bioRxiv Science⌕ Search

Biology subjects

Johnson, R. F.

Publications and source records attributed to Johnson, R. F..

14 recordsLinked to original sources

Biodiversity data portals as methodological filters for iNaturalist: how platform choice can shape biodiversity assessments

iNaturalist has rapidly grown to become one of the largest contributors of global biodiversity data, being widely used in academic research, to support and inform applied conservation, and to help develop policy indicators for decision makers. However, the availability of iNaturalist data varies based on the digital platform it is accessed from. Here, we assess whether the pathway used to access iNaturalist data from three commonly available biodiversity data sources: iNaturalist, the Global Biodiversity Information Facility (GBIF) and ESRIs ArcGIS Online, alters occurrence record availability and downstream analyses for ecological inference. First, we investigate iNaturalist data availability on ArcGIS Online and find that the reduced field metadata for record location and obscuration information can lead to biased assumptions in the spatial ranges of sensitive species. Second, when assessing iNaturalist records available through GBIF, we find that restrictive Creative Commons observation licenses prevent an average of 26.1% of iNaturalist Research Grade records from being exported to GBIF, and this can lead to differences in environmental niche analysis when compared to datasets including all available research grade records. Understanding differences in platform licensing when integrating across biodiversity data repositories is another consideration for researchers and practitioners when conducting biodiversity assessments. Our results show that the pathway through which iNaturalist data are accessed can function as a methodological filter, potentially altering spatial coverage, the climatic conditions represented by occurrence datasets, and downstream ecological analysis.

ecology↗

Intranasal Replicating Adenovirus type 4-SARS-CoV-2 Recombinants Induce Superior Immune Response Durability and Efficacy in Preclinical Testing Compared to Standard Intramuscular Vaccines

The portfolio of next generation COVID-19 vaccines would benefit from candidates that induce durable systemic and mucosal immune responses that would lessen person-to-person transmission. We constructed an intranasal (IN) replication-competent adenovirus type 4 recombinant platform to express SARS-CoV-2 Spike variants (Ad4-S) and assessed immunogenicity and efficacy in the Syrian hamster model. Although both IN Ad4-S and intramuscular (IM) vaccines (Ad26.CoV2.S and mRNA-1273) induced serum binding antibodies, only Ad4-S induced a robust mucosal response in the nasal cavity. IN Ad4-S vaccination induced serum neutralizing titers equivalent to or greater than IM vaccination but more durable up to 6 months. Upon challenge, IN immunization also resulted in less weight loss, greater breadth and durability of restriction of viral replication, and less lung pathology than IM immunization up to 268 days after immunization. These data support the potential of the IN Ad4 vaccine platform to reduce transmission of SARS-CoV-2 and other respiratory viruses with pandemic potential.

immunology↗

Global monitoring of wildlife mortality through participatory science in near-real time

Detection of wildlife mortality events is critical for timely conservation and natural resource management. We present an open-source, web-based decision support tool that queries, aggregates and summarizes participatory science data from iNaturalist to monitor mortality events worldwide. We demonstrate the effectiveness of this approach using four case studies spanning taxonomic, spatial, and temporal scales. In Canada and the United States, high peaks of bird mortality coincided with zoonotic risk during avian influenza outbreaks. Across Latin America, we detected 75 mortality events of critically endangered species. In California, recorded mammal mortality was associated with human infrastructure, including proximity to roads, and to a lesser extent, the human footprint. Mortality of pumas (Puma concolor) was detected across nine countries, highlighting the need for international cooperation to conserve mobile species. Our tool enables resource managers to flag emerging threats and empowers participatory scientists to monitor and integrate mortality records for conservation.

ecology↗

Intranasal parainfluenza virus-vectored vaccine expressing SARS-CoV-2 spike protein of Delta or Omicron B.1.1.529 induces mucosal and systemic immunity and protects hamsters against homologous and heterologous challenge

The continuous emergence of new SARS-CoV-2 variants requires that COVID vaccines be updated to match circulating strains. We generated B/HPIV3-vectored vaccines expressing 6P-stabilized S protein of the ancestral, B.1.617.2/Delta, or B.1.1.529/Omicron variants as pediatric vaccines for intranasal immunization against HPIV3 and SARS-CoV-2 and characterized these in hamsters. Following intranasal immunization, these B/HPIV3 vectors replicated in the upper and lower respiratory tract and induced mucosal and serum anti-S IgA and IgG. B/HPIV3 expressing ancestral or B.1.617.2/Delta-derived S-6P induced serum antibodies that effectively neutralized SARS-CoV-2 of the ancestral and B.1.617.2/Delta lineages, while the cross-neutralizing potency of B.1.1.529/Omicron S-induced antibodies was lower. Despite the lower cross-neutralizing titers induced by B/HPIV3 expressing S-6P from B.1.1.529/Omicron, a single intranasal dose of all three versions of B/HPIV3 vectors was protective against matched or heterologous WA1/2020, B.1.617.2/Delta or BA.1 (B.1.1.529.1)/Omicron challenge; hamsters were protected from challenge virus replication in the lungs, while low levels of challenge virus were detectable in the upper respiratory tract of a small number of animals. Immunization also protected against lung inflammatory response after challenge, with mild inflammatory cytokine induction associated with the slightly lower level of cross-protection of WA1/2020 and B.1.617.2/Delta variants against the BA.1/Omicron variant. Serum antibodies elicited by all vaccine candidates were broadly reactive against 20 antigenic variants, but the antigenic breadth of antibodies elicited by B/HPIV3-expressed S-6P from the ancestral or B.1.617.2/Delta variant exceeded that of the S-6P B.1.1.529/Omicron expressing vector. These results will guide development of intranasal B/HPIV3 vectors with S antigens matching circulating SARS-CoV-2 variants. Author SummaryIntranasal COVID vaccines have the potential to stimulate respiratory mucosal immunity, effectively restricting replication of SARS-CoV-2 in the respiratory tract, thereby reducing virus shedding and transmission. To develop pediatric vaccines for intranasal immunization against HPIV3 and SARS-CoV-2, we use live-attenuated bovine-human parainfluenza virus vaccine, a pediatric intranasal parainfluenza virus vaccine candidate, designed to express the stabilized SARS-CoV-2 spike protein. We compared the immunogenicity and breadth of protection of the B/HPIV3-expressed ancestral, B.1.617.2/Delta, or B.1.1.529/Omicron variants following intranasal immunization in hamsters. All three B/HPIV3 vectors replicated in the respiratory tract, induced mucosal and serum anti-S IgA and IgG, and were protective in the hamster model against matched or heterologous WA1/2020, B.1.617.2/Delta or BA.1 (B.1.1.529.1)/Omicron SARS-CoV-2 challenge. Serum antibodies elicited by all intranasal vaccine candidates were broadly reactive against 20 antigenic variants of SARS-CoV-2, but the antigenic breadth of antibodies elicited by B/HPIV3-expressed stabilized S from the ancestral or B.1.617.2/Delta variant exceeded that of the S-6P B.1.1.529/Omicron expressing vector. Thus, these intranasal vectored SARS-CoV-2 vaccine candidates induce cross-protective SARS-CoV-2 immunity with antigenic breadth similar to that of injectable SARS-CoV-2 vaccines. These results will guide development of intranasal COVID vaccines based on B/HPIV3 vectors with S antigens matching current SARS-CoV-2 variants.

microbiology↗

Why didnt the nudibranch cross the ocean? Understanding biogeographic and evolutionary relationships of Hermissenda (Nudibranchia: Myrrhinidae) Bergh, 1878

In the aftermath of the 2011 east Japanese earthquake and tsunami, anthropogenic debris from the east coast of Japan floated across the Pacific Ocean to the west coast of North America. One such vessel from Iwate Prefecture arrived on the coast of Oregon, and the fouling community included specimens identified as the nudibranch Hermissenda crassicornis, which was previously thought to range from Japan to Baja California but has since been split into three species: H. crassicornis (Alaska to southern CA), H. opalescens (British Columbia to Baja California), and H. emurai (Japan, Korea, Russian Far East). Previous work suggested that all of the motile invertebrates found in the tsunami debris fouling community were either pelagic or Japanese in origin. Our study sought to determine whether the nudibranch specimens collected from the Iwate vessel were, according to the new classification system, only H. emurai or whether the Eastern Pacific Hermissenda were present as well. Results from DNA sequencing and morphological analysis suggest that specimens of H. crassicornis, as it is currently recognized, and H. opalescens were found on the vessel. This finding indicates either that these species settled after arrival to the west coast of North America or that H. crassicornis and H. opalescens is found in Japan, suggesting Hermissenda ranges need to be investigated further. Occurrence data shared on the iNaturalist platform were also used to assess current ranges. Our phylogenetic tree and haplotype network constructed from COI data from all Hermissenda species indicate that H. opalescens and H. emurai are most closely related with H. opalescens sister to the clade that contains H. opalescens and H. emurai. This study demonstrates the power of combining volunteer naturalist data with lab-collected data to understand evolutionary relationships, species ranges, and biogeography.

zoology↗

The inflammatory microenvironment of the lung at the time of infection governs innate control of SARS-CoV-2 replication

SARS-CoV-2 infection leads to vastly divergent clinical outcomes ranging from asymptomatic infection to fatal disease. Co-morbidities, sex, age, host genetics and vaccine status are known to affect disease severity. Yet, how the inflammatory milieu of the lung at the time of SARS-CoV-2 exposure impacts the control of viral replication remains poorly understood. We demonstrate here that immune events in the mouse lung closely preceding SARS-CoV-2 infection significantly impact viral control and we identify key innate immune pathways required to limit viral replication. A diverse set of pulmonary inflammatory stimuli, including resolved antecedent respiratory infections with S. aureus or influenza, ongoing pulmonary M. tuberculosis infection, ovalbumin/alum-induced asthma or airway administration of defined TLR ligands and recombinant cytokines, all establish an antiviral state in the lung that restricts SARS-CoV-2 replication upon infection. In addition to antiviral type I interferons, the broadly inducible inflammatory cytokines TNF and IL-1 precondition the lung for enhanced viral control. Collectively, our work shows that SARS-CoV-2 may benefit from an immunologically quiescent lung microenvironment and suggests that heterogeneity in pulmonary inflammation that precedes or accompanies SARS-CoV-2 exposure may be a significant factor contributing to the population-wide variability in COVID-19 disease outcomes.

immunology↗

Pre-existing interferon gamma conditions the lung to mediate early control of SARS-CoV-2

Interferons (IFNs) are critical for anti-viral host defence. Type-1 and type-3 IFNs are typically associated with early control of viral replication and promotion of inflammatory immune responses; however, less is known about the role of IFN{gamma} in anti-viral immunity, particularly in the context of SARS-CoV-2. We have previously observed that lung infection with attenuated bacteria Mycobacterium bovis BCG achieved though intravenous (iv) administration provides strong protection against SARS-CoV-2 (SCV2) infection and disease in two mouse models. Assessment of the pulmonary cytokine milieu revealed that iv BCG induces a robust IFN{gamma} response and low levels of IFN{beta}. Here we examined the role of ongoing IFN{gamma} responses due to pre-established bacterial infection on SCV2 disease outcomes in two murine models. We report that IFN{gamma} is required for iv BCG induced reduction in pulmonary viral loads and that this outcome is dependent on IFN{gamma} receptor expression by non-hematopoietic cells. Further analysis revealed that BCG infection promotes the upregulation of interferon-stimulated genes (ISGs) with reported anti-viral activity by pneumocytes and bronchial epithelial cells in an IFN{gamma}-dependent manner, suggesting a possible mechanism for the observed protection. Finally, we confirmed the importance of IFN{gamma} in these anti-viral effects by demonstrating that the recombinant cytokine itself provides strong protection against SCV2 challenge when administered intranasally. Together, our data show that a pre-established IFN{gamma} response within the lung is protective against SCV2 infection, suggesting that concurrent or recent infections that drive IFN{gamma} may limit the pathogenesis of SCV2 and supporting possible prophylactic uses of IFN{gamma} in COVID-19 management.

immunology↗

Helminth exposure protects against murine SARS-CoV-2 infection through macrophage dependent T cell activation

Helminth endemic regions report lower COVID-19 morbidity and mortality. Here, we show that lung remodeling from a prior infection with a lung migrating helminth, Nippostrongylus brasiliensis, enhances viral clearance and survival of human-ACE2 transgenic mice challenged with SARS-CoV-2 (SCV2). This protection is associated with a lymphocytic infiltrate including an increased accumulation of pulmonary SCV2-specific CD8+ T cells and anti-CD8 antibody depletion abrogated the N. brasiliensis-mediated reduction in viral loads. Pulmonary macrophages with a type-2 transcriptional signature persist in the lungs of N. brasiliensis exposed mice after clearance of the parasite and establish a primed environment for increased antigen presentation. Accordingly, depletion of macrophages ablated the augmented viral clearance and accumulation of CD8+ T cells driven by prior N. brasiliensis infection. Together, these findings support the concept that lung migrating helminths can limit disease severity during SCV2 infection through macrophage-dependent enhancement of anti-viral CD8+ T cell responses. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/515832v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1c17a22org.highwire.dtl.DTLVardef@13967b3org.highwire.dtl.DTLVardef@1c723a7org.highwire.dtl.DTLVardef@f5e038_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Evaluation of endogenous and therapeutic 25-hydroxycholesterols in murine models of pulmonary SARS-CoV-2 infection

Oxysterols (i.e., oxidized cholesterol species) have complex roles in biology. 25-hydroxycholesterol (25HC), a product of activity of cholesterol-25-hydroxylase (CH25H) upon cholesterol, has recently been shown to be broadly antiviral, suggesting therapeutic potential against SARS-CoV-2. However, 25HC can also amplify inflammation and tissue injury and be converted by CYP7B1 to 7,25HC, a lipid with chemoattractant activity via the G protein-coupled receptor, EBI2/GPR183. Here, using in vitro studies and two different murine models of SARS-CoV-2 infection, we investigate the effects of these two oxysterols on SARS-CoV-2 pneumonia. We show that while 25HC and enantiomeric-25HC are antiviral in vitro against human endemic coronavirus-229E, they did not inhibit SARS-CoV-2; nor did supplemental 25HC reduce pulmonary SARS-CoV-2 titers in the K18-human ACE2 mouse model in vivo. 25HC treatment also did not alter immune cell influx into the airway, airspace cytokines, lung pathology, weight loss, symptoms, or survival but was associated with increased airspace albumin, an indicator of microvascular injury, and increased plasma pro-inflammatory cytokines. Conversely, mice treated with the EBI2/GPR183 inhibitor NIBR189 displayed a modest increase in lung viral load only at late time points, but no change in weight loss. Consistent with these findings, although Ch25h was upregulated in the lungs of SARS-CoV-2-infected WT mice, lung viral titers and weight loss in Ch25h-/- and Gpr183-/- mice infected with the beta variant were similar to control animals. Taken together, endogenous 25-hydroxycholesterols do not significantly regulate early SARS-CoV-2 replication or pathogenesis and supplemental 25HC may have pro-injury rather than therapeutic effects in SARS-CoV-2 pneumonia.

immunology↗

IL-10 suppresses T cell expansion while promoting tissue-resident memory cell formation during SARS-CoV-2 infection in rhesus macaques

The pro- and anti-inflammatory pathways that determine the balance of inflammation and viral control during SARS-CoV-2 infection are not well understood. Here we examine the roles of IFN{gamma} and IL-10 in regulating inflammation, immune cell responses and viral replication during SARS-CoV-2 infection of rhesus macaques. IFN{gamma} blockade tended to decrease lung inflammation based on 18FDG-PET/CT imaging but had no major impact on innate lymphocytes, neutralizing antibodies, or antigen-specific T cells. In contrast, IL-10 blockade transiently increased lung inflammation and enhanced accumulation of virus-specific T cells in the lower airways. However, IL-10 blockade also inhibited the differentiation of virus-specific T cells into airway CD69+CD103+ TRM cells. While virus-specific T cells were undetectable in the nasal mucosa of all groups, IL-10 blockade similarly reduced the frequency of total TRM cells in the nasal mucosa. Neither cytokine blockade substantially affected viral load and infection ultimately resolved. Thus, in the macaque model of mild COVID-19, the pro- and anti-inflammatory effects of IFN{gamma} and IL-10 have no major role in control of viral replication. However, IL-10 has a key role in suppressing the accumulation of SARS-CoV-2-specific T cells in the lower airways, while also promoting TRM at respiratory mucosal surfaces.

immunology↗

Intranasal pediatric parainfluenza virus-vectored SARS-CoV-2 vaccine candidate is protective in macaques

Pediatric SARS-CoV-2 vaccines are needed that elicit immunity directly in the airways, as well as systemically. Building on pediatric parainfluenza virus vaccines in clinical development, we generated a live-attenuated parainfluenza virus-vectored vaccine candidate expressing SARS-CoV-2 prefusion-stabilized spike (S) protein (B/HPIV3/S-6P) and evaluated its immunogenicity and protective efficacy in rhesus macaques. A single intranasal/intratracheal dose of B/HPIV3/S-6P induced strong S-specific airway mucosal IgA and IgG responses. High levels of S-specific antibodies were also induced in serum, which efficiently neutralized SARS-CoV-2 variants of concern. Furthermore, B/HPIV3/S-6P induced robust systemic and pulmonary S-specific CD4+ and CD8+ T-cell responses, including tissue-resident memory cells in lungs. Following challenge, SARS-CoV-2 replication was undetectable in airways and lung tissues of immunized macaques. B/HPIV3/S-6P will be evaluated clinically as pediatric intranasal SARS-CoV-2/parainfluenza virus type 3 vaccine. One-Sentence SummaryIntranasal parainfluenza virus-vectored COVID-19 vaccine induces anti-S antibodies, T-cell memory and protection in macaques.

immunology↗

Characteristic and quantifiable COVID-19-like abnormalities in CT- and PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing an exponentially increasing number of coronavirus disease 19 (COVID-19) cases globally. Prioritization of medical countermeasures for evaluation in randomized clinical trials is critically hindered by the lack of COVID-19 animal models that enable accurate, quantifiable, and reproducible measurement of COVID-19 pulmonary disease free from observer bias. We first used serial computed tomography (CT) to demonstrate that bilateral intrabronchial instillation of SARS-CoV-2 into crab-eating macaques (Macaca fascicularis) results in mild-to-moderate lung abnormalities qualitatively characteristic of subclinical or mild-to-moderate COVID-19 (e.g., ground-glass opacities with or without reticulation, paving, or alveolar consolidation, peri-bronchial thickening, linear opacities) at typical locations (peripheral>central, posterior and dependent, bilateral, multi-lobar). We then used positron emission tomography (PET) analysis to demonstrate increased FDG uptake in the CT-defined lung abnormalities and regional lymph nodes. PET/CT imaging findings appeared in all macaques as early as 2 days post-exposure, variably progressed, and subsequently resolved by 6-12 days post-exposure. Finally, we applied operator-independent, semi-automatic quantification of the volume and radiodensity of CT abnormalities as a possible primary endpoint for immediate and objective efficacy testing of candidate medical countermeasures.

microbiology↗

Clinical Characterization of Host Response to Simian Hemorrhagic Fever Virus Infection in Permissive and Refractory Hosts: A Model for Determining Mechanisms of VHF Pathogenesis

Simian hemorrhagic fever virus (SHFV) causes a fulminant and typically lethal viral hemorrhagic fever (VHF) in macaques (Cercopithecinae: Macaca spp.) but causes subclinical infections in patas monkeys (Cercopithecinae: Erythrocebus patas). This difference in disease course offers a unique opportunity to compare host-responses to infection by a VHF-causing virus in biologically similar susceptible and refractory animals. Patas and rhesus monkeys were inoculated side-by-side with SHFV. In contrast to the severe disease observed in rhesus monkeys, patas monkeys developed a limited clinical disease characterized by changes in complete blood counts, serum chemistries, and development of lymphadenopathy. Viremia was measurable 2 days after exposure and its duration varied by species. Infectious virus was detected in terminal tissues of both patas and rhesus monkeys. Varying degrees of overlap in changes in serum concentrations of IFN-{gamma}, MCP-1, and IL-6 were observed between patas and rhesus monkeys, suggesting the presence of common and species-specific cytokine responses to infection. Similarly, quantitative immunohistochemistry of terminal livers and whole blood flow cytometry revealed varying degrees of overlap in changes in macrophages, natural killer cells, and T-cells. The unexpected degree of overlap in host-response suggests that relatively small subsets of a hosts response to infection may be responsible for driving pathogenesis that results in a hemorrhagic fever. Furthermore, comparative SHFV infection in patas and rhesus monkeys offers an experimental model to characterize host-response mechanisms associated with viral hemorrhagic fever and evaluate pan-viral hemorrhagic fever countermeasures.\n\nIMPORTANCEHost-response mechanisms involved in pathogenesis of VHFs remain poorly understood. An underlying challenge is separating beneficial, inconsequential, and detrimental host-responses during infection. The comparison of host-responses to infection with the same virus in biologically similar animals that have drastically different disease manifestations allows for the identification of pathogenic mechanisms. SHFV, a surrogate virus for human VHF-causing viruses likely causes subclinical infection in African monkeys such as patas monkeys but can cause severe disease in Asian macaque monkeys. Data from the accompanying article by Buechler et al. support that infection of macaques and baboons with non-SHFV simarteviruses can establish persistent or long-term subclinical infections. Baboons, macaques, and patas monkeys are relatively closely taxonomically related (Cercopithecidae: Cercopithecinae) and therefore offer a unique opportunity to dissect how host-response differences determine disease outcome in VHFs.

immunology↗

Subclinical infection of macaques and baboons with a baboon simartevirus

Simarteviruses (Arteriviridae: Simartevirus) are commonly found at high titers in the blood of African monkeys but do not cause overt disease in these hosts. In contrast, simarteviruses cause severe disease in Asian macaques upon accidental or experimental transmission. Here, we sought to better understand the host-dependent drivers of simartevirus pathogenesis by infecting olive baboons (n=4) and rhesus macaques (n=4) with the simartevirus Southwest baboon virus 1 (SWBV-1). Surprisingly, none of the animals in our study showed signs of disease following SWBV-1 inoculation. Three animals (two rhesus monkeys and one olive baboon) became infected and sustained high levels of SWBV-1 viremia for the duration of the study. The course of SWBV-1 infection was highly predictable: plasma viremia peaked between 1x107 and 1x108 vRNA copies/ml at 3-10 days post-inoculation, which was followed by a relative nadir and then establishment of a stable set-point between 1x106 and 1x107 vRNA copies/ml for the remainder of the study (56 days). We characterized cellular and antibody responses to SWBV-1 infection in these animals, demonstrating that macaques and baboons mount similar responses to SWBV-1 infection, yet these responses are ineffective at clearing SWBV-1 infection. SWBV-1 sequencing revealed the accumulation of non-synonymous mutations in a region of the genome that corresponds to an immunodominant epitope in the simartevirus major envelope glycoprotein GP5, which likely contribute to viral persistence by enabling escape from host antibodies.\n\nOne Sentence SummarySimartevirus infection has multiple disease manifestations following cross-species transmission.\n\nAccessible Summary/ImportanceSimarteviruses are known to infect African monkeys, such as olive baboons, without causing overt disease. In contrast, accidental infection of Asian monkeys, such as rhesus monkeys, has resulted in severe and often fatal disease. We used a simartevirus found circulating among captive olive baboons (Southwest baboon virus 1; SWBV-1) to experimentally infect both olive baboons and rhesus monkeys to model infection with the same virus in both natural and non-natural hosts. Surprisingly, neither baboons nor macaques displayed any laboratory abnormalities or signs of disease over the course of infection, despite robust SWBV-1 replication. In the accompanying study by Cornish et al., a similar experimental approach was undertaken: African patas monkeys and rhesus monkeys were infected with the simartevirus simian hemorrhagic fever virus (SHFV). In contrast to our study, SHFV caused disease in both of these hosts, albeit with much more severe disease developing in the macaques. Interestingly, we observed similar levels of immune cell activation in simartevirus-infected animals across both studies, suggesting that finer nuances of the host response, and perhaps properties of each individual simartevirus, may influences pathogenicity of these viruses in primates. Taken together, our collective findings highlight the wide clinical spectrum of simartevirus infection, ranging from highly-lethal hemorrhagic disease to persistent infection without any overt signs of disease, even in non-natural primate hosts.

microbiology↗