successfully with peptide insertions on their surface.

One-Step Purification Strategy for Cowpea Chlorotic Mottle Virus-Like Particles Produced by the IC-BEVS.

Virus-like particles (VLP) of the cowpea chlorotic mottle virus (CCMV), a plant virus, have been shown to be safe and noncytotoxic vehicles for delivering various cargos, including nucleic acids and peptides, and as scaffolds for presenting epitopes. Thus, CCMV-VLP have acquired increasing attention to be used in fields such as gene therapy, drug delivery, and vaccine development. Regardless of their production method, most reports purify CCMV-VLP through a series of ultracentrifugation steps using sucrose density gradient ultracentrifugation, which is a complex and time-consuming process. Here, the use of anion exchange chromatography is described as a one-step protocol for purification of CCMV-VLP produced by the insect cell-baculovirus expression vector system (IC-BEVS).

Plant Virus-Like Particles for RNA Delivery.

Plant viruses such as brome mosaic virus and cowpea chlorotic mottle virus are effectively purified through PEG precipitation and sucrose cushion ultracentrifugation. Increasing ionic strength and an alkaline pH cause the viruses to swell and disassemble into coat protein subunits. The coat proteins can be reassembled into stable virus-like particles (VLPs) that carry anionic molecules at low ionic strength and through two-step dialysis from neutral pH to acidic buffer. VLPs have been extensively studied due to their ability to protect and deliver cargo, particularly RNA, while avoiding degradation under physiological conditions. Furthermore, chemical functionalization of the surface of VLPs allows for the targeted drug delivery. VLPs derived from plants have demonstrated great potential in nanomedicine by offering a versatile platform for drug delivery, imaging, and therapeutic applications.

Differential Severe Acute Respiratory Syndrome Coronavirus 2-Specific Humoral Response in Inactivated Virus-Vaccinated, Convalescent, and Breakthrough-Infected Subjects.

BACKGROUND: We sought to identify potential antigens for discerning between humoral responses elicited after vaccination with CoronaVac (a severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] inactivated vaccine), natural infection, or breakthrough infection. METHODS: Serum samples obtained from volunteers immunized with CoronaVac (2 and 3 doses), breakthrough case patients, and from convalescent individuals were analyzed to determine the immunoglobulin (Ig) G responses against 3 structural and 8 nonstructural SARS-CoV-2 antigens. RESULTS: Immunization with CoronaVac induced higher levels of antibodies against the viral membrane (M) protein compared with convalescent subjects both after primary vaccination and after a booster dose. Individuals receiving a booster dose displayed equivalent levels of IgG antibodies against the nucleocapsid (N) protein, similar to convalescent subjects. Breakthrough case patients produced the highest antibody levels against the N and M proteins. Antibodies against nonstructural viral proteins were present in >50% of the convalescent subjects. CONCLUSIONS: Vaccinated individuals elicited a different humoral response compared to convalescent subjects. The analysis of particular SARS-CoV-2 antigens could be used as biomarkers for determining infection in subjects previously vaccinated with CoronaVac.

Expanding the Repertoire of the Plant-Infecting Ophioviruses through Metatranscriptomics Data.

Ophioviruses (genus Ophiovirus, family Aspiviridae) are plant-infecting viruses with non-enveloped, filamentous, naked nucleocapsid virions. Members of the genus Ophiovirus have a segmented single-stranded negative-sense RNA genome (ca. 11.3-12.5 kb), encompassing three or four linear segments. In total, these segments encode four to seven proteins in the sense and antisense orientation, both in the viral and complementary strands. The genus Ophiovirus includes seven species with viruses infecting both monocots and dicots, mostly trees, shrubs and some ornamentals. From a genomic perspective, as of today, there are complete genomes available for only four species. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and molecular characterization of 33 novel viruses with genetic and evolutionary cues of ophioviruses. Genetic distance and evolutionary insights suggest that all the detected viruses could correspond to members of novel species, which expand the current diversity of ophioviruses ca. 4.5-fold. The detected viruses increase the tentative host range of ophioviruses for the first time to mosses, liverwort and ferns. In addition, the viruses were linked to several Asteraceae, Orchidaceae and Poaceae crops/ornamental plants. Phylogenetic analyses showed a novel clade of mosses, liverworts and fern ophioviruses, characterized by long branches, suggesting that there is still plenty of unsampled hidden diversity within the genus. This study represents a significant expansion of the genomics of ophioviruses, opening the door to future works on the molecular and evolutionary peculiarity of this virus genus.

Nanomechanical and Vibrational Signature of Chikungunya Viral Particles.

Chikungunya virus (CHIKV) belongs to the genus Alphaviridae, with a single-stranded positive-sense RNA genome of 11.8 kbp encoding a polyprotein that generates both non-structural proteins and structural proteins. The virus is transmitted by the Aedes aegypti and A. albopictus mosquitoes, depending on the location. CHIKV infection leads to dengue-like musculoskeletal symptoms and has been responsible for several outbreaks worldwide since its discovery in 1952. Patients often experience fever, headache, muscle pain, joint swelling, and skin rashes. However, the ultrastructural and mechanical properties of CHIKV have not been fully characterized. Thus, this study aims to apply a physical approach to investigate CHIKV's ultrastructural morphology and mechanical properties, using atomic force microscopy and Raman spectroscopy as the main tools. Using nanomechanical assays of AFM and a gold nanoparticles substrate for Raman signal enhancement, we explored the conformational plasticity, morphology, vibrational signature, and nanomechanical properties of the chikungunya virus, providing new information on its ultrastructure at the nanoscale and offering a novel understanding of the virus' behavior upon mechanical disruptions besides its molecular composition.

Quantitative electrostatic force tomography for virus capsids in interaction with an approaching nanoscale probe.

Electrostatic interactions are crucial for the assembly, disassembly and stability of proteinaceous viral capsids. Moreover, at the molecular scale, elucidating the organization and structure of the capsid proteins in response to an approaching nanoprobe is a major challenge in biomacromolecular research. Here, we report on a generalized electrostatic model, based on the Poisson-Boltzmann equation, that quantifies the subnanometric electrostatic interactions between an AFM tip and a proteinaceous capsid from molecular snapshots. This allows us to describe the contributions of specific amino acids and atoms to the interaction force. We show validation results in terms of total electrostatic forces with previous semi-empirical generalized models at available length scales (d > 1 nm). Then, we studied the interaction of the Zika capsid with conical and spherical AFM tips in a tomography-type analysis to identify the most important residues and atoms, showing the localized nature of the interaction. This method can be employed for the interpretation of force microscopy experiments in fundamental virological characterization and in diverse nanomedicine applications, where specific regions of the protein cages are aimed to electrostatically interact with molecular sized functionalized inhibitors, or tailoring protein-cage functional properties for nucleic acid delivery.

Pseudomonas-tailed lytic phages: genome mechanical analysis and putative correlation with virion morphogenesis yield.

Aim: To unveil a putative correlation between phage genome flexibility and virion morphogenesis yield. Materials & methods: A deeper analysis of the mechanical properties of three Pseudomonas aeruginosa lytic phage genomes was undertaken, together with full genome cyclizability calculations. Results & conclusion: A putative correlation was established among phage genome flexibility, eclipse timeframe and virion particle morphogenesis yield, with a more flexible phage genome leading to a higher burst size and a more rigid phage genome leading to lower burst sizes. The results obtained are highly relevant to understand the influence of the phage genome plasticity on the virion morphogenesis yield inside the infected bacterial host cells and assumes particular relevance in the actual context of bacterial resistance to antibiotics.

ICTV Virus Taxonomy Profile: Potyviridae 2022.

The family Potyviridae includes plant viruses with single-stranded, positive-sense RNA genomes of 8-11 kb and flexuous filamentous particles 650-950 nm long and 11-20 nm wide. Genera in the family are distinguished by the host range, genomic features and phylogeny of the member viruses. Most genomes are monopartite, but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Potyviridae, which is available at ictv.global/report/potyviridae.

Epitranscriptomic regulation of HIV-1 full-length RNA packaging.

During retroviral replication, the full-length RNA serves both as mRNA and genomic RNA. However, the mechanisms by which the HIV-1 Gag protein selects the two RNA molecules that will be packaged into nascent virions remain poorly understood. Here, we demonstrate that deposition of N6-methyladenosine (m6A) regulates full-length RNA packaging. While m6A deposition by METTL3/METTL14 onto the full-length RNA was associated with increased Gag synthesis and reduced packaging, FTO-mediated demethylation promoted the incorporation of the full-length RNA into viral particles. Interestingly, HIV-1 Gag associates with the RNA demethylase FTO in the nucleus and contributes to full-length RNA demethylation. We further identified two highly conserved adenosines within the 5'-UTR that have a crucial functional role in m6A methylation and packaging of the full-length RNA. Together, our data propose a novel epitranscriptomic mechanism allowing the selection of the HIV-1 full-length RNA molecules that will be used as viral genomes.

Exposing cryptic epitopes on the Venezuelan equine encephalitis virus E1 glycoprotein prior to treatment with alphavirus cross-reactive monoclonal antibody allows blockage of replication early in infection.

Eastern equine encephalitis virus (EEEV), western equine encephalitis virus (WEEV) and Venezuelan equine encephalitis virus (VEEV) can cause fatal encephalitis in humans and equids. Some MAbs to the E1 glycoprotein are known to be cross-reactive, weakly neutralizing in vitro but can protect from disease in animal models. We investigated the mechanism of neutralization of VEEV infection by the broadly cross-reactive E1-specific MAb 1A4B-6. 1A4B-6 protected 3-week-old Swiss Webster mice prophylactically from lethal VEEV challenge. Likewise, 1A4B-6 inhibited virus growth in vitro at a pre-attachment step after virions were incubated at 37 °C and inhibited virus-mediated cell fusion. Amino acid residue N100 in the fusion loop of E1 protein was identified as critical for binding. The potential to elicit broadly cross-reactive MAbs with limited virus neutralizing activity in vitro but that can inhibit virus entry and protect animals from infection merits further exploration for vaccine and therapeutic developmental research.

The stressed life of a lipid in the Zika virus membrane.

Protein-lipid interactions modulate a plethora of physiopathologic processes and have been the subject of countless studies. However, these kinds of interactions in the context of viral envelopes have remained relatively unexplored, partially because the intrinsically small dimensions of the molecular systems escape to the current resolution of experimental techniques. However, coarse-grained and multiscale simulations may fill that niche, providing nearly atomistic resolution at an affordable computational price. Here we use multiscale simulations to characterize the lipid-protein interactions in the envelope of the Zika Virus, a prominent member of the Flavivirus genus. Comparisons between the viral envelope and simpler molecular systems indicate that the viral membrane is under extreme pressures and asymmetric forces. Furthermore, the dense net of protein-protein contacts established by the envelope proteins creates poorly solvated regions that destabilize the external leaflet leading to a decoupled dynamics between both membrane layers. These findings lead to the idea that the Flaviviral membrane may store a significant amount of elastic energy, playing an active role in the membrane fusion process.

Dengue Virus Capsid-Protein Dynamics in Live Infected Cells Studied by Pair Correlation Analysis.

It has become increasingly evident that unveiling the mechanisms of virus entry, assembly, and virion release is fundamental for identifying means for preventing viral spread and controlling viral disease. Due to virus mobility and structural and/or functional heterogeneity among viral particles, high spatiotemporal resolution single-virus/single-particle techniques are required to capture the behavior of viral particles inside infected cells.In this chapter, we present fluorescence imaging analysis methods for studying the mobility of fluorescently labeled dengue virus (DENV) proteins in live infected cells. Some of the most recent Fluorescence Fluctuation Spectroscopy (FFS) methods will be presented and, in particular, the pair Correlation Functions (pCF) approach will be discussed. The pCF method does not require individual molecule isolation, as in a particle-tracking experiment, to capture single viral protein behavior. In this regard, image acquisition is followed by the spatiotemporal cross-correlation function at increasing time delays, yielding a quantitative view of single-particle mobility in intact live infected cells.We provide a general overview and a practical guidance for the implementation of advanced FFS techniques, and the pair Correlation Functions analysis, as quantitative tools to reveal insights into previously unreported DENV mechanisms. We expect this protocol report will serve as an incentive for further applying correlation imaging studies in virology research.

In Vitro Generation of Human Antibody-Secreting Cells Through the Stimulation of PBMCs with Dengue Virus Particles.

The Dengue pathophysiology has had several aspects determined over the years. However, some points remain elusive, such as the metabolic factors that regulate the massive B cell differentiation into antibody-secreting cells observed in Dengue patients. In this chapter, we describe an in vitro method capable of mimicking this Dengue-induced cell expansion. More specifically, this approach allows dengue virus-stimulated peripheral blood mononuclear cells (PBMCs) from healthy individuals to enhance the frequency of phenotypical and functional antibody-secreting cells (ASCs) after 7 days of culture. A manuscript recently published by Bonezi and colleagues displays results generated through this methodology.

Avaliação da infecção por Parvovírus Humano B19 em diferentes grupos populacionais: diagnóstico diferencial e aspectos imunopatogênicos da infecção aguda e persistente / Evaluation of Human Parvovirus B19 infection in different population groups: differential diagnosis and immunopathogenic aspects of acute and persistent infection

A infecção pelo Parvovírus B19 (B19V) pode ocorrer em indivíduos imunocompetentes e imunocomprometidos, de todas as faixas etárias, e se caracteriza por ser aguda e autolimitada, podendo levar a quadros de doença exantemática (DE), doença febril aguda (DFA), doença renal crônica (DRC) e falência hepática aguda (FHA). O diagnóstico diferencial de B19V nessas populações, muitas vezes, não ocorre e estudos sobre a prevalência do B19V são antigos e escassos, não refletindo a atualidade. Marcadores da infecção podem ser detectados na circulação e em diferentes tipos de tecidos, inclusive em tecidos não eritroides, por meses ou anos. A infecção pode levar a manifestações clínicas graves, que requer tratamento hospitalar, e a doenças inflamatórias atípicas, como: cardiomiopatia, artrite reumatoide, hepatite e vasculite. No entanto, a detecção de B19V DNA não implica necessariamente na presença de vírions infecciosos e na associação do B19V com essas manifestações atípicas. Dessa forma, o objetivo do trabalho foi otimizar técnicas de PCR em tempo real para quantificação do B19V DNA e de detecção de partículas virais infecciosas, a fim de realizar o diagnóstico diferencial da infecção pelo B19V em pacientes com DE, DFA, DRC e FHA. Para o diagnóstico da infecção, amostras de diferentes populações foram testadas: DE (n=54), DFA (n=60), DRC (n=221), e FHA (n=30). Amostras de soro (e de tecido hepático para FHA) foram submetidas a avaliação de marcadores sorológicos (IgM e IgG anti-B19V) e moleculares do B19V, a fim de determinar a fase da infecção em que o paciente se encontrava. Para a avaliação de marcadores moleculares, a metodologia de PCR quantitativo e em tempo real foi otimizada e permitiu um diagnóstico sensível e específico do B19V DNA. Além disso, a presença de vírions em amostras de pacientes com B19V (n=10) e de macacos cynomolgus (n=4) infectados experimentalmente foram avaliadas por meio da técnica de pré-tratamento das amostras com uma enzima endonuclease. O teste molecular (qPCR) otimizado durante o estudo, apresentou sensibilidade e especificidade de 100%. O ensaio com a endonuclease revelou que a maioria das amostras de soro humano tornou-se B19V DNA negativa após o pré-tratamento, indicando que não eram infecciosas. Foi observado prevalências do B19V DNA em 5,5% dos pacientes com DE; 6,6% em DFA; 65,6% em DRC, e 23,3% em FHA. Como conclusão a técnica de qPCR otimizada no presente estudo foi efetiva para o esclarecimento de casos da infecção por B19V e é adequada para diagnóstico diferencial. Além disso, o teste laboratorial baseado em endonuclease possibilitou a discriminação do B19V DNA (se encapsidado em vírions ou não). Portanto, estes testes podem ser utilizados para esclarecer o papel do B19V como agente etiológico associado a diversas manifestações clínicas. As prevalências encontradas nesse estudo indicam que o B19V está circulando entre os diversos grupos populacionais estudados e deve ser feita uma melhor vigilância da infecção, pois está presente tanto em indivíduos imunocompetentes como em imunocomprometidos. Além disso, os resultados sugerem a importância da inclusão de B19V no diagnóstico laboratorial diferencial, não apenas para fins epidemiológicos, mas também para o manejo adequado do paciente.

Parvovirus B19 (B19V) infection can occur in immunocompetent and immunocompromised individuals of all group ages and is characterized as acute and self limiting, which can lead to rash disease (RD), acute febrile illness (AFI), chronic kidney disease (CKD), and acute liver failure (ALF). Differential diagnosis of B19V in these populations often does not occur and studies on the prevalence of B19V are scarce, outdated, and do not reflect the current situation. B19V markers of acute infection can be detected in the circulation and in different tissue types, including non-erythroid tissues, for months to years and may lead to severe clinical manifestations, requiring hospital treatment, and to atypical inflammatory diseases, such as cardiomyopathy, rheumatoid arthritis, hepatitis, and vasculitis. However, the detection of B19V DNA does not necessarily imply the presence of infectious virions and the causal relation between B19V and atypical manifestations could not be proved yet. Thus, the aim of this study was to standardize the real-time PCR for quantification of B19V DNA and detection of infectious viral particles in order to perform the differential diagnosis of the B19V infection in RD, AFI, CKD, and ALF patients. For the diagnosis of the infection, samples from different populations were tested: RD (n=54), AFI (n=60), CKD (n=221), and ALF (n=30). Serum samples (and hepatic tissue for ALF) were submitted to the evaluation of B19V serological status (anti-B19V IgM and IgG antibodies) and molecular markers, in order to determine the stage of infection in which the patient is. For the evaluation of molecular markers, a quantitative real-time PCR methodology was optimized and allowed a sensitive and specific diagnosis of B19V DNA. In addition, the presence of virions in samples from patients with B19V (n=10) and from cynomolgus monkeys (n=4) experimentally infected were evaluated by endonuclease enzyme pretreatment. The molecular test optimized during the study showed 100% sensitivity and specificity. The endonuclease treatment assay revealed that most human serum samples became negative after pretreatment, as indicative of non-infective particles. Concerning the prevalence of B19V DNA: 5.5% were obtained in patients with RD; 6.6% in AFI; 65.6% in CKD, and 23.3% in ALF. In conclusion, the qPCR technique optimized in the present study was effective for clarifying cases of B19V infection and is suitable for differential diagnosis. In addition, the endonuclease-based laboratory test made it possible to discriminate B19V DNA (whether encapsidated in virions or not). Therefore, these tests can be used to clarify the role of B19V as an etiologic agent associated with several clinical manifestations. The prevalence found in this study indicate that B19V is circulating among the different populational groups that have been studied and better surveillance of the infection should be carried out, as it is present in both immunocompetent and immunocompromised individuals. In addition, the results suggest the importance of including B19V in the differential laboratory diagnosis, not only for epidemiological purposes but also for the proper management of the patient.

Interaction of Spike protein and lipid membrane of SARS-CoV-2 with Ursodeoxycholic acid, an in-silico analysis.

Numerous repositioned drugs have been sought to decrease the severity of SARS-CoV-2 infection. It is known that among its physicochemical properties, Ursodeoxycholic Acid (UDCA) has a reduction in surface tension and cholesterol solubilization, it has also been used to treat cholesterol gallstones and viral hepatitis. In this study, molecular docking was performed with the SARS-CoV-2 Spike protein and UDCA. In order to confirm this interaction, we used Molecular Dynamics (MD) in "SARS-CoV-2 Spike protein-UDCA". Using another system, we also simulated MD with six UDCA residues around the Spike protein at random, naming this "SARS-CoV-2 Spike protein-6UDCA". Finally, we evaluated the possible interaction between UDCA and different types of membranes, considering the possible membrane conformation of SARS-CoV-2, this was named "SARS-CoV-2 membrane-UDCA". In the "SARS-CoV-2 Spike protein-UDCA", we found that UDCA exhibits affinity towards the central region of the Spike protein structure of - 386.35 kcal/mol, in a region with 3 alpha helices, which comprises residues from K986 to C1032 of each monomer. MD confirmed that UDCA remains attached and occasionally forms hydrogen bonds with residues R995 and T998. In the presence of UDCA, we observed that the distances between residues atoms OG1 and CG2 of T998 in the monomers A, B, and C in the prefusion state do not change and remain at 5.93 ± 0.62 and 7.78 ± 0.51 Å, respectively, compared to the post-fusion state. Next, in "SARS-CoV-2 Spike protein-6UDCA", the three UDCA showed affinity towards different regions of the Spike protein, but only one of them remained bound to the region between the region's heptad repeat 1 and heptad repeat 2 (HR1 and HR2) for 375 ps of the trajectory. The RMSD of monomer C was the smallest of the three monomers with a value of 2.89 ± 0.32, likewise, the smallest RMSF was also of the monomer C (2.25 ± 056). In addition, in the simulation of "SARS-CoV-2 membrane-UDCA", UDCA had a higher affinity toward the virion-like membrane; where three of the four residues remained attached once they were close (5 Å, to the centre of mass) to the membrane by 30 ns. However, only one of them remained attached to the plasma-like membrane and this was in a cluster of cholesterol molecules. We have shown that UDCA interacts in two distinct regions of Spike protein sequences. In addition, UDCA tends to stay bound to the membrane, which could potentially reduce the internalization of SARS-CoV-2 in the host cell.

Quantification of airborne SARS-CoV-2 genomic particles in different hospital settings.

We quantified the presence of SARS-CoV-2 RNA in the air of different hospital settings and the autopsy room of the largest medical centre in Sao Paulo, Brazil. Real-time reverse-transcription PCR was used to determine the presence of the envelope protein of SARS-CoV-2 and the nucleocapsid protein genes. The E-gene was detected in 5 out of 6 samples at the ICU-COVID-19 ward and in 5 out of 7 samples at the ward-COVID-19. Similarly, in the non-dedicated facilities, the E-gene was detected in 5 out of 6 samples collected in the ICU and 4 out of 7 samples in the ward. In the necropsy room, 6 out of 7 samples were positive for the E-gene. When both wards were compared, the non-COVID ward presented a significantly higher concentration of the E-gene than in the COVID-19 ward (p = 0.003). There was no significant difference in E-gene concentration between the ICU-COVID-19 and the ICU (p = 0.548). Likewise, there was no significant difference among E-gene concentrations found in the autopsy room versus the ICUs and wards (dedicated or not) (p = 0.245). Our results show the widespread presence of aerosol contamination in different hospital units.