Viral Assay Research Articles

Distal protein-protein interactions contribute to nirmatrelvir resistance

SARS-CoV-2 main protease, Mpro, is responsible for processing the viral polyproteins into individual proteins, including the protease itself. Mpro is a key target of anti-COVID-19 therapeutics such as nirmatrelvir (the active component of Paxlovid). Resistance mutants identified clinically and in viral passage assays contain a combination of active site mutations (e.g., E166V, E166A, L167F), which reduce inhibitor binding and enzymatic activity, and non-active site mutations (e.g., P252L, T21I, L50F), which restore the fitness of viral replication. To probe the role of the non-active site mutations in fitness rescue, here we use an Mpro triple mutant (L50F/E166A/L167F) that confers nirmatrelvir drug resistance with a viral fitness level similar to the wild-type. By comparing peptide and full-length Mpro protein as substrates, we demonstrate that the binding of Mpro substrate involves more than residues in the active site. Particularly, L50F and other non-active site mutations can enhance the Mpro dimer-dimer interactions and help place the nsp5-6 substrate at the enzyme catalytic center. The structural and enzymatic activity data of Mpro L50F, L50F/E166A/L167F, and others underscore the importance of considering the whole substrate protein in studying Mpro and substrate interactions, and offers important insights into Mpro function, resistance development, and inhibitor design.

P-670. Differences in Adenovirus Type Detection in Children with Acute Respiratory Illness versus Healthy Controls: New Vaccine Surveillance Network (NVSN) 2016-2019

Abstract Background Human adenovirus (HAdV) is a common cause of acute respiratory illness (ARI) in children, ranging from asymptomatic to life-threatening disease. While previous studies have examined asymptomatic vs HAdV ARI infections, few have analyzed HAdV species and type. We compared frequencies of common HAdV ARI types among children with ARI vs. healthy controls (HCs). Comparison of demographics and HAdV detection between children with ARI and healthy controls: New Vaccine Surveillance Network 12/01/2016–11/30/2019 (N=1,393). Methods Data were analyzed from the New Vaccine Surveillance Network, a multicenter, prospective surveillance network at 7 U.S. children’s hospitals that enrolled children < 18 years with ARI (fever and/or respiratory symptoms) from emergency departments or inpatient settings during 12/01/16–11/30/19. HCs (ARI symptom free ≥3 days and no vomiting/diarrhea ≥14 days) were matched by age and near date of enrollment, and enrolled from outpatient clinics. Nasal and/or throat swabs were tested using molecular assays for HAdV and other respiratory viruses. HAdV-positive specimens were tested by real-time PCR for 11 common respiratory HAdV types representing species B, C, and E based on unique sequences in the hexon gene. Demographics, HAdV species, and HAdV types from HAdV-positive children with ARI were compared to those from HAdV-positive HCs. Percent of HAdV species detections stratified by ARI cases and healthy controls: New Vaccine Surveillance Network 12/01/2016–11/30/2019 Results 1,330 HAdV detections from ARI cases and 63 from HCs were included. Children with HAdV ARI were older, more frequently attended daycare, had higher viral load (based on cycle threshold value), and had more frequent viral co-detection compared to HCs (Table 1). HAdV-C predominated in both ARI and HC groups (Fig. 1); HAdV-C2 was most common, followed by HAdV-C1 (Fig. 2). Among HAdV-positive patients, those with ARI more frequently had HAdV-B detection than HCs (22.3% vs. 1.6%, p< 0.001). HAdV-positive HCs more frequently had HAdV-C detected than HAdV-positive ARI cases (95.2% vs 73.8%, p< 0.001). HAdV-C1 was more likely to be detected in HCs than those with ARI (28.9% vs. 41.3%, p=0.03), and HAdV-B3 was only detected in those with ARI. Percent of HAdV type detections stratified by ARI cases and healthy controls: NVSN, 12/01/2016–11/30/2019. Conclusion While HAdV-C was most frequent in all children, HAdV-B was more often detected in those with ARI than HCs, suggesting that different HAdV species and types have different symptom phenotypes, including HAdV-B3. Further investigations into the identification of specific HAdV types responsible for ARI are necessary. Disclosures Rangaraj Selvarangan, BVSc, PhD, D(ABMM), FIDSA, FAAM, Abbott: Grant/Research Support|Abbott: Honoraria|BioMerieux: Grant/Research Support|Cepheid: Grant/Research Support|Diasorin: Grant/Research Support|GSK: Advisor/Consultant|Hologic: Grant/Research Support|Luminex: Grant/Research Support|Qiagen: Grant/Research Support Christopher J. Harrison, MD, GSK: Grant/Research Support|Medscape: Honoraria|Merck: Grant/Research Support|Pfizer: Grant/Research Support|UpToDate: Honoraria Pedro A. Piedra, MD, Merck: Grant/Research Support|Novavax: Grant/Research Support|Sanofi-Pasteur: Grant/Research Support|Shionogi: Grant/Research Support Mary A. Staat, MD, MPH, Cepheid: Grant/Research Support|Merck: Grant/Research Support|Pfizer: Grant/Research Support|Up-To-Date: Honoraria Elizabeth P. Schlaudecker, MD, MPH, Pfizer: Grant/Research Support|Sanofi Pasteur: Advisor/Consultant Geoffrey A. Weinberg, MD, Inhalon: Advisor/Consultant|Merck & Company: Honoraria for textbook chapter preparation Janet A. Englund, MD, Abbvie: Advisor/Consultant|AstraZeneca: Advisor/Consultant|AstraZeneca: Grant/Research Support|GlaxoSmithKline: Advisor/Consultant|GlaxoSmithKline: Grant/Research Support|Meissa Vaccines: Advisor/Consultant|Merck: Advisor/Consultant|Pfizer: Board Member|Pfizer: Grant/Research Support|Pfizer: Speaker at meeting|SanofiPasteur: Advisor/Consultant|Shinogi: Advisor/Consultant James Chappell, MD, PhD, Merck: Grant/Research Support Natasha B. Halasa, MD, MPH, Merck: Grant/Research Support

P-2066. Impact of XXB 1.5 Monovalent Booster Vaccination on Mucosal and Systemic Immune Responses in Healthy Adults

Abstract Background The FDA recently approved the first monovalent XBB1.5 booster vaccine. However, the mechanism by which this vaccine stimulates mucosal and systemic immune responses has been understudied.Figure 1.Impact of XBB 1.5 vaccination on viral neutralization titers using pseudo virus assay (left panel) and ACE2 inhibition assay (right panel).Each dot (white) represents a single serum sample tested in parallel with a post-vaccination sample (colored dot) for each of the 28 participants. The mean fold increase in neutralization titers pre- and post-vaccination are shown for Wuhan, XBB 1.5, and BA5 variants. All increases in neutralization titers are significant to P<0.0001 by employing Wilcoxon matched-pairs signed rank test. Methods We examined 28 participants' serum and saliva one week before and two to three weeks after the XBB1.5 mRNA vaccination for neutralizing and binding antibodies to Wuhan and XBB1.5 S protein.Figure 2:Inhibition of ACE2 binding to different S variants by saliva samples pre- and post-vaccination with XBB1.5 monovalent booster.Paired samples represent the percent ACE2 binding inhibition in participants before and after vaccination. Vaccination induced a 1.7-fold increase in ACE2 neutralization in saliva to XBB1.5 (p<0.0001) and 1.2-fold increase in ACE2 neutralization to Wuhan (p=0.03). Significance tested between pre and post-vaccination by Wilcoxon matched-paired sign rank test. *** p<0.001, **** p<0.0001. Results We observed a 2.9 to 2.6-fold and 5.0 to 7.8-fold increase in Wuhan and XBB1.5 serum neutralization titers following mRNA vaccination using pseudovirus and ACE2 neutralization assays respectively, that closely correlated with a rise in binding antibodies to S protein. Vaccination induced a 1.7-fold increase in ACE2 neutralization in saliva to XBB1.5 (p< 0.0001) and 1.2-fold increase in ACE2 neutralization to Wuhan (p=0.03). This increase in neutralization Ab levels in saliva failed to correlate with the number and time of prior COVID-19 infections, vaccination status, type of vaccine, or concomitant rise in S-specific IgA or IgG in saliva or serum. Depletion of IgA or IgG in saliva following vaccination demonstrated that IgA was primarily responsible for the increase in ACE2 blocking activity (mean reduction in blocking activity with IgA depletion=68%, range, 58-81%) compared to IgG (mean reduction=27%, range 0-71%).Figure 3.Role of IgA on percent reduction in ACE2 inhibition in saliva. Depletion of IgA or IgG in saliva following vaccination demonstrated that IgA was primarily responsible for the increase in ACE2 blocking activity (mean reduction in blocking activity with IgA depletion=68%, range, 58-81%) compared to IgG (mean reduction=27%, range 0-71%). Statistical analysis done using unpaired t test. Conclusion The XBB1.5 monovalent vaccine boosts systemic and mucosal viral neutralization antibody levels, primarily to the XBB1.5 variant. Most people have hybrid immunity to SARS-CoV2 now, so mRNA vaccines boost mucosal immune response better than observed earlier in the pandemic. Increased oral mucosal immunity may reduce the risk of COVID-19 progressing to pneumonia and more severe disease. Disclosures All Authors: No reported disclosures

Selective phosphodiesterase 4 inhibitor roflumilast reduces inflammation and lung injury in models of betacoronavirus infection in mice.

We aimed to understand the potential therapeutic and anti-inflammatory effects of the phosphodiesterase-4 (PDE4) inhibitor roflumilast in models of pulmonary infection caused by betacoronaviruses. Mice were infected intranasally with murine hepatitis virus (MHV-3) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Roflumilast was given to MHV-3-infected mice therapeutically at doses of 1mg/kg or 10mg/kg, or prophylactically at 10mg/kg. In SARS-CoV-2-infected mice, roflumilast was given therapeutically at a dose of 10mg/kg. Lung histopathology, chemokines (CXCL-1 and CCL2), cytokines (IL-1β, IL-6, TNF, IFN-γ, IL-10 and TGFβ), neutrophil immunohistochemical staining (Ly6G+ cells), macrophage immunofluorescence staining (F4/80+ cells), viral titration plaque assay, real-time PCR virus detection, and blood cell counts were examined. Therapeutic treatment with roflumilast at 10mg/kg reduced lung injury in SARS-CoV-2 or MHV-3-infected mice without compromising viral clearance. In MHV-3-infected mice, reduced lung injury was associated with decreased chemokines levels, prevention of neutrophil aggregates and reduced macrophage accumulation in the lung tissue. However, the prophylactic treatment strategy with roflumilast increased lung injury in MHV-3-infected mice. Our findings indicate that therapeutic treatment with roflumilast reduced lung injury in MHV-3 and SARS-CoV-2 lung infections. Given the protection induced by roflumilast in inflammation, PDE4 targeting could be a promising therapeutic avenue worth exploring following severe viral infections of the lung.

Mixed lipopeptide-based mucosal vaccine candidate induces cross-variant immunity and protects against SARS-CoV-2 infection in hamsters.

The global dissemination of SARS-CoV-2 led to a worldwide pandemic in March 2020. Even after the official downgrading of the COVID-19 pandemic, infection with SARS-CoV-2 variants continues. The rapid development and deployment of SARS-CoV-2 vaccines helped to mitigate the pandemic to a great extent. However, the current vaccines are suboptimal; they elicit incomplete and short-lived protection and are ineffective against evolving virus variants. Updating the spike antigen according to the prevailing variant and repeated boosters is not the long-term solution. We have designed a lipopeptide-based, mucosal, pan-coronavirus vaccine candidate, derived from highly conserved and/or functional regions of the SARS-CoV-2 spike, nucleocapsid, and membrane proteins. Our studies demonstrate that the designed lipopeptides (LPMix) induced both cellular and humoral (mucosal and systemic) immune responses upon intranasal immunization in mice. Furthermore, the antibodies bound to the wild-type and mutated S proteins of SARS-CoV-2 variants of concern, including Alpha, Beta, Delta and Omicron, and also led to efficient neutralization in a surrogate viral neutralization assay. Our sequence alignment and 3-dimensional molecular modeling studies demonstrated that spike-derived epitopes, P1 and P2, are sequentially and/or structurally conserved among the SARS-CoV-2 variants. The addition of a novel mucosal adjuvant, heat-killed Caulobacter crescentus, to the lipopeptide vaccine significantly bolstered mucosal antibody responses. Finally, the lipopeptide-based intranasal vaccine demonstrated significant improvement in lung pathologies in a hamster model of SARS-CoV-2 infection. These studies are fundamentally important and open new avenues in the investigation of an innovative, broadly protective intranasal vaccine platform for SARS-CoV-2 and its variants.

Optimization of a micro-scale air–liquid-interface model of human proximal airway epithelium for moderate throughput drug screening for SARS-CoV-2

BackgroundMany respiratory viruses attack the airway epithelium and cause a wide spectrum of diseases for which we have limited therapies. To date, a few primary human stem cell-based models of the proximal airway have been reported for drug discovery but scaling them up to a higher throughput platform remains a significant challenge. As a result, most of the drug screening assays for respiratory viruses are performed on commercial cell line-based 2D cultures that provide limited translational ability.MethodsWe optimized a primary human stem cell-based mucociliary airway epithelium model of SARS-CoV-2 infection, in 96-well air–liquid-interface (ALI) format, which is amenable to moderate throughput drug screening. We tested the model against SARS-CoV-2 parental strain (Wuhan) and variants Beta, Delta, and Omicron. We applied this model to screen 2100 compounds from targeted drug libraries using a high throughput-high content image-based quantification method.ResultsThe model recapitulated the heterogeneity of infection among patients with SARS-CoV-2 parental strain and variants. While there were heterogeneous responses across variants for host factor targeting compounds, the two direct-acting antivirals we tested, Remdesivir and Paxlovid, showed consistent efficacy in reducing infection across all variants and donors. Using the model, we characterized a new antiviral drug effective against both the parental strain and the Omicron variant.ConclusionThis study demonstrates that the 96-well ALI model of primary human mucociliary epithelium can recapitulate the heterogeneity of infection among different donors and SARS-CoV-2 variants and can be used for moderate throughput screening. Compounds that target host factors showed variability among patients in response to SARS-CoV-2, while direct-acting antivirals were effective against SARS-CoV-2 despite the heterogeneity of patients tested.

Current methods for detecting and assessing HIV-1 antibody resistance.

Antiretroviral therapy is the standard treatment for HIV, but it requires daily use and can cause side effects. Despite being available for decades, there are still 1.5 million new infections and 700,000 deaths each year, highlighting the need for better therapies. Broadly neutralizing antibodies (bNAbs), which are highly active against HIV-1, represent a promising new approach and clinical trials have demonstrated the potential of bNAbs in the treatment and prevention of HIV-1 infection. However, HIV-1 antibody resistance (HIVAR) due to variants in the HIV-1 envelope glycoproteins (HIV-1 Env) is not well understood yet and poses a critical problem for the clinical use of bNAbs in treatment. HIVAR also plays an important role in the future development of an HIV-1 vaccine, which will require elicitation of bNAbs to which the circulating strains are sensitive. In recent years, a variety of methods have been developed to detect, characterize and predict HIVAR. Structural analysis of antibody-HIV-1 Env complexes has provided insight into viral residues critical for neutralization, while testing of viruses for antibody susceptibility has verified the impact of some of these residues. In addition, in vitro viral neutralization and adaption assays have shaped our understanding of bNAb susceptibility based on the envelope sequence. Furthermore, in vivo studies in animal models have revealed the rapid emergence of escape variants to mono- or combined bNAb treatments. Finally, similar variants were found in the first clinical trials testing bNAbs for the treatment of HIV-1-infected patients. These structural, in vitro, in vivo and clinical studies have led to the identification and validation of HIVAR for almost all available bNAbs. However, defined assays for the detection of HIVAR in patients are still lacking and for some novel, highly potent and broad-spectrum bNAbs, HIVAR have not been clearly defined. Here, we review currently available approaches for the detection, characterization and prediction of HIVAR.

Assessing the Effectiveness of Fast-Track Diagnostic Kit for Detecting Viral Gastroenteritis Agents.

Viral gastroenteritis is a significant global health concern. An effective, rapid, and easy-to-use diagnostic tool is essential for screening causative viruses. Forty-eight samples, known to be infected with one of the following viruses: norovirus, group A rotavirus, astrovirus, adenovirus, and sapovirus determined by reverse transcription-PCR and nucleotide sequencing, were evaluated by the Fast Track Diagnostics (FTD) viral gastroenteritis assay. The assay demonstrated 100% specificity for all viruses and matched the RT-PCR sensitivity for norovi-rus GI, classic human astrovirus, adenovirus, and sapovirus. It identified norovirus GII and rotavirus with 87.5% and 85.7% sensitivity, respectively. However, its sensitivity for detecting novel human astrovirus MLB and VA was lower, at 35%. The FTD viral gastroenteritis assay can effectively screen simultaneously for norovirus GI, GII, group A rotavirus, adenovirus, and sapovirus in clinical settings. The study also suggests that improved detection methods are necessary for novel astrovirus strains.

Anti-nucleocapsid SARS-CoV-2 antibody seroprevalence in previously infected persons with immunocompromising conditions-United States, 2020-2022.

People with immunocompromising conditions (IC) are at increased risk of severe COVID-19 and death. These individuals show weaker immunogenicity following vaccination than individuals without IC, yet immunogenicity after SARS-CoV-2 infection is poorly understood. To address this gap, the presence of infection-induced antibodies in sera following a positive COVID-19 test result was compared between patients with and without IC. A commercial laboratory provided patient data gathered during July 2020-February 2022 on COVID-19 viral test results and antibody assay results, which included infection-induced (anti-N) antibody presence. Participants were categorized into having or not having IC based on if there was an indicative diagnostic code on their health record for a five-year period prior to the study period. Anti-N presence in sera from people with a positive COVID-19 test result was compared by IC status for four post-infection periods: 14-90, 91-180, 181-365, and 365+ days. A longitudinal, logistic regression produced adjusted odds ratios comparing anti-N prevalence among specimens with and without associated IC, adjusted for age, sex, residence in a metro area, and social vulnerability index (SVI) tertile. Data included 17,025 anti-N test results from 14,690 patients, 1,424 (9.7%) of which had at least one IC on record. In an adjusted comparison to patients without IC, patients with any IC were 0.61 times as likely to have infection-induced antibodies (99% CI: 0.40-0.93), during the 14-90 days following infection. Similar patterns were found when comparing people with two specific types of IC to people without any IC: (1) solid malignancies and (2) other intrinsic immune conditions. These findings stress the importance of prevention measures for people with IC, such as additional vaccination doses and consistent mask use before and after a documented infection.

Accurate predictions of SARS-CoV-2 infectivity from comprehensive analysis

An unprecedented amount of SARS-CoV-2 data has been accumulated compared with previous infectious diseases, enabling insights into its evolutionary process and more thorough analyses. This study investigates SARS-CoV-2 features as it evolved to evaluate its infectivity. We examined viral sequences and identified the polarity of amino acids in the receptor binding motif (RBM) region. We detected an increased frequency of amino acid substitutions to lysine (K) and arginine (R) in variants of concern (VOCs). As the virus evolved to Omicron, commonly occurring mutations became fixed components of the new viral sequence. Furthermore, at specific positions of VOCs, only one type of amino acid substitution and a notable absence of mutations at D467 were detected. We found that the binding affinity of SARS-CoV-2 lineages to the ACE2 receptor was impacted by amino acid substitutions. Based on our discoveries, we developed APESS, an evaluation model evaluating infectivity from biochemical and mutational properties. In silico evaluation using real-world sequences and in vitro viral entry assays validated the accuracy of APESS and our discoveries. Using Machine Learning, we predicted mutations that had the potential to become more prominent. We created AIVE, a web-based system, accessible at https://ai-ve.org to provide infectivity measurements of mutations entered by users. Ultimately, we established a clear link between specific viral properties and increased infectivity, enhancing our understanding of SARS-CoV-2 and enabling more accurate predictions of the virus.

TaqMan-based quantitative real-time polymerase chain reaction assay to detect porcine circovirus-like virus.

The aim of this study was to develop a rapid, sensitive and highly specific TaqMan quantitative real-time polymerase chain reaction PCR (qPCR) assay for porcine circovirus-like virus (PCLV). The primers and probe were designed based on the conserved regions of the PCLV ORF4 gene. The assay has a good detection performance (y=-3.3257x+ 1.482, R2=0.9905), with a limit of detection of 10 copies, which was 100 times more sensitive than conventional PCR (cPCR). No cross-reactivity was observed with other common viruses. The intra- and inter-assay coefficients of variation were less than 1.25%. 36 fecal samples were analyzed using this method, detecting a positivity rate of 8.33% (3/36) that was higher than the cPCR detected. In summary, the established assay for PCLV detection has high specificity, sensitivity, and reproducibility and can be used as a tool for clinical diagnosis and epidemiological investigation.

Common Chemical Plasticizer Di(2-Ethhylhexyl) Phthalate Exposure Exacerbates Coxsackievirus B3 Infection.

HeLa cervical cancer cells, human induced pluripotent stem cell-derived brain-like endothelial cells (iBECs), and Caco-2 colon carcinoma cells were exposed to 40 µg/mL DEHP for 24 h prior to infecting with enhanced green fluorescent protein (EGFP)-expressing CVB. The severity of the infection was evaluated via fluorescence microscopy and flow cytometry-based viral EGFP detection, viral plaque assay on tissue culture media, and Western blotting to detect VP1 viral capsid protein. Interferon-associated proteins such as interferon regulatory factor (IRF) 3, IRF7, interferon-induced transmembrane (IFITM) 2, and IFITM3 were measured by Western blotting. The roles of IFITM2 and IFITM3 in the context of CVB infection were evaluated via siRNA silencing. We found that DEHP drastically increased CVB infection in each of the cell types we tested, and, while the cellular processes underlying DEHP's proviral properties were not entirely clear, we observed that DEHP may subvert CVB-induced interferon signaling and elevate levels of IFITMs, which appeared to bolster CVB infection. DEHP may represent a major environmental factor associated with the severity of CVB infection. Further understanding of how DEHP exacerbates infection may better elucidate its potential role as a proviral environmental factor.

Performance evaluation of the high-throughput quantitative Alinity m Epstein-Barr virus assay.

Epstein-Barr virus (EBV) infection and reactivation are associated with increased risk for post-transplant lymphoproliferative disorders (PTLD) in transplant recipients with the development of PTLD occurring predominantly within a year of transplant. Quantitative PCR for EBV is used to monitor the viral load of EBV with a negative result as a good negative predictor of PTLD. Nucleic acid amplification tests (NAATs) with high sensitivity and specificity are available on fully automated high-throughput instruments to provide accurate quantitation and improve test result turn-around time. This study evaluates the analytical and clinical performance of one such NAAT, the Alinity m EBV assay.

Establishment and application of a duplex fluorescent quantitative PCR assay for H9N2 subtype avian influenza virus and infectious bronchitis virus.

The H9N2 subtype of avian influenza virus (AIV) and infectious bronchitis virus (IBV) are important avian viruses that cause respiratory symptoms in poultry, and can form mixed infections. In this study, primers and probes were designed based on the HA gene of H9N2 and the 5' noncoding region of IBV, respectively, and a fluorescent quantitative RT-PCR assay was established for simultaneous detection of these two pathogens. The reaction system and conditions were optimized. The method only detected AIV subtype H9N2 and IBV and no other viruses, confirming its high specificity. The assay detected 13.5 copies/μL and 1.66 copies/μL of H9N2 and IBV in clinical samples, respectively. The coefficients of variation for intra- and interassay repeatability were < 3%. The established method was used to analyze 254 clinical samples (oropharyngeal and cloacal swabs) from Hubei Province, China; 98.82% were positive for both pathogens. In summary, a duplex fluorescent quantitative RT-PCR method capable of simultaneously detecting AIV subtype H9N2 and IBV was established. It is specific, sensitive, and reproducible, and can be used for diagnosis of a variety of clinical samples. It provides a technological means for the rapid and simultaneous detection of both pathogens, and thus can facilitate clinical diagnosis and epidemiological investigations.

Evaluating the antiviral efficacy and specificity of chlorogenic acid and related herbal extracts against SARS-CoV-2 variants via spike protein binding intervention

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus infect the respiratory tract through surface proteins, causing similar symptoms. Since the onset of the COVID-19 pandemic, both viruses have posed significant ongoing global health threats. Like the influenza virus, SARS-CoV-2 evolves into variants that can reduce vaccine efficacy. Thus, herbal medicines are being explored as supplementary options to enhance protection against these infections. This study aimed to investigate the therapeutic potential of chlorogenic acid (3-CQA) and related extracts from green coffee beans and Echinacea purpurea against SARS-CoV-2 variants and H1N1 infection. The methods employed included an ELISA-based trimeric spike protein binding assay, viral infection assays, plaque assays, and molecular docking studies. Results showed that 3-CQA blocked spike protein/angiotensin converting enzyme 2 (ACE2) binding for most SARS-CoV-2 variants of concern, except the Delta variant. Extracts from Green coffee bean and E. purpurea effectively blocked all variants tested. Additionally, antibodies blocked spike protein binding up to Omicron BA.2. Molecular docking suggested that 3-CQA binding to Omicron BA.1, BA.2, and BA.4, though not to the Delta spike protein, may lead to steric hindrance, preventing receptor-binding domain interactions with ACE2. Finally, both 3-CQA and E. purpurea extract showed preventive effects against H1N1 viral infection, though with lower potency compared to SARS-CoV-2. In conclusion, 3-CQA has potential as a phytoconstituent marker for herbs with bioactive properties against SARS-CoV-2 and H1N1 viral infections.

Mitochondrial resilience and antioxidant defence against HIV-1: unveiling the power of Asparagus racemosus extracts and Shatavarin IV.

Asparagus racemosus (AR), an Ayurvedic botanical, possesses various biological characteristics, yet its impact on HIV-1 replication remains to be elucidated. This study aimed to investigate the inhibitory effects of AR root extracts and its principal bioactive molecule, Shatavarin IV (Shatavarin), on HIV-1 replication and their role in mitigating mitochondrial dysfunction during HIV-1 infection, utilizing both in vitro and in silico methodologies. The cytotoxicity of the extracts was evaluated using MTT and ATPlite assays. In vitro anti-HIV-1 activity was assessed in TZM-bl cells against X4 and R5 subtypes, and confirmed in peripheral blood mononuclear cells using HIV-1 p24 antigen capture ELISA and viral copy number assessment. Mechanistic insights were obtained through enzymatic assays targeting HIV-1 Integrase, Protease and Reverse Transcriptase. Shatavarin's activity was also validated via viral copy number and p24 antigen capture assays, along with molecular interaction studies against key HIV-1 replication enzymes. HIV-1 induced mitochondrial dysfunction was evaluated by detecting mitochondrial reactive oxygen species (ROS), calcium accumulation, mitochondrial potential, and caspase activity within the infected cells. Non-cytotoxic concentrations of both aqueous and hydroalcoholic extracts derived from Asparagus racemosus roots displayed dose-dependent inhibition of HIV-1 replication. Notably, the hydroalcoholic extract exhibited superior Reverse Transcriptase activity, complemented by moderate activity observed in the Protease assay. Molecular interaction studies revealed that Shatavarin IV, the key bioactive constituent of AR, formed hydrogen bonds within the active binding pocket site residues crucial for HIV replication enzyme catalysis, suggesting its potential in attenuating HIV-1 infection. Mitochondrial dysfunction induced by HIV-1 infection, marked by increased oxidative stress, mitochondrial calcium overload, loss of mitochondrial membrane potential, and elevated caspase activity, was effectively mitigated by treatment with AR extracts and Shatavarin IV. These findings underscore the potential of AR extracts and Shatavarin IV as antiviral agents, while enhancing mitochondrial function during HIV-1 infection. In conclusion, Asparagus racemosus extracts, particularly Shatavarin IV, demonstrate promising inhibitory effects against HIV-1 replication while concurrently ameliorating mitochondrial dysfunction induced by the virus. These findings suggest the therapeutic potential of AR extracts and Shatavarin in combating HIV-1 infection and improving mitochondrial health.

SARS-CoV-2 outbreak in lions, tigers and hyenas at Denver Zoo.

In late 2019, SARS-CoV-2 spilled-over from an animal host into humans, where it efficiently spread, resulting in the COVID-19 pandemic. Through both natural and experimental infections, we learned that many animal species are susceptible to SARS-CoV-2. Importantly, animals in close proximity to humans, including companion, farmed, and those at zoos and aquariums, became infected, and many studies demonstrated transmission to/from humans in these settings. In this study, we first review the literature of SARS-CoV-2 infections in tigers and lions, and compare species, sex, age, virus and antibody detection assay, and types, frequency and length of clinical signs, demonstrating broad heterogeneity amongst infections. We then describe a SARS-CoV-2 outbreak in lions, tigers and hyenas at Denver Zoo in late 2021. Animals were tested for viral RNA (vRNA) for four months. Lions had significantly more viral RNA in nasal swabs than both tigers and hyenas, and many individual lions experienced viral recrudescence after weeks of undetectable vRNA. Infectious virus was correlated with high levels of vRNA and was more likely to be detected earlier during infection. Four months post-infection, all tested animals generated robust neutralizing antibody titers. Animals were infected with Delta lineage AY.20 identical to a variant circulating at less than 1% in Colorado humans at that time, suggesting a single spillover event from an infected human spread within and between species housed at the zoo. Better understanding of epidemiology and susceptibility of SARS-CoV-2 infections in animals is critical to limit the current and future spread and protect animal and human health.

The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir.

Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are investigational antiretroviral agents that potently impair virion maturation by inducing hyper-multimerization of IN and inhibiting its interaction with viral genomic RNA. The pyrrolopyridine-based ALLINI pirmitegravir (PIR) has recently advanced into phase 2a clinical trials. Previous cell culture-based viral breakthrough assays identified the HIV-1(Y99H/A128T IN) variant that confers substantial resistance to this inhibitor. Here, we have elucidated the unexpected mechanism of viral resistance to PIR. Although both Tyr99 and Ala128 are positioned within the inhibitor binding V-shaped cavity at the IN catalytic core domain (CCD) dimer interface, the Y99H/A128T IN mutations did not substantially affect the direct binding of PIR to the CCD dimer or functional oligomerization of full-length IN. Instead, the drug-resistant mutations introduced a steric hindrance at the inhibitor-mediated interface between CCD and C-terminal domain (CTD) and compromised CTD binding to the CCDY99H/A128T + PIR complex. Consequently, full-length INY99H/A128T was substantially less susceptible to the PIR-induced hyper-multimerization than the WT protein, and HIV-1(Y99H/A128T IN) conferred >150-fold resistance to the inhibitor compared with the WT virus. By rationally modifying PIR, we have developed its analog EKC110, which readily induced hyper-multimerization of INY99H/A128T in vitro and was ~14-fold more potent against HIV-1(Y99H/A128T IN) than the parent inhibitor. These findings suggest a path for developing improved PIR chemotypes with a higher barrier to resistance for their potential clinical use.IMPORTANCEAntiretroviral therapies save the lives of millions of people living with HIV (PLWH). However, the evolution of multi-drug-resistant viral phenotypes is a major clinical problem, and there are limited or no treatment options for heavily treatment-experienced PLWH. Allosteric HIV-1 integrase inhibitors (ALLINIs) are a novel class of antiretroviral compounds that work by a unique mechanism of binding to the non-catalytic site on the viral protein and inducing aberrant integrase multimerization. Accordingly, ALLINIs potently inhibit both wild-type HIV-1 and all drug-resistant viral phenotypes that have so far emerged against currently used therapies. Pirmitegravir, a highly potent and safe investigational ALLINI, is currently advancing through clinical trials. Here, we have elucidated the structural and mechanistic bases behind the emergence of HIV-1 integrase mutations in infected cells that confer resistance to pirmitegravir. In turn, our findings allowed us to rationally develop an improved ALLINI with substantially enhanced potency against the pirmitegravir-resistant virus.

Evaluation and comparison of performances of six commercial NSP ELISA assays for foot and mouth disease virus in Thailand

ELISA kits that detect antibodies to the non-structural protein (NSP) of the foot-and-mouth disease virus (FMDV), commonly referred to as NSP-ELISA, can distinguish between vaccinated and naturally infected animals. They can play an essential role in demonstrating ‘proof-of-freedom’ during the control of FMD. Although various NSP-ELISA kits are available in Thailand, information regarding their performance is lacking. To select the most appropriate NSP-ELISA kit for our specific purpose, we must compare their performance using carefully characterized sera. This will ensure that we maximize the benefits of our testing. In this study, six NSP-ELISA kits sold in Thailand―Biovet, ID Screen, VDPro, IDEXX, PrioCHECK, and KUcheck-F―were evaluated and compared. A total of 800 serum samples were examined, including samples from 357 cattle and 29 buffaloes in outbreak areas, as well as 14 swine serum samples from the Vaccine Quality Control Unit of the Bureau of Veterinary Biologics, Ministry of Agriculture and Cooperation, Thailand. Four hundred samples were confirmed to originate from animals infected with FMDV through ELISA typing (n = 11, tested as representative samples in each farm) and/or RT-PCR (n = 400, all samples), serving as positive control sera. Additionally, 400 negative control sera were obtained from Japan (97 cattle and 300 pigs) and Australia (3 goats), certified by the World Organisation for Animal Health as ‘free of FMD’. The sensitivity and specificity of the six tests were determined based on the results obtained from two-by-two tables. Cohen’s kappa statistics were calculated for the six tests to assess their concordance, and the diagnostic accuracy of the assays was also determined. For all six NSP-ELISA kits, the sensitivity ranged from 97.75 to 99.50%, and the specificity ranged from 97.25 to 100%. Cohen’s kappa statistics ranged from 0.96 to 1.00, and diagnostic accuracy ranged from 98.13 to 99.75%. The study results indicated that the test kits have statistically similar sensitivity, specificity, concordance, and diagnostic accuracy, suggesting they can be used interchangeably. However, ID Screen demonstrated the highest sensitivity and specificity among all kits tested. Therefore, if a single kit were to be selected from the six evaluated, ID Screen would be the most appropriate choice. These findings can aid in selecting the most suitable test kit. Therefore, it is recommended to consider purchasing a diverse range of effective test kits. Furthermore, these findings can provide guidance for expanding the use of test kits, particularly with the growing availability of NSP-ELISA kits in the market.

Diagnostic yield of stains for infectious organisms in esophageal or gastroesophageal junction biopsies with esophagitis*

ABSTRACT Stains frequently performed to exclude infectious etiologies in esophagitis include Grocott methenamine silver (GMS) and periodic acid–Schiff (PAS) as well as immunohistochemistry (IHC) assays for cytomegalovirus (CMV) and herpes simplex virus (HSV). The diagnostic yield of these tests, in this situation, has not been well studied. We retrospectively reviewed 261 esophageal biopsies, which had one or more of the above tests performed. The diagnostic yield for GMS and PAS was 8%, while CMV and HSV immunohistochemistry had a diagnostic yield of 1% and 0%, respectively. Our study suggests that routine use of ancillary labeling techniques in esophagitis biopsies may be of limited utility and have low diagnostic yield.