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The potential for future coronavirus outbreaks highlights the need to broadly target this group of pathogens. We used an epitope-agnostic approach to identify six monoclonal antibodies that bind to spike proteins from all seven human-infecting coronaviruses. All six antibodies target the conserved fusion peptide region adjacent to the S2′ cleavage site. COV44-62 and COV44-79 broadly neutralize alpha- and betacoronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants BA.2 and BA.4/5, albeit with lower potency than receptor binding domain–specific antibodies. In crystal structures of COV44-62 and COV44-79 antigen-binding fragments with the SARS-CoV-2 fusion peptide, the fusion peptide epitope adopts a helical structure and includes the arginine residue at the S2′ cleavage site. COV44-79 limited disease caused by SARS-CoV-2 in a Syrian hamster model. These findings highlight the fusion peptide as a candidate epitope for next-generation coronavirus vaccine development.

Background False positivity may hinder the utility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological tests in sub-Saharan Africa. Methods From 312 Malian samples collected before 2020, we measured antibodies to the commonly tested SARS-CoV-2 antigens and 4 other betacoronaviruses by enzyme-linked immunosorbent assay (ELISA). In a subset of samples, we assessed antibodies to a panel of Plasmodium falciparum antigens by suspension bead array and functional antiviral activity by SARS-CoV-2 pseudovirus neutralization assay. We then evaluated the performance of an ELISA using SARS-CoV-2 spike protein and receptor-binding domain developed in the United States using Malian positive and negative control samples. To optimize test performance, we compared single- and 2-antigen approaches using existing assay cutoffs and population-specific cutoffs. Results Background reactivity to SARS-CoV-2 antigens was common in prepandemic Malian samples. The SARS-CoV-2 reactivity varied between communities, increased with age, and correlated negligibly/weakly with other betacoronavirus and P falciparum antibodies. No prepandemic samples demonstrated functional activity. Regardless of the cutoffs applied, test specificity improved using a 2-antigen approach. Test performance was optimal using a 2-antigen assay with population-specific cutoffs (sensitivity, 73.9% [95% confidence interval {CI}, 51.6–89.8]; specificity, 99.4% [95% CI, 97.7–99.9]). Conclusions We have addressed the problem of SARS-CoV-2 seroassay performance in Africa by using a 2-antigen assay with cutoffs defined by performance in the target population.

Objective Assess the presence, durability, and neutralization capacity of SARS-CoV-2-specific antibodies in breastfeeding infants’ stools, mother’s plasma, and human milk following maternal vaccination.DesignThirty-seven mothers and 25 infants were enrolled between December 2020 and November 2021 for this prospective observational study. Human milk, maternal plasma, and infants' stools were collected pre-vaccination and at periods up to 6 months following COVID-19 vaccine series initiation/completion. SARS-CoV-2 antibody levels and their neutralization capacities were assessed in collected samples. Results SARS-CoV-2-specific IgA and IgG levels were higher in infant stool post-maternal vaccination amongst milk-fed compared to pre-COVID controls. Human milk and plasma SARS-CoV-2-specific IgA and IgG concentrations decreased over 6 months post-vaccination but remained higher than pre-vaccination levels. We observed improved neutralization capacity in milk antibodies over time.ConclusionsThe presence of neutralizing SARS-CoV-2-specific antibodies in infant stool following maternal vaccination offers further evidence of the lasting transfer of these antibodies through breastfeeding and their protective effect.

We investigated the function of the newly discovered myosin family protein myosin 18A (Myo18A) in Ab-mediated immunity by generating B cell–conditional Myo18A-deficient mice. Myo18A deficiency led to expansion of bone marrow progenitor B cells and mature B cells in secondary lymphoid organs. Myo18A-deficient mice displayed serum IgM hyperglobulinemia and increased splenic IgM-secreting cells, with older mice switching to IgG1 hyperglobulinemia and autoantibody development. Immunization of Myo18A-deficient mice with inactivated influenza virus led to development of more potent neutralizing Abs against the major Ag hemagglutinin, associated with persistent accumulation of Ag-specific germinal center B cells and more Ag-specific bone marrow plasma cells. In vitro stimulation with TLR7 and BCR ligands revealed a greater ability of Myo18A-deficient B cells to differentiate into Ab-secreting cells, associated with higher AID and Blimp-1 expression. Overall, our study demonstrates that Myo18A is a novel negative regulator of B cell homeostasis, differentiation, and humoral immunity.

Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5-1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.

SARS-CoV-2 nucleocapsid protein (N) induces strong antibody and T cell responses. Although considered to be localized in the cytosol, we readily detect N on the surface of live cells. N released by SARS-CoV-2 infected cells or N-expressing transfected cells binds to neighboring cells by electrostatic high-affinity binding to heparan sulfate and heparin, but not other sulfated glycosaminoglycans. N binds with high affinity to 11 human chemokines, including CXCL12β, whose chemotaxis of leukocytes is inhibited by N from SARS-CoV-2, SARS-CoV-1, and MERS CoV. Anti-N Abs bound to the surface of N expressing cells activate Fc receptor-expressing cells. Our findings indicate that cell surface N manipulates innate immunity by sequestering chemokines and can be targeted by Fc expressing innate immune cells. This, in combination with its conserved antigenicity among human CoVs, advances its candidacy for vaccines that induce cross-reactive B and T cell immunity to SARS-CoV-2 variants and other human CoVs, including novel zoonotic strains.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the third coronavirus in less than 20 years to spillover from an animal reservoir and cause severe disease in humans. High impact respiratory viruses such as pathogenic beta-coronaviruses and influenza viruses, as well as other emerging respiratory viruses, pose an ongoing global health threat to humans. There is a critical need for physiologically relevant, robust and ready to use, in vitro cellular assay platforms to rapidly model the infectivity of emerging respiratory viruses and discover and develop new antiviral treatments. Here, we validate in vitro human alveolar and tracheobronchial tissue equivalents and assess their usefulness as in vitro assay platforms in the context of live SARS-CoV-2 and influenza A virus infections. We establish the cellular complexity of two distinct tracheobronchial and alveolar epithelial air liquid interface (ALI) tissue models, describe SARS-CoV-2 and influenza virus infectivity rates and patterns in these ALI tissues, the viral-induced cytokine production as it relates to tissue-specific disease, and demonstrate the pharmacologically validity of these lung epithelium models as antiviral drug screening assay platforms.

In December 2020, efficacious COVID-19 vaccines were approved for use and since, millions have been immunized against SARS-CoV-2, the virus responsible for COVID-19. It is known that administration of the COVID-19 vaccine leads to increased SARS-CoV-2 specific antibodies in plasma and human milk. While this increase has been studied, the durability, longevity, and efficacy of these antibodies remains unknown. Historically, human milk serves a vital role in providing protection and nutrients to infants, and with COVID-19 vaccines not approved for children under five, immunity and protection from vaccinated mothers is likely a crucial barrier for infant safety. This study aimed at determining how long these antibodies remain in plasma and milk after COVID-19 vaccination, how effective these antibodies are at neutralizing SARS-CoV-2, and if antibodies are detectable in breastfeeding infant stool after mother has been vaccinated. This study found that concentrations of SARS-CoV-2 specific IgA and IgG decrease over 6 months post vaccine, but remain higher than pre-vaccination levels in plasma and milk. Although post-neutralization efficacy decreased over a 6-month period in plasma, using a pseudo-type vaccine neutralization assay, neutralization efficacy in human milk became more robust over the same period. Notably, we found elevated levels of SARS-CoV-2 specific IgA and IgG and neutralization within the stool of breastfeeding infants, post COVID vaccination compared to pre-COVID stool. Although further studies will be needed to determine the full extent of this passive immunity, these studies implicate the maternal/infant transfer of neutralizing SARS-CoV-2 specific antibodies through human milk subsequent to vaccination. Supported by Children's Miracle Network

The B cell antibody response is tightly regulated to facilitate pathogen-specific immunity and prevent self-reactivity, with actin cytoskeleton dynamics playing an important role in regulating B cell activation. The newly discovered unconventional myosin family protein Myosin 18A (Myo18A) is most closely related to Myo2A, and regulates important cellular processes in non-lymphoid cells. Myo18A is expressed in both precursor and mature B cells, and interacts with ezrin, Myo2A and tyrosine phosphorylated proteins suggesting that it may regulate physiological functions of B cells. We investigated the function of Myo18A in antibody-mediated immunity by generating B cell-conditional Myo18A-deficient mice. Basally, Myo18A deficiency led to expansion of both bone marrow progenitor B cells, and mature B cells in secondary lymphoid organs. Myo18A-deficient mice displayed serum IgM hyperglobulinemia with greater levels of splenic IgM secreting cells, with older mice switching to IgG1 hyperglobulinemia and autoantibody development. Immunization of Myo18A-deficient mice with inactivated influenza virus led to development of more potent neutralizing antibodies against the major antigen hemagglutinin, associated with early expansion and persistent accumulation of antigen-specific germinal center B cells. In vitro stimulation with TLR7 and BCR ligands revealed a greater ability of Myo18A-deficient B cells to differentiate into antibody secreting cells, and induce Blimp-1 expression. Overall, our study demonstrates that Myo18A is a novel negative regulator of B cell homeostasis, differentiation, self-tolerance and humoral immunity. Supported by an NIH grant (R21 AI117350) to Neetu Gupta

This review focuses on the methods and current trends in determination of neuraminidases (NAs) activity and evaluation of neuraminidase inhibitors (NAIs) by means of biochemical assays. These methods can be used, in principle, for any type of sialidase, with regard to substrate specificity and optimal conditions for enzymatic reaction. Considering the range of organisms producing sialidases, this review omits cell-based assays (plaque assays and study of cytopathic effect) and animal model studies, which are reviewed elsewhere concerning specific organisms. The present review also provides the brief introductory survey of role of sialic acids and neuraminidases, but main focus is on the methods of determining neuraminidase activity and evaluating neuraminidase inhibitors. The future prospect of improvement in analytical techniques regarding the enzymatic activity of sialidases is briefly outlined.

Serological tests are an indispensable tool to understand the epidemiology of the SARS-CoV-2 pandemic, particularly in areas where molecular diagnostics are limited. Poor assay performance may hinder the utility of these tests, including high rates of false-positivity previously reported in sub-Saharan Africa. From 312 Malian samples collected prior to 2020, we measured antibodies to the commonly tested SARS-CoV-2 antigens and four other betacoronaviruses by ELISA, and assessed functional cross-reactivity in a subset by SARS-CoV-2 pseudovirus neutralization assay. We then evaluated the performance of an ELISA developed in the US, using two-antigen SARS-CoV-2 spike protein and receptor-binding domain. To optimize test performance, we compared single and two-antigen approaches using existing assay cutoffs and population-specific cutoffs for Malian control samples (positive and negative). Background reactivity to SARS-CoV-2 antigens was common in pre-pandemic samples compared to US controls (43.4% (135/311) for spike protein, 22.8% (71/312) for RBD, and 33.9% (79/233) for nucleocapsid protein). SARS-CoV-2 reactivity correlated weakly with other betacoronavirus reactivity, varied between Malian communities, and increased with age. No pre-pandemic samples demonstrated functional activity. Regardless of the cutoffs applied, specificity improved using a two-antigen approach. Test performance was optimal using a two-antigen assay with population-specific cutoffs derived from ROC curve analysis [Sensitivity: 73.9% (51.6-89.8), Specificity: 99.4% (97.7-99.9)]. In the setting of high background reactivity, such as sub-Saharan Africa, SARS-CoV-2 serological assays need careful qualification is to characterize the epidemiology of disease, prevent unnecessary harm, and allocate resources for targeted control measures.

Avian influenza A(H7N9) epidemics have a fatality rate of approximately 40%. Previous studies reported that low pathogenic avian influenza (LPAI)-derived candidate vaccine viruses (CVVs) are poorly immunogenic. Here, we assess the immunogenicity and efficacy of a highly pathogenic avian influenza (HPAI) A/Guangdong/17SF003/2016 (GD/16)-extracted hemagglutinin (eHA) vaccine. GD/16 eHA induces robust H7-specific antibody responses in mice with a marked adjuvant antigen-sparing effect. Mice immunized with adjuvanted GD/16 eHA are protected from the lethal LPAI and HPAI H7N9 challenges, in stark contrast to low antibody titers and high mortality in mice receiving adjuvanted LPAI H7 eHAs. The protection correlates well with the magnitude of the H7-specific antibody response (IgG and microneutralization) or HA group 2 stem-specific IgG. Inclusion of adjuvanted GD/16 eHA in heterologous prime-boost improves the immunogenicity and protection of LPAI H7 HAs in mice. Our findings support the inclusion of GD/16-derived CVV in the pandemic preparedness vaccine stockpile.

Background: Serological tests are an indispensable tool to understand the epidemiology of the SARS-CoV-2 pandemic, particularly in areas where molecular diagnostics are limited. Poor assay performance may hinder the utility of these tests, including high rates of false-positivity previously reported in sub-Saharan Africa. Methods: From 312 Malian samples collected prior to 2020, we measured antibodies to the commonly tested SARS-CoV-2 antigens and four other betacoronaviruses by ELISA, and assessed functional cross-reactivity in a subset by SARS-CoV-2 pseudovirus neutralization assay. We then evaluated the performance of a two-antigen test developed in the US, using SARS-CoV-2 spike protein and receptor-binding domain ELISA measurements. To optimize test performance, we compared single and two-antigen approaches using existing assay cutoffs and population-specific cutoffs for Malian control samples (positive and negative). Findings: Background reactivity to SARS-CoV-2 antigens was common in pre-pandemic samples compared to US controls (43·4% (135/311) for spike protein, 22·8% (71/312) for RBD, and 33·9% (79/233) for nucleocapsid protein). SARS-CoV-2 reactivity correlated weakly with other betacoronavirus reactivity, varied between Malian communities, and increased with age. No pre-pandemic samples demonstrated functional activity. Regardless of the cutoffs applied, specificity improved using a two-antigen approach. Test performance was optimal using a two-antigen assay with population-specific cutoffs derived from ROC curve analysis [Sensitivity: 73·9% (51·6-89·8), Specificity: 99·4% (97·7-99·9)]. Interpretation: In the setting of high background reactivity, such as sub-Saharan Africa, SARS-CoV-2 serological assays need careful qualification is to characterize the epidemiology of disease, prevent unnecessary harm, and allocate resources for targeted control measures. Funding: This project was funded by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, as well as the National Cancer Institute, National Institutes of Health. Declaration of Interests: The authors declare no conflicts of interest. Ethics Approval Statement: All pre-pandemic samples were collected during NIH-sponsored studies that were approved by the Malian USTTB FMPOS human research ethics committee and the NIAID/NIH institutional review board. Convalescent PCR-confirmed COVID-19 US positive control samples (n=10) were provided by the Adventist Hospital, Maryland. De-identified residual clinical samples for non-human subject research were obtained in accordance with 45 CFR 46. Convalescent samples were collected as part of a Public Health surveillance activity in collaboration with the Malian Ministry of Health COVID-19 Coordination Unit and with the approval of the USTTB FMOS-FAPH ethics committee (No2020/114/CE/FMOS/FAPH).

Immunodominance defines the hierarchical immune response to competing antigens in complex immunogens. Little is known regarding B cell and antibody immunodominance despite its importance to immunity to viruses and other pathogens. We show that B cells and serum antibodies from inbred mice demonstrate a reproducible immunodominance hierarchy to the five major antigenic sites in the influenza A virus hemagglutinin globular domain. The hierarchy changes as the immune response progresses and depending on antigen formulation and delivery. Passive antibody transfer and sequential infection experiments demonstrate “original antigenic suppression”, where antibodies suppress memory responses to the priming antigenic site. Our study provides a template for attaining deeper understanding of antibody immunodominance to viruses and other immunogens.

We studied the ability of monoclonal Abs (mAbs) recognizing the major hemagglutinin (HA) antigenic sites to inhibit neuraminidase (NA) cleavage of sialic acids on fetuin. We show that virion associated-NA activity in the enzyme linked lectin assay (ELLA) is largely dependent on HA-mediated attachment of virions to immobilized fetuin. For a Sb-antigenic site specific mAb, there is a nearly perfect correlation between neuraminidase inhibition and blocking virus attachment to immobilized fetuin. By contrast, Sa-, Ca-, and Cb- antigenic site specific mAbs block NA activity in ELLA or the traditional thiobarbituric acid assay by sterically interfering with NA access to substrate. We conclude first, that ELLA with intact virus can only be used to measure anti-NA Abs if sera lack HA-specific Abs, and second, that anti-HA Abs block NA activity by both limiting virion interaction with sialic acid containing surfaces and by sterically limiting NA access to sialic acids attached to macromolecules.

A major obstacle to vaccination against antigenically variable viruses is skewing of antibody responses to variable immunodominant epitopes. For influenza virus hemagglutinin (HA), the immunodominance of the variable head impairs responses to the highly conserved stem. Here, we show that head immunodominance depends on the physical attachment of head to stem. Stem immunogenicity is enhanced by immunizing with stem-only constructs or by increasing local HA concentration in the draining lymph node. Surprisingly, coimmunization of full-length HA and stem alters stem-antibody class switching. Our findings delineate strategies for overcoming immunodominance, with important implications for human vaccination.

Frequent mutation of its major antibody target, the glycoprotein hemagglutinin, ensures that the influenza virus is perennially both a rapidly emerging virus and a major threat to public health. One type of mutation escapes immunity by adding a glycan onto an area of hemagglutinin that many antibodies recognize. This study revealed that these glycan changes follow a simple temporal pattern. Every 5 to 7 years, hemagglutinin adds a new glycan, up to a limit. After this limit is reached, no net additions of glycans occur. Instead, glycans are swapped or lost at longer intervals. Eventually, a pandemic replaces the terminally glycosylated hemagglutinin with a minimally glycosylated one from the animal reservoir, restarting the cycle. This pattern suggests the following: (i) some hemagglutinins are evolved for this decades-long process, which is both defined by and limited by successive glycan addition; and (ii) hemagglutinin's antibody dominance and its capacity for mutations are highly adapted features that allow influenza to outpace our antibody-based immunity., Human antibody-based immunity to influenza A virus is limited by antigenic drift resulting from amino acid substitutions in the hemagglutinin (HA) head domain. Glycan addition can cause large antigenic changes but is limited by fitness costs to viral replication. Here, we report that glycans are added to H1 and H3 HAs at discrete 5-to-7-year intervals, until they reach a functional glycan limit, after which glycans are swapped at approximately 2-fold-longer intervals. Consistent with this pattern, 2009 pandemic H1N1 added a glycan at residue N162 over the 2015–2016 season, an addition that required two epistatic HA head mutations for complete glycosylation. These strains rapidly replaced H1N1 strains globally, by 2017 dominating H3N2 and influenza B virus strains for the season. The pattern of glycan modulation that we outline should aid efforts for tracing the epidemic potential of evolving human IAV strains.

Due to its superior molecular sensitivity, surgical management of breast cancer now often includes preoperative dynamic contrast enhanced magnetic resonance imaging (DCE-MRI). Nevertheless, statistics indicate that, in practice, tumor size is frequently misestimated leading to incomplete resections, and consequently, repeat surgeries. Our group developed a surgical specimen assessment technique, called intraoperative photoacoustic screening (iPAS), based on photoacoustic tomography and with the capability to visualize whole breast tumors. The system was deployed at a breast surgical center and used to scan freshly excised breast tissue specimens belonging to 12 patients. This report compares breast cancer imaging performance by iPAS to that of DCE-MRI, and pathology.

High re-excision rates in breast conserving surgery call for a new intraoperative approach to the lumpectomy specimen evaluation problem. The unique intraoperative photoacoustic screening (iPAS) system, presented here, demonstrated the capability of photoacoustic tomography (PAT) to deliver optical sensitivity and specificity, along with over 2 cm imaging depth, in a true clinical setting. Highly specialized acoustic transducers enabled the evaluation of tumor extent, shape, morphology and position within lumpectomy specimens measuring up to 11 cm in diameter. Comparison with conventional ultrasound (US) and x-ray imaging validated the performance of iPAS. This approach shines a light towards more effective soft tissue abnormality assessment.

Photoacoustic tomography (PAT) has excellent sensitivity for hemoglobin and lipids, which make up much of human breast tissue. Our group has focused on intraoperative PAT applied to tissues obtained during breast-conserving surgery (BCS). In BCS, the tumor is excised with a margin of healthy tissue to ensure tumor removal. Margin detection can be difficult and re-excision surgeries are required in 10 to 25% of cases. Our first-generation intraoperative PAT system was capable of 3D imaging specimens up to 11 cm in diameter and several centimeters thick. The system used a semi-circular ring of low frequency transducers, resulting in a 2.5 mm spatial resolution. The current objective is to improve spatial resolution using higher frequency transducers. An array was constructed with 41 circular transducers positioned on two concentric circular rungs with a single point of focus. An optical window at the center allowed illumination. The array was tested with imaging phantoms consisting of written words on a clear plastic bag, 108 µm polyester monofilament arranged as parallel lines with spacing varying from 1 mm to 8 mm, and finally with porcine tissues. The array was positioned above and perpendicular to the imaging area and raster scanned. Signal averaging was implemented, and images were reconstructed with universal back projection. Image analysis demonstrated a 400 μm spatial resolution, but with low penetration depth and low sensitivity. Results suggest the transducers could improve spatial resolution of the first-generation intraoperative PAT system by 6-fold.

With a lifetime risk of 1 in 8, breast cancer continues to be a major concern for women and their physicians. The optimal treatment of the disease depends on the stage of the cancer at diagnosis, which is typically assessed using medical imaging. However, currently employed imaging systems for breast tumor measurement rarely agree perfectly. Our group developed an Intraoperative Photoacoustic Screening (iPAS) soft tissue scanner featuring high bulk tissue sensitivity, a clinically compatible scan-time of 6 min, imaging depths greater than 2 cm and the capability to visualize whole breast tumors based on their lipid, rather than hemoglobin, profile. Here, we report on the first clinical experience with breast cancer patients by comparing tumor-measurement using iPAS, preoperative dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) and gold-standard pathology. Tumor size was measured volumetrically for iPAS and DCE-MRI, and separately using maximum diameters for pathology, DCE-MRI and iPAS. Comparisons were performed using Pearson’s correlation coefficients, and the non-parametric Wilcoxon signed-rank test. Twelve consecutive patients were included in the study, contingent on pathologically documented invasive carcinoma. iPAS volumetric tumor size was positively correlated to DCE-MRI (Pearson’s r = 0.78, p = 0.003) and not significantly different (Wilcoxon, p = 0.97). In comparison to pathology, tumor diameters given by iPAS were positively correlated (Pearson’s r = 0.87, p = 0.0002) and significantly different (Wilcoxon, p = 0.0015). The results indicated that volumetric-measurement of invasive breast tumors with iPAS is similar to that of DCE-MRI. On the other hand, tumor diameter measurements were less reliable. Beyond enhancing surgical specimen examination, an extension of this technology to diagnostic imaging promises a new perspective on tumor assessment, potentially improving our current understanding and treatment of breast cancer.

SummaryBroadly neutralizing antibodies (Abs) that bind the influenza virus hemagglutinin (HA) stem may enable universal influenza vaccination. Here, we show that anti-stem Abs sterically inhibit viral neuraminidase activity against large substrates, with activity inversely proportional to the length of the fibrous NA stalk that supports the enzymatic domain. By modulating NA stalk length in recombinant IAVs, we show that anti-stem Abs inhibit virus release from infected cells by blocking NA, accounting for theirin vitroneutralization activity. NA inhibition contributes to anti-stem Ab protection in influenza infected mice, likely due at least in part to NA-mediated inhibition of FcγR dependent activation of innate immune cells by antibody bound to virions. FDA approved NA inhibitors enhance anti-stem based Fcγdependent immune cell activation, raising the possibility of therapeutic synergy between NA inhibitors and anti-stem mAb treatment in humans.

Rapid antigenic evolution enables the persistence of seasonal influenza A and B viruses in human populations despite widespread herd immunity. Understanding viral mechanisms that enable antigenic evolution is critical for designing durable vaccines and therapeutics. Here, we utilize the primerID method of error-correcting viral population sequencing to reveal an unexpected role for hemagglutinin (HA) glycosylation in compensating for fitness defects resulting from escape from anti-HA neutralizing antibodies. Antibody-free propagation following antigenic escape rapidly selected viruses with mutations that modulated receptor binding avidity through the addition of N-linked glycans to the HA globular domain. These findings expand our understanding of the viral mechanisms that maintain fitness during antigenic evolution to include glycan addition, and highlight the immense power of high-definition virus population sequencing to reveal novel viral adaptive mechanisms., Author summary Seasonal influenza A viruses (IAV) cause tens of thousands of deaths and tens of billions of dollars in economic costs every year in the U.S. alone, despite widespread pre-exposure and vaccination. IAV persists within the human population by evading herd immunity through the continual accumulation of immune escape substitutions in a process known as antigenic drift. Unfortunately, the specific mechanisms that facilitate IAV antigenic drift remain unclear, making it difficult to design more efficacious, escape-proof vaccines. Here, we used a high-definition population sequencing approach to understand how IAV tolerates the accumulation of immune escape substitutions during antigenic drift without losing fitness. We found that the virus rapidly acquired N-linked glycan structures on the hemagglutinin (HA) protein following escape from a panel of neutralizing antibodies. Glycosylation of HA alleviated the deleterious effects of immune escape substitutions on interactions with host cell receptors. These results expand our understanding of the mechanisms that facilitate IAV immune evasion, and highlight the immense power of high-definition virus population sequencing to reveal novel viral adaptive mechanisms.

A major obstacle to vaccination to antigenically variable viruses is skewing of antibody responses to immunodominant epitopes. For influenza virus hemagglutinin (HA), the immunodominance of the variable head impairs responses to the highly conserved stem. Here, we show that head immunodominance depends on the physical attachment of head to stem. Stem immunogenicity is enhanced by immunizing with stem only-constructs or by increasing local HA concentration in the draining lymph node. Surprisingly, co-immunization of HA and stem alters stem-antibody class switching. Our findings delineate strategies for overcoming immunodominance with important implications for human vaccination.

Probing the limits of CD8+ T cell immunosurveillance, we inserted the SIINFEKL peptide into influenza A virus (IAV)-negative strand gene segments. Although IAV genomic RNA is considered noncoding, there is a conserved, relatively long open reading frame present in segment 8, encoding a potential protein termed NEG8. The biosynthesis of NEG8 from IAV has yet to be demonstrated. Although we failed to detect NEG8 protein expression in IAV-infected mouse cells, cell surface Kb-SIINFEKL complexes are generated when SIINFEKL is genetically appended to the predicted C terminus of NEG8, as shown by activation of OT-I T cells in vitro and in vivo. Moreover, recombinant IAV encoding of SIINFEKL embedded in the negative strand of the neuraminidase-stalk coding sequence also activates OT-I T cells in mice. Together, our findings demonstrate both the translation of sequences on the negative strand of a single-stranded RNAvirus and its relevance in antiviral immunosurveillance. Fil: Hickman, Heather D.. National Institute Of Allergy And Infectious Diseases; Fil: Mays, Jacqueline W.. National Institute Of Allergy And Infectious Diseases; Fil: Gibbs, James. National Institute Of Allergy And Infectious Diseases; Fil: Kosik, Ivan. National Institute Of Allergy And Infectious Diseases; Fil: Magadan, Javier Guillermo. National Institute Of Allergy And Infectious Diseases; . Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo; Argentina Fil: Takeda, Kazuyo. Food And Drug Administration; Fil: Das, Suman. National Institute Of Allergy And Infectious Diseases; Fil: Reynoso, Glennys V.. National Institute Of Allergy And Infectious Diseases; Fil: Ngudiankama, Barbara F.. National Institute Of Allergy And Infectious Diseases; Fil: Wei, Jiajie. National Institute Of Allergy And Infectious Diseases; Fil: Shannon, John P.. National Institute Of Allergy And Infectious Diseases; Fil: McManus, Daniel. National Institute Of Allergy And Infectious Diseases; Fil: Yewdell, Jonathan W.. National Institute Of Allergy And Infectious Diseases

Rapid antigenic evolution enables the persistence of seasonal influenza A and B viruses in human populations despite widespread herd immunity. Understanding viral mechanisms that enable antigenic evolution is critical for designing durable vaccines and therapeutics. Here, we utilize the primerID method of error-correcting viral population sequencing to reveal an unexpected role for hemagglutinin (HA) glycosylation in compensating for fitness defects resulting from escape from anti-HA neutralizing antibodies. Antibody-free propagation following antigenic escape rapidly selected viruses with mutations that modulated receptor binding avidity through the addition of N-linked glycans to the HA globular domain. These findings expand our understanding of the viral mechanisms that maintain fitness during antigenic evolution to include glycan addition, and highlight the immense power of high-definition virus population sequencing to reveal novel viral adaptive mechanisms. Fil: Kosik, Ivan. National Institute of Allergy and Infectious Diseases; Estados Unidos Fil: Ince, William L.. National Institute of Allergy and Infectious Diseases; Estados Unidos. National Center For Toxicological Research. Food And Drug Administration; Estados Unidos Fil: Gentles, Lauren E.. National Institute of Allergy and Infectious Diseases; Estados Unidos Fil: Oler, Andrew J.. National Institute of Allergy and Infectious Diseases; Estados Unidos Fil: Kosikova, Martina. National Center For Toxicological Research. Food And Drug Administration; Estados Unidos Fil: Angel, Matthew. National Institute of Allergy and Infectious Diseases; Estados Unidos Fil: Magadan, Javier Guillermo. National Institute of Allergy and Infectious Diseases; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; Argentina Fil: Xie, Hang. National Center For Toxicological Research. Food And Drug Administration; Estados Unidos Fil: Brooke, Christopher B.. University of Illinois at Urbana; Estados Unidos Fil: Yewdell, Jonathan W.. National Institute of Allergy and Infectious Diseases; Estados Unidos

Adaptive immunity to influenza A virus is limited by frequent mutations in the immunodominant head of hemagglutinin (HA). Over the last century, the upward trend in HA-head glycosylation indicates glycan addition can increase fitness, but its role in viral evolution remains unclear. Here, we report glycan evolution follows a clock-like rhythm, pacing the timeline, trajectory, and replacement of HA. Following pandemic introduction, glycans are added to HA at 4- to 6-year intervals, until a functional glycan limit is reached, after which, at 9- to 12-year intervals, glycans are either swapped between different sites, or the HA is replaced by a novel pandemic virus. Using this, we predicted the appearance of the newest glycan on pH1N1 HA. Phylogeographic reconstruction suggests these highly fit strains originated in the Middle East, before rapidly replacing all strains globally. Going forward, we can use this simple algorithm to forecast future glycan evolution and identify seasons with higher pandemic potential.

High re-excision rates in breast-conserving surgery call for a new intraoperative approach to the lumpectomy margin evaluation problem. The unique intraoperative imaging system, presented here, demonstrated the capability of photoacoustic tomography (PAT) to deliver optical sensitivity and specificity, along with over 2-cm imaging depth, in a clinical setting. The system enabled the evaluation of tumor extent, shape, morphology, and position within lumpectomy specimens measuring up to 11 cm in diameter. The investigation included all major breast cancer-related lesions, such as invasive ductal carcinoma (IDC), multifocal IDC, ductal carcinoma in situ and combinations of these variants. Coregistration with established ultrasound (US) technology, as well as comparison to specimen radiography, validated the performance of PAT, which appeared to facilitate better tumor visualization. Contrary to expected PA contrast mechanisms, PAT images of hemoglobin distribution correlated poorly with US-determined tumor location, while hypointense regions in lipid-weighted PAT images were in better agreement with US.

Influenza A virions possess two surface glycoproteins—the hemagglutinin (HA) and neuraminidase (NA)—which exert opposite functions. HA attaches virions to cells by binding to terminal sialic acid residues on glycoproteins/glycolipids to initiate the infectious cycle, while NA cleaves terminal sialic acids, releasing virions to complete the infectious cycle. Antibodies specific for HA or NA can protect experimental animals from IAV pathogenesis and drive antigenic variation in their target epitopes that impairs vaccine effectiveness in humans. Here, we review progress in understanding HA/NA co-evolution as each acquires epistatic mutations to restore viral fitness to mutants selected in the other protein by host innate or adaptive immune pressure. We also discuss recent exciting findings that antibodies to HA can function in vivo by blocking NA enzyme activity to prevent nascent virion release and enhance Fc receptor-based activation of innate immune cells.

Although influenza DNA vaccine research has focused mainly on viral hemagglutinin and has led to promising results, other virion proteins have also shown some protective potential. In this work, we explored the potential of a DNA vaccine based on the PB1 protein to protect BALB/c mice against lethal influenza A virus infection. The DNA vaccine consisted of pTriEx4 plasmid expressing PB1. As a positive control, a pTriEx4 plasmid expressing influenza A virus HA was used. Two weeks after three subcutaneous doses of DNA vaccine, the mice were challenged intranasally with 1 LD50 of A/Puerto Rico/8/34 (H1N1) virus, and PB1- and HA-specific antibodies, survival rate, body weight change, viral mRNA load, infectious virus titer in the lungs, cytokines IL-2, IL-4 and IL-10, and granzyme-B were measured. The results showed that (i) the PB1-expressing DNA vaccine provided a fair protective immunity in the mouse model and (ii) viral structural proteins such as PB1 represent promising antigens for DNA vaccination against influenza A.

Human infections with avian influenza A viruses (IAVs) without or with clinical symptoms of disease were recently reported from several continents, mainly in high risk groups of people, who came into the contact with infected domestic birds or poultry. It was shown that avian IAVs are able to infect humans directly without previous adaptation, however, their ability to replicate and to cause a disease in this new host can differ. No spread of these avian IAVs among humans has been documented until now, except for one case described in Netherlands in the February of 2003 in people directly involved in handling IAV (H7N7)-infected poultry. The aim of our work was to examine whether a low pathogenic avian IAV can induce a virus-specific immune response of biological relevancy, in spite of its restricted replication in mammals. As a model we used a low pathogenic virus A/Duck/Czechoslovakia/1956 (H4N6) (A/Duck), which replicated well in MDCK cells and produced plaques on cell monolayers, but was unable to replicate productively in mouse lungs. We examined how the immune system of mice responds to the intranasal application of this non-adapted avian virus. Though we did not prove the infectious virus in lungs of mice following A/Duck application even after its multiple passaging in mice, we detected virus-specific vRNA till day 8 post infection. Moreover, we detected virus-specific mRNA and de novo synthesized viral nucleoprotein (NP) and membrane protein (M1) in lungs of mice on day 2 and 4 after exposure to A/Duck. Virus-specific antibodies in sera of these mice were detectable by ELISA already after a single intranasal dose of A/Duck virus. Not only antibodies specific to the surface glycoprotein hemagglutinin (HA) were induced, but also antibodies specific to the NP and M1 of IAV were detected by Western blot and their titers increased after the second exposure of mice to this virus. Importantly, antibodies neutralizing virus A/Duck were proved in mouse immune sera after the second dose of virus and a slight increase of mRNA expression of immune mediators tumor necrosis factor alpha (TNF-α) and IP10 has been observed in lungs of these mice 48 hr after the infection. These observations correspond to the limited replication ability of the virus in mice and provided an important information about its ability to induce virus-specific antibodies, including those neutralizing virus, even without the previous virus adaptation to the new mammalian host. Such antibodies could consequently influence the immune potential of exposed individuals and their defensive capability against the newly emerged, even more virulent IAV.

Hickman, H. D., J. W. Mays, J. Gibbs, I. Kosik, J. G. Magadan, K. Takeda, S. Das, G. V. Reynoso, B. F. Ngudiankama, J. Wei, J. P. Shannon, D. McManus, and J. W. Yewdell. 2018. Influenza A virus negative strand RNA is translated for CD8+ T cell immunosurveillance. J. Immunol. 201: [1222–1228][1

In this work we simulated in a mouse model a naturally occurring situation of humans, who overcame an infection with epidemic strains of influenza A, and were subsequently exposed to avian influenza A viruses (IAV). The antibody response to avian IAV in mice previously infected with human IAV was analyzed. We used two avian IAV (A/Duck/Czechoslovakia/1956 (H4N6) and the attenuated virus rA/Viet Nam/1203-2004 (H5N1)) as well as two human IAV isolates (virus A/Mississippi/1/1985 (H3N2) of medium virulence and A/Puerto Rico/8/1934 (H1N1) of high virulence). Two repeated doses of IAV of H4 or of H5 virus elicited virus-specific neutralizing antibodies in mice. Exposure of animals previously infected with human IAV (of H3 or H1 subtype) to IAV of H4 subtype led to the production of antibodies neutralizing H4 virus in a level comparable with the level of antibodies against the human IAV used for primary infection. In contrast, no measurable levels of virus-neutralizing (VN) antibodies specific to H5 virus were detected in mice infected with H5 virus following a previous infection with human IAV. In both cases the secondary infection with avian IAV led to a significant increase of the titer of VN antibodies specific to the corresponding human virus used for primary infection. Moreover, cross-reactive HA2-specific antibodies were also induced by sequential infection. By virtue of these results we suggest that the differences in the ability of avian IAV to induce specific antibodies inhibiting virus replication after previous infection of mice with human viruses can have an impact on the interspecies transmission and spread of avian IAV in the human population.

The aim of the present study was to identify what influences the short half-life of the influenza A virus PB1-F2 protein and whether a prolonged half-life affects the properties of this molecule. We hypothesized that the short half-life of PB1-F2 could conceal the phenotype of the protein. Because proteasome degradation might be involved in PB1-F2 degradation, we focused on ubiquitination, a common label for proteasome targeting. A cluster of lysine residues was demonstrated as an ubiquitination acceptor site in evolutionary and functionally distinct proteins. The PB1-F2 sequence alignment revealed a cluster of lysines on the carboxy terminal end of PB1-F2 in almost all of the GenBank sequences available to date. Using a proximity ligation assay, we identified ubiquitination as a novel posttranslational modification of PB1-F2. Changing the lysines at positions 73, 78, and 85 to arginines suppressed the ubiquitination of A/Puerto Rico/8/1934 (H1N1)-derived PB1-F2. The mutation of the C-terminal lysine residue cluster positively affected the overall expression levels of avian A/Honk Kong/156/1997 (H5N1)- and mammalian A/Puerto Rico/8/1934 (H1N1)-derived PB1-F2. Moreover, increased PB1-F2 copy numbers strengthened the functions of this virus in the infected cells. The results of a minigenome luciferase reporter assay revealed an enhancement of viral RNA-dependent RNA polymerase activity in the presence of stabilized PB1-F2, regardless of viral origin. IFNβ antagonism was enhanced in 293T cells transfected with a plasmid expressing stabilized K→R mutant variants of PB1-F2. Compared with PB1-F2 wt, the loss of ubiquitination enhanced the antibody response after DNA vaccination. In summary, we revealed that PB1-F2 is an ubiquitinated IAV protein, and this posttranslational modification plays a central role in the regulation of the biological functions of this protein.

PB1-F2 protein of influenza A virus (IAV) was cloned in a plum pox virus (PPV) genome-based vector and attempts to express it in biolistically transfected Nicotiana benthamiana plants were performed. The vector-insert construct replicated in infected plants properly and was stable during repeated passage by mechanical inoculation, as demonstrated by disease symptoms and immunoblot detection of PPV capsid protein, while PB1-F2-specific band was more faint. We showed that it was due its low solubility. Modification of sample preparation (denaturation/solubilization preceding the centrifugation of cell debris) led to substantial signal enhancement. Maximal level of PB1-F2 expression in plants was observed 12 days post inoculation (dpi). Only 1% SDS properly solubilized the protein, other detergents were much less efficient. Solubilization with 8M urea released approximately 50% of PB1-F2 from the plant tissues, thus the treatment with this removable chaotropic agent may be a good starting point for the purification of the protein for eventual functional studies in the future.

Photoacoustic imaging (PAI) has been proposed as a non-invasive technique for imaging neonatal brain injury. Since PAI combines many of the merits of both optical and ultrasound imaging, images with high contrast, high resolution, and a greater penetration depth can be obtained when compared to more traditional optical methods. However, due to the strong attenuation and reflection of photoacoustic pressure waves at the skull bone, PAI of the brain is much more challenging than traditional methods (e.g. near infrared spectroscopy) for optical interrogation of the neonatal brain. To evaluate the potential limits the skull places on 3D PAI of the neonatal brain, we constructed a neonatal skull phantom (1.4-mm thick) with a mixture of epoxy and titanium dioxide powder that provided acoustic insertion loss (1-5MHz) similar to human infant skull bone. The phantom was molded into a realistic infant skull shape by means of a CNCmachined mold that was based upon a 3D CAD model. To evaluate the effect of the skull bone on PAI, a photoacoustic point source was raster scanned within the phantom brain cavity to capture the imaging operator of the 3D PAI system (128 ultrasound transducers in a hemispherical arrangement) with and without the intervening skull phantom. The resultant imaging operators were compared to determine the effect of the skull layer on the PA signals in terms of amplitude loss and time delay. © 2013 Copyright SPIE.