Mutational pressure drives enhanced release of proteasome-generated public CD8+ T cell epitopes from SARS-CoV-2 RBD of Omicron and its current lineages (preprint)

The COVID-19 pandemic was the most dramatic in the newest history with nearly 7 million deaths and global impact on mankind. Here we report binding index of 305 HLA class I molecules from 18,771 unique haplotypes of 28,104 individuals to 821 peptides experimentally observed from spike protein RBD of 5 main SARS-CoV-2 strains hydrolyzed by human proteasomes with constitutive and immune catalytic phenotypes. Our data read that 4 point mutations in the hACE2-binding region RBD496-513 of Omicron B1.1.529 strain results in a dramatic increase of proteasome-mediated release of two public HLA class I epitopes. Global population analysis of HLA class I haplotypes, specific to these peptides, demonstrated decreased mortality of human populations enriched in these haplotypes from COVID-19 after but not before December, 2021, when Omicron became dominant SARS-CoV-2 strain. Noteworthy, currently circulating BA.2.86 and JN.1 lineages contain no amino acid substitutions in RBD496-513 thus preserving identified core epitopes.

Enhanced mucosal B- and T-cell responses against SARS-CoV-2 after heterologous intramuscular mRNA prime/intranasal protein boost vaccination with a combination adjuvant. (preprint)

Current COVID-19 mRNA vaccines delivered intramuscularly (IM) induce effective systemic immunity, but with suboptimal immunity at mucosal sites, limiting their ability to impart sterilizing immunity. There is strong interest in rerouting immune responses induced in the periphery by parenteral vaccination to the portal entry site of respiratory viruses, such as SARS-CoV-2, by mucosal vaccination. We previously demonstrated the combination adjuvant, NE/IVT, consisting of a nanoemulsion (NE) and an RNA-based RIG-I agonist (IVT) induces potent systemic and mucosal immune responses in protein-based SARS-CoV-2 vaccines administered intranasally (IN). Herein, we demonstrate priming IM with mRNA followed by heterologous IN boosting with NE/IVT adjuvanted recombinant antigen induces strong mucosal and systemic antibody responses and enhances antigen-specific T cell responses in mucosa-draining lymph nodes compared to IM/IM and IN/IN prime/boost regimens. While all regimens induced cross-neutralizing antibodies against divergent variants and sterilizing immunity in the lungs of challenged mice, mucosal vaccination, either as homologous prime/boost or heterologous IN boost after IM mRNA prime was required to impart sterilizing immunity in the upper respiratory tract. Our data demonstrate the benefit of hybrid regimens whereby strong immune responses primed via IM vaccination are rerouted by IN vaccination to mucosal sites to provide optimal protection to SARS-CoV-2.

COVID-19 mortality in the Philippines: a province-level analysis, 2020-2023 (preprint)

Objective: To investigate the COVID-19 mortality in Philippine provinces from 2020 to 2023. Methods: We calculated the crude (CMR) and age-standardised mortality rates (ASMR) of the Philippine provinces from the national COVID-19 surveillance data from January 18, 2020 to May 9, 2023. With Spearman's method, we then performed a correlation analysis between the rates and four independent variables, namely, poverty incidence, population density, hospital beds per 100 000 population and proportion of elderly population (>=65). Results: The province with the highest ASMR is Benguet with 207.83 deaths per 100 000 population, followed by Cagayan, Bataan, Nueva Vizcaya, Quirino, National Capital Region, Isabela, Cebu, Aurora and Davao del Sur. Meanwhile, the province with the lowest ASMR is Tawi-Tawi with 2.22 deaths per 100 000 population, followed by Sulu, Masbate, Misamis Occidental, Camarines Norte, Sarangani, Camiguin, Sultan Kudarat, Southern Leyte, Catanduanes and Batanes. Among the independent variables, poverty incidence and hospital beds per 100 000 population were found to independently predict CMR and ASMR. Discussion: The results of this analysis provides a starting point for the investigation of COVID-19 mortality in Philippine provinces. The ranking of provinces by ASMR reveals the provinces with the highest and lowest rates, while the results of the correlation analysis, linked with findings from previous studies, explain the ranking, including surveillance issues that are related to health-care access and health-seeking behaviour. Our study paves the way for investigating factors that need to be considered and more closely investigated to get a clearer picture to inform decision-making, which affects millions of lives in communities across the Philippines' provinces.

Carboxylated graphene: A novel approach for enhanced IgA-SARS-CoV-2 electrochemical biosensing (preprint)

Biosensors comprise devices that use a material of biological nature as receptors connected to transducers, these devices are capable of capturing biorecognition signals, called a primary signal, and converting it to a measurable signal. In this study, we report the synthesis of carboxylated graphene (CG) through a carboxylation method in acid medium and further characterization of the materials by different techniques such as scanning electron microscopy, energy-dispersive X-ray spectroscopy, Raman spectroscopy, thermal gravimetric analysis, and X-ray diffraction. Also, the surface of the screen-printed carbon electrodes (SPCEs) was modified with CG for subsequent immobilization of N-protein of SARS-CoV-2, which allowed the detection of antibodies (IgA-SARS-CoV-2). The electrical properties and response of the biosensor were investigated using electrochemical techniques (cyclic voltammetry and electrochemical impedance spectroscopy). Through the chemical characterization techniques, it was possible to confirm the success of the CG synthesis process. The biosensor fabricated shown to be able to detect IgA-SARS-CoV-2 in the range of 1:1000 to1:200 v/v in phosphate buffer solution (PBS) and the limit of detection calculated was 1:1601 v/v. this perspective they comprise a wide range of applications due to its advantages, such as the possibility of a shorter response time, reproducibility, the miniaturization of detection devices such as the use of screen-printed electrodes, the use of small amounts of sample, the high sensitivity and specificity, low limits of detection and the integration of nano materials that make it possible to improve the detected signal.

Temporal Analysis of Drifting Hashtags in Textual Data Streams: A Graph-Based Application (preprint)

Social media has played an important role since its emergence. People use the internet to express opinions about anything, making social media platforms a social sensor. Initially supported by Twitter, the hashtags are now in use on several social media platforms. Hashtags are helpful to tag, track, and group posts on similar topics. In this paper, we analyze hashtag drifts over time using concepts from graph analysis and textual data streams using the Girvan-Newman method to uncover hashtag communities in annual snapshots. More specifically, we analyzed the #mybodymychoice hashtag between 2018 and 2022. In addition, we offer insights about some hashtags found in the study. Furthermore, our approach can be useful for monitoring changes over time in opinions and sentiment patterns about an entity on social media. Even though the hashtag #mybodymychoice was initially coupled with women's rights, abortion, and bodily autonomy, we observe that it suffered drifts during the studied period across topics such as drug legalization, vaccination, political protests, war, and civil rights. The year 2021 was the most significant drifting year, in which the communities detected suggest that #mybodymychoice significantly drifted to vaccination and Covid-19-related topics.

SSRI Use During Acute COVID-19 Infection Associated with Lower Risk of Long COVID Among Patients with Depression (preprint)

Background: Long COVID, also known as post-acute sequelae of COVID-19 (PASC), is a poorly understood condition with symptoms across a range of biological domains that often have debilitating consequences. Some have recently suggested that lingering SARS-CoV-2 virus in the gut may impede serotonin production and that low serotonin may drive many Long COVID symptoms across a range of biological systems. Therefore, selective serotonin reuptake inhibitors (SSRIs), which increase synaptic serotonin availability, may prevent or treat Long COVID. SSRIs are commonly prescribed for depression, therefore restricting a study sample to only include patients with depression can reduce the concern of confounding by indication. Methods: In an observational sample of electronic health records from patients in the National COVID Cohort Collaborative (N3C) with a COVID-19 diagnosis between September 1, 2021, and December 1, 2022, and pre-existing major depressive disorder, the leading indication for SSRI use, we evaluated the relationship between SSRI use at the time of COVID-19 infection and subsequent 12-month risk of Long COVID (defined by ICD-10 code U09.9). We defined SSRI use as a prescription for SSRI medication beginning at least 30 days before COVID-19 infection and not ending before COVID-19 infection. To minimize bias, we estimated the causal associations of interest using a nonparametric approach, targeted maximum likelihood estimation, to aggressively adjust for high-dimensional covariates. Results: We analyzed a sample (n = 506,903) of patients with a diagnosis of major depressive disorder before COVID-19 diagnosis, where 124,928 (25%) were using an SSRI. We found that SSRI users had a significantly lower risk of Long COVID compared to nonusers (adjusted causal relative risk 0.90, 95% CI (0.86, 0.94)). Conclusion: These findings suggest that SSRI use during COVID-19 infection may be protective against Long COVID, supporting the hypothesis that serotonin may be a key mechanistic biomarker of Long COVID.

Humoral Immune Response to the SARS-CoV-2 Spike Protein Receptor Binding Motif Linear Epitopes (preprint)

Abstract: The worldwide spread of SARS-CoV-2 has led to a significant economic and social burden on a global scale. Even though the pandemic has concluded, there remains apprehension regarding the emergence of highly transmissible variants capable of evading immunity induced by either vaccination or prior infection. The success of viral penetration is the specific amino acid residues of the Receptor Binding Motif (RBM) involved in viral attachment. This region interacts with the cellular receptor ACE2, triggering a neutralizing antibody (nAb) response. In this study, we have evaluated the immunogenicity of serum from individuals who received either a single dose or a combination of different vaccines against the original SARS-CoV-2 strain and mutated linear RBM. Despite a modest antibody response to the wild-type SARS-CoV-2 RBM, the Omicron variants exhibit four mutations in the RBM (S477N, T478K, E484A, F486V) that result in even lower antibody titers. The primary immune responses observed were directed towards IgA and IgG. While nAbs typically target the RBD, our investigation has unveiled a reduced seroreactivity within the RBD's crucial subregion, the RBM. This deficiency may have implications for the generation of protective nAbs. Evaluation of S1WT and S2WT RBM peptides binding to nAbs using microscale thermophoresis revealed a higher affinity (35 nM) for the S2WT sequence (GSTPCNGVEGFNCYF), which includes the FNCY patch. Our findings suggest that the linear RBM of SARS-CoV-2 is not an immunodominant region in vaccinated individuals. Comprehending the intricate dynamics of the humoral response, its interplay with viral evolution, and host genetics is crucial for formulating effective vaccination strategies, not only targeting SARS-CoV-2 but also anticipating potential future coronaviruses.

Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody (preprint)

SUMMARY/ABSTRACTThree coronaviruses have spilled over from animal reservoirs into the human population and caused deadly epidemics or pandemics. The continued emergence of coronaviruses highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using LIBRA-seq, we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these antibodies, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryo-EM structure of 54043-5 bound to the pre-fusion S2 subunit of the SARS-CoV-2 spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses, including ADCC and ADCP. In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.

Intestinal helminth infection impairs vaccine-induced T cell responses and protection against SARS-CoV-2 (preprint)

Although vaccines have reduced COVID-19 disease burden, their efficacy in helminth infection endemic areas is not well characterized. We evaluated the impact of infection by Heligmosomoides polygyrus bakeri (Hpb), a murine intestinal hookworm, on the efficacy of an mRNA vaccine targeting the Wuhan-1 spike protein of SARS-CoV-2. Although immunization generated similar B cell responses in Hpb-infected and uninfected mice, polyfunctional CD4+ and CD8+ T cell responses were markedly reduced in Hpb-infected mice. Hpb-infected and mRNA vaccinated mice were protected against the ancestral SARS-CoV-2 strain WA1/2020, but control of lung infection was diminished against an Omicron variant compared to animals immunized without Hpb infection. Helminth mediated suppression of spike-specific CD8+ T cell responses occurred independently of STAT6 signaling, whereas blockade of IL-10 rescued vaccine-induced CD8+ T cell responses. In mice, intestinal helminth infection impairs vaccine induced T cell responses via an IL-10 pathway and compromises protection against antigenically shifted SARS-CoV-2 variants.

Time Series Forecasting of HIV/AIDS in the Philippines Using Deep Learning: Does COVID-19 Epidemic Matter? (preprint)

With a 676% growth rate in HIV incidence between 2010 and 2021, the HIV/AIDS epidemic in the Philippines is the one that is spreading the quickest in the western Pacific. Although the full effects of COVID-19 on HIV services and development are still unknown, it is predicted that such disruptions could lead to a significant increase in HIV casualties. Therefore, the nation needs some modeling and forecasting techniques to foresee the spread pattern and enhance the governments prevention, treatment, testing, and care program. In this study, the researcher uses Multilayer Perceptron Neural Network to forecast time series during the period when the COVID-19 pandemic strikes the nation, using statistics taken from the HIV/AIDS and ART Registry of the Philippines. After training, validation, and testing of data, the study finds that the predicted cumulative cases in the nation by 2030 will reach 145,273. Additionally, there is very little difference between observed and anticipated HIV epidemic levels, as evidenced by reduced RMSE, MAE, and MAPE values as well as a greater coefficient of determination. Further research revealed that the Philippines seems far from achieving Sustainable Development Goal 3 of Project 2030 due to an increase in the nations rate of new HIV infections. Despite the detrimental effects of COVID-19 spread on HIV/AIDS efforts nationwide, the Philippine government, under the Marcos administration, must continue to adhere to the United Nations 90-90-90 targets by enhancing its ART program and ensuring that all vital health services are readily accessible and available.

Time to publication in medical education journals: An analysis of publication timelines during COVID-19 (2019-2022) (preprint)

IntroductionCOVID-19 changed scholarly publishing. Yet, its impact on medical education publishing is unstudied. Because journal articles and their corresponding publication timelines can influence academic success, the field needs updated publication timelines to set evidence-based expectations for academic productivity. This study attempts to answer the following research questions: did publication timelines significantly change around the time of COVID-19 and, if so, how? MethodsWe conducted a bibliometric study; our sample included articles published between January 2018, and December 2022, that appeared in the Medical Education Journals List-24 (MEJ-24). We clustered articles into three time-based groups (pre-COVID, COVID-overlap, and COVID-endemic), and two subject-based groups (about COVID-19 and not about COVID-19). We downloaded each articles metadata from the National Library of Medicine and analyzed data using descriptive statistics, analysis of variance, and post-hoc tests to compare mean time differences across groups. ResultsOverall, time to publish averaged 300.8 days (SD = 200.8). One-way between-groups ANOVA showed significant differences between the three time-based groups F (2, 7473) = 2150.7, p <.001. The post-hoc comparisons indicated that COVID-overlap articles took significantly longer (n = 1470, M= 539; SD = 210.6) as compared to pre-COVID (n = 1281; M = 302; SD = 172.5) and COVID-endemic articles (n = 4725; M = 226; SD = 136.5). Notably, COVID-endemic articles were published in significantly less time than pre-pandemic articles, p < .001. DiscussionLonger publication time was most pronounced for COVID-overlap articles. Publication timelines for COVID-endemic articles have shortened. Future research should explore how the shift in publication timelines has shaped medical education scholarship.

Virological characteristics of the SARS-CoV-2 JN.1 variant (preprint)

The SARS-CoV-2 BA.2.86 lineage, first identified in August 2023, is phylogenetically distinct from the currently circulating SARS-CoV-2 Omicron XBB lineages, including EG.5.1 and HK.3. Comparing to XBB and BA.2, BA.2.86 carries more than 30 mutations in the spike (S) protein, indicating a high potential for immune evasion. BA.2.86 has evolved and its descendant, JN.1 (BA.2.86.1.1), emerged in late 2023. JN.1 harbors S:L455S and three mutations in non-S proteins. S:L455S is a hallmark mutation of JN.1: we have recently shown that HK.3 and other "FLip" variants carry S:L455F, which contributes to increased transmissibility and immune escape ability compared to the parental EG.5.1 variant. Here, we investigated the virological properties of JN.1.

COVID-19 infection wave mortality from surveillance data in the Philippines using machine learning (preprint)

ObjectiveThe Philippines has had several COVID-19 infection waves brought about by different strains and variants of SARS-CoV-2. This study aimed to describe COVID-19 outcomes by infection waves using machine learning. MethodsWe used a cross-sectional surveillance data review design using the DOH COVID DataDrop data set as of September 24, 2022. We divided the data set into infection wave data sets based on the predominant COVID-19 variant(s) of concern during the identified time intervals: ancestral strain (A0), Alpha/Beta variant (AB), Delta variant (D), and Omicron variant (O). Descriptive statistics and machine learning models were generated from each infection wave data set. ResultsOur final data set consisted of 3 896 206 cases and ten attributes including one label attribute. Overall, 98.39% of cases recovered while 1.61% died. The Delta wave reported the most deaths (43.52%), while the Omicron wave reported the least (10.36%). The highest CFR was observed during the ancestral wave (2.49%), while the lowest was seen during the Omicron wave (0.61%). Higher age groups generally had higher CFRs across all infection waves. The A0, AB and D models had up to four levels with two or three splits for each node. The O model had eight levels, with up to 16 splits in some nodes. Of the ten attributes, only age was included in all the decision tree models, while region of residence was included in the O model. F-score and specificity were highest using naive Bayes in all four data sets. Area under the curve (AUC) was highest in the naive Bayes models for the A0, AB and D models, while sensitivity was highest in the decision tree models for the A0, AB and O models. DiscussionThe ancestral, Alpha/Beta and Delta variants seem to have similar transmission and mortality profiles. The Omicron variant caused lesser deaths despite being more transmissible. Age remained a significant predictor of death regardless of infection wave. We recommend constant timely analysis of available data especially during public health events and emergencies.

Antiviral humoral immunity against SARS-CoV-2 Omicron subvariants induced by XBB.1.5 monovalent vaccine in infection-naive and XBB-infected individuals (preprint)

To control infection with SARS-CoV-2 Omicron XBB subvariants, the XBB.1.5 monovalent mRNA vaccine has been available since September 2023. However, we have found that natural infection with XBB subvariants, including XBB.1.5, does not efficiently induce humoral immunity against the infecting XBB subvariants. These observations raise the possibility that the XBB.1.5 monovalent vaccine may not be able to efficiently induce humoral immunity against emerging SARS-CoV-2 variants, including a variety of XBB subvariants (XBB.1.5, XBB.1.16, XBB.2.3, EG.5.1 and HK.3) as well as BA.2.86. To address this possibility, we collected two types of sera from individuals vaccinated with the XBB.1.5 vaccine; those who had not been previously infected with SARS-CoV-2 and those who had been infected with XBB subvariants prior to XBB.1.5 vaccination. We collected sera before and 3-4 weeks after vaccination, and then performed a neutralization assay using these sera and pseudoviruses.

Social determinants of adult COVID-19 vaccine acceptance and uptake in a Brazilian urban informal community: a longitudinal time-to-event study (preprint)

Residents of informal urban settlements have a high risk of COVID-19 exposure and have less access to medical care, making vaccine-driven prevention critical in this vulnerable population. Despite robust vaccination campaigns in Brazil, vaccine uptake and timing continue to be influenced by social factors and contribute to health disparities. To address this, we conducted a sequential survey in a cohort of 717 adults in an urban favela in Salvador, Brazil where participants were interviewed in 2020, before vaccines were rolled out, and in 2022, after primary and booster dose distribution. We collected data on demographics, social characteristics, and COVID-19 vaccination status and intent. Primary series uptake was high (91.10% for 1st dose and 94.74% for 2nd dose among eligible); however, booster uptake was lower (63.51% of eligible population) at the time of the second interview, suggesting a decreasing interest in vaccination. To account for both vaccine refusal and delays, we conducted a Cox time-to-event analysis of dose uptake using sequential independent outcomes. Exposure times were determined by dose eligibility date to account for age and comorbidities. Intent to vaccinate in 2020 (hazard ratio [HR]: 1.54, CI: [1.05, 1.98]) and age (HR: 1.27, CI: [1.01, 2.08]) were associated with higher vaccination rates for the 1st dose. Males were less likely to receive the 1st dose (HR: 0.61, CI: [0.35, 0.83]), and, compared to catholics, 2nd dose uptake was lower for those identifying with Pentecostalism (HR: 0.49, CI: [0.37, 0.66]) and without a religion (HR: 0.49, CI: [0.37, 0.66]), with the latter association disappearing after controlling by age. Risk perception was associated with 2nd dose uptake (HR: 1.15, CI: [1.08, 1.26]). The role of sex and religion in vaccination behavior highlights the need for targeted outreach and interfacing with local organizations. The data offers lessons to build a long-term COVID-19 vaccination strategy beyond availability.

The Antiviral Mechanism of Action of Molnupiravir in Humans with COVID-19 (preprint)

Meaningful metrics of antiviral activity are essential for determining the efficacy of therapeutics in human clinical trials. Molnupiravir (MOV) is a broadly acting antiviral nucleoside analog prodrug that acts as a competitive alternative substrate for the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). We developed an assay, Culture-PCR, to better understand the impact of MOV therapy on infectious SARS-CoV-2. Culture-PCR revealed MOV eliminated infectious virus within 48 hours in the nasopharyngeal compartment, the upper airway location with the greatest levels of infectious virus. MOV therapy was associated with increases in mutations across the viral genome but select regions were completely unaffected, thus identifying regions where mutation likely abrogates infectivity. MOV therapy did not alter the magnitude or neutralization capacity of the humoral immune response, a documented correlate of protection. Thus, we provide holistic insights into the function of MOV in adults with COVID-19.

Virological characteristics of the SARS-CoV-2 Omicron HK.3 variant harboring the "FLip" substitution (preprint)

In November 2023, SARS-CoV-2 XBB descendants, including EG.5.1 (XBB.1.9.2.5.1), the currently predominant lineage, are circulating worldwide according to Nextstrain. EG.5.1 has a characteristic amino acid substitution in the spike protein (S), S:F456L, which contributes to its escape from humoral immunity. EG.5.1 has further evolved, and its descendant lineage harboring S:L455F (i.e., EG.5.1+S:L455F) emerged and was named HK.3 (XBB.1.9.2.5.1.1.3). HK.3 was initially discovered in East Asia and is rapidly spreading worldwide. Notably, the XBB subvariants bearing both S:L455F and S:F456L substitutions, including HK.3, are called the "FLip" variants. These FLip variants, such as JG.3 (XBB.1.9.2.5.1.3.3), JF.1 (XBB.1.16.6.1) and GK.3 (XBB.1.5.70.3), have emerged convergently, suggesting that the acquisition of these two substitutions confers a growth advantage to XBB in the human population. Here, we investigated the virological properties of HK.3 as a representative of the FLip variants.

Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury (preprint)

Acute kidney injury (AKI) in COVID-19 patients is associated with high mortality and morbidity. Critically ill COVID-19 patients are at twice the risk of in-hospital mortality compared to non-COVID AKI patients. We know little about the cell-specific mechanism in the kidney that contributes to worse clinical outcomes in these patients. New generation single cell technologies have the potential to provide insights into physiological states and molecular mechanisms in COVID-AKI. One of the key limitations is that these patients are severely ill posing significant risks in procuring additional biopsy tissue. We recently generated single nucleus RNA-sequencing data using COVID-AKI patient biopsy tissue as part of the human kidney atlas. Here we describe this approach in detail and report deeper comparative analysis of snRNAseq of 4 COVID-AKI, 4 reference, and 6 non-COVID-AKI biopsies. We also generated and analyzed urine transcriptomics data to find overlapping COVID-AKI-enriched genes and their corresponding cell types in the kidney from snRNA-seq data. We identified all major and minor cell types and states by using by using less than a few cubic millimeters of leftover tissue after pathological workup in our approach. Differential expression analysis of COVID-AKI biopsies showed pathways enriched in viral response, WNT signaling, kidney development, and cytokines in several nephron epithelial cells. COVID-AKI profiles showed a much higher proportion of altered TAL cells than non-COVID AKI and the reference samples. In addition to kidney injury and fibrosis markers indicating robust remodeling we found that, 17 genes overlap between urine cell COVID-AKI transcriptome and the snRNA-seq data from COVID-AKI biopsies. A key feature was that several of the distal nephron and collecting system cell types express these markers. Some of these markers have been previously observed in COVID-19 studies suggesting a common mechanism of injury and potentially the kidney as one of the sources of soluble factors with a potential role in disease progression. Translational StatementThe manuscript describes innovation, application and discovery that impact clinical care in kidney disease. First, the approach to maximize use of remnant frozen clinical biopsies to inform on clinically relevant molecular features can augment existing pathological workflow for any frozen tissue without much change in the protocol. Second, this approach is transformational in medical crises such as pandemics where mechanistic insights are needed to evaluate organ injury, targets for drug therapy and diagnostic and prognostic markers. Third, the cell type specific and soluble markers identified and validated can be used for diagnoses or prognoses in AKI due to different etiologies and in multiorgan injury.

Virological characteristics of the SARS-CoV-2 BA.2.86 variant (preprint)

In late 2023, a lineage of SARS-CoV-2 emerged and was named the BA.2.86 variant. BA.2.86 is phylogenetically distinct from other Omicron sublineages identified so far, displaying an accumulation of over 30 amino acid mutations in its spike protein. Here, we performed multiscale investigations to reveal the virological characteristics of the BA.2.86 variant. Our epidemic dynamics modeling suggested that the relative reproduction number of BA.2.86 is significantly higher than that of EG.5.1. Experimental studies showed that four clinically-available antivirals were effective against BA.2.86. Although the fusogenicity of BA.2.86 spike is similar to that of the parental BA.2 spike, the intrinsic pathogenicity of BA.2.86 in hamsters was significantly lower than that of BA.2. Since the growth kinetics of BA.2.86 is significantly lower than that of BA.2 in both in vitro cell cultures and in vivo, it is suggested that the attenuated pathogenicity of BA.2.86 is due to its decreased replication capacity.

Nonspecific membrane bilayer perturbations by ivermectin underlie SARS-CoV-2 in vitro activity (preprint)

Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five- to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates.