Search

In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the UK. By the end of 2020, 49% of all SARS-CoV-2 genome sequences globally had been generated as part of the COG-UK programme, and to date, this system has generated >3 million SARS-CoV-2 genomes. Rapidly and reliably analysing this unprecedented number of genomes was an enormous challenge. To fulfil this need and to inform public health decision-making, we developed a centralized pipeline that performs quality control, alignment, and variant calling and provides the global phylogenetic context of sequences. We present this pipeline and describe how we tailored it as the pandemic progressed to scale with the increasing amounts of data and to provide the most relevant analyses on a daily basis., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press.)

The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different 'catchments' and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 O’Toole et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard., Results: As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories., Conclusions: Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI's BioSample database., (© The Author(s) 2022. Published by Oxford University Press GigaScience.)

We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single-nucleotide polymorphisms and deletions that are characteristic of the B.1.1.7 variant of concern but lack the full complement of lineage-defining mutations. Instead, the remainder of their genomes share contiguous genetic variation with non-B.1.1.7 viruses circulating in the same geographic area at the same time as the recombinants. In four instances, there was evidence for onward transmission of a recombinant-origin virus, including one transmission cluster of 45 sequenced cases over the course of 2 months. The inferred genomic locations of recombination breakpoints suggest that every community-transmitted recombinant virus inherited its spike region from a B.1.1.7 parental virus, consistent with a transmission advantage for B.1.1.7's set of mutations., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Motivation: Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolating and sequencing DNA directly from an environment (metagenomics). Recovering the genomic sequences of all isoforms of a given gene across all organisms in a metagenomic sample would aid evolutionary and ecological insights into microbial ecosystems with potential benefits for medicine and biotechnology. A significant obstacle to this goal arises from the lack of a computationally tractable solution that can recover these sequences from sequenced read fragments. This poses a problem analogous to reconstructing the two sequences that make up the genome of a diploid organism (i.e. haplotypes) but for an unknown number of individuals and haplotypes., Results: The problem of single individual haplotyping was first formalized by Lancia et al. in 2001. Now, nearly two decades later, we discuss the complexity of 'haplotyping' metagenomic samples, with a new formalization of Lancia et al.'s data structure that allows us to effectively extend the single individual haplotype problem to microbial communities. This work describes and formalizes the problem of recovering genes (and other genomic subsequences) from all individuals within a complex community sample, which we term the metagenomic individual haplotyping problem. We also provide software implementations for a pairwise single nucleotide variant (SNV) co-occurrence matrix and greedy graph traversal algorithm., Availability and Implementation: Our reference implementation of the described pairwise SNV matrix (Hansel) and greedy haplotype path traversal algorithm (Gretel) is open source, MIT licensed and freely available online at github.com/samstudio8/hansel and github.com/samstudio8/gretel, respectively., (© The Author(s) 2021. Published by Oxford University Press.)

Extensive global sampling and sequencing of the pandemic virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have enabled researchers to monitor its spread and to identify concerning new variants. Two important determinants of variant spread are how frequently they arise within individuals and how likely they are to be transmitted. To characterize within-host diversity and transmission, we deep-sequenced 1313 clinical samples from the United Kingdom. SARS-CoV-2 infections are characterized by low levels of within-host diversity when viral loads are high and by a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with minimal persistence of shared diversity, patterns that are readily observable on the phylogenetic tree. Our results suggest that transmission-enhancing and/or immune-escape SARS-CoV-2 variants are likely to arise infrequently but could spread rapidly if successfully transmitted., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)

Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Background: Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition., Findings: We sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning., Conclusions: We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines., (© The Author(s) 2019. Published by Oxford University Press.)

Unlabelled: : We present Goldilocks: a Python package providing functionality for collecting summary statistics, identifying shifts in variation, discovering outlier regions and locating and extracting interesting regions from one or more arbitrary genomes for further analysis, for a user-provided definition of interesting., Availability and Implementation: Goldilocks is freely available open-source software distributed under the MIT licence. Source code is hosted publicly at https://github.com/SamStudio8/goldilocks and the package may also be installed using pip install goldilocks. Documentation can be found at https://goldilocks.readthedocs.org, Contact: : msn@aber.ac.uk, Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2016. Published by Oxford University Press.)

Corneal graft rejection is primarily a CD4(+) T cell-mediated mechanism in which macrophages may play an important inflammatory role. CD200Fc fusion protein is an artificial agonist of CD200R1, a receptor expressed predominantly on myeloid cells, engagement of which is known to down-regulate macrophage function. We therefore wished to test whether CD200Fc could be used as a therapeutic agent to prolong corneal graft survival. The distribution of CD200R1 and CD200, its natural ligand, was examined by immunohistology in the cornea and conjunctiva of unoperated rats and rats that had received corneal allografts. Mouse CD200Fc was injected subconjunctivally into transplanted rats on six occasions from the day of surgery until day 10 after transplantation. Control groups received injections of mouse IgG or diluent PBS. Allo-transplants were also performed in CD200(-/-) and control mice. The ability of CD200Fc to bind rat macrophages in vitro and to inhibit nitric oxide production was tested. Mean day of rejection in CD200Fc, IgG and PBS-treated rats was 12, 10 and 9 respectively (p=0.24). Mean day of rejection in CD200(-/-) and wild type mice was 17.5 and 16.0 respectively (p=0.07). Mouse CD200Fc bound to rat macrophages in a dose-dependent manner, but was unable to inhibit nitric oxide production. The fact that treatment with CD200Fc did not inhibit graft rejection and the failure of CD200 deficiency to affect graft survival suggests that local targeting of the CD200-CD200R axis to suppress macrophage activation is not a useful therapeutic strategy in corneal graft rejection., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Purpose: The purpose of our study is to develop a pre-clinical model of corneal graft rejection in the semi-inbred NIH minipig as a model of human rejection., Methods: NIH minipigs received corneal allografts with MHC and minor mismatches, or minor mismatches alone. Clinical rejection was monitored, and major subsets of leukocytes and ingress of vessels were quantified post-mortem by automated digital methods. Spectratypes of recipient T-cell receptor β-subunit variable region (TRβV) were analyzed. The capacity of pig corneal endothelial cells to proliferate in vivo was assessed., Results: Autografts (n = 5) and SLA(cc) to SLA(cc) allografts (minor mismatches, n = 5) were not rejected. Median graft survival of SLA(dd) and SLA(bb) allografts in SLA(cc) strain recipients (major and minor mismatches) was 57 (n = 10) and 67 (n = 6) days, respectively. Rejected grafts did not recover clarity in vivo, and corneal endothelial cells did not proliferate in organ culture after cryo-injury. There were significantly more leukocytes in clinically rejected versus accepted grafts (P < 0.0001) and in transplanted versus contralateral eyes (P < 0.0001). Numbers of T-cells were significantly greater in clinically accepted grafts versus autografts and in rejected grafts versus accepted (P < 0.005 for most subsets). There were significant differences in TRβV spectratype between graft groups in cornea, but not in draining lymph node or blood (P < 0.05)., Conclusions: The NIH minipig offers a robust model of human rejection suitable for immunological or therapeutic studies. In particular, there is limited capacity for corneal endothelial repair in vivo, and histological evidence suggests that allosensitization of the recipient may develop in the absence of clinical rejection.

Swine are a frequent species of choice for testing new surgical procedures and for transplantation studies. However, information concerning best practice to prepare pigs for surgery and postoperative treatment and monitoring is limited, despite a perception that preoperative socialization is beneficial. Therefore we examined the effect of preoperative visits by project personnel on compliance of 26 National Institutes of Health (NIH) minipigs subject to corneal transplantation. We briefly describe sedation and anaesthesia protocols developed for surgery and multiple postoperative interventions in order to facilitate interpretation of data relating to pig compliance. Preoperative visit variables and measures of preoperative socialization were correlated with postoperative outcome. Principal component analysis (PCA) of postoperative outcome variables identified a factor accounting for 53.5% of the variance that was significantly associated with two factors derived from PCA of preoperative factors (accounting, respectively, for 54.7% and 26.0% of the variance; P = 0.019 for the overall model, P = 0.041 and 0.040 for factors 1 and 2, respectively), such that more time spent with pigs before surgery and higher socialization scores were associated with less postoperative stress and difficulty of eye medication. Moreover, two of the preoperative visit variables, time spent with only one person in the pen and time spent with two or more people in the pen, contributed predominantly to PCA factors 1 and 2, respectively, indicating that they were fulfilling two qualitatively different requirements for socialization. We conclude that NIH minipigs are fully compliant with anaesthetic and postoperative experimental procedures provided they are well-socialized to project personnel before surgery.

Purpose: To investigate cytokine production by leukocytes in aqueous humor (AH) during corneal graft rejection and nitric oxide (NO) production by macrophages as a potential mediator of graft damage., Methods: Rats received corneal allotransplants and were killed during acute rejection. Leukocytes in AH that expressed tumor necrosis factor (TNF)-alpha, interferon (IFN)-gamma, and interleukin (IL)-10 were quantified by flow cytometry. Isograft and further allograft recipients were killed, and sectioned corneas with conjunctivae were examined by histology for production of inducible nitric oxide synthase (iNOS), NO, and nitrotyrosine (NT)., Results: Between 80% and 90% of T cells, NK cells, and macrophages in AH expressed TNF-alpha, and at least 20% expressed IL-10. However, IFN-gamma was undetectable unless cells were first stimulated in vitro with PMA and ionomycin, which yielded IFN-gamma in 25% of cells. iNOS(+) macrophages were identified in donor cornea and AH, correlating precisely with rejection. Cells producing low levels of NO (NO(dim) cells) were found in donor stroma, but NT(+) cells were rare. Both NT(+) and NO(+) cells were rare in the anterior chamber (AC) or attached to corneal endothelium. NT(+) macrophages that were also NO(bright) were associated with sutures in allograft and isograft recipients and within conjunctivae, either scattered or in leukocyte aggregates., Conclusions: IFN-gamma synthesis is lacking in the AC during rejection, correlating with lack of NO but not of iNOS expression. NO does not appear to mediate endothelial cell death. NT and high levels of NO production are associated with nonspecific inflammatory cells.

MNL1, the Candida albicans homologue of an orphan Msn2-like gene (YER130c in Saccharomyces cerevisiae) has no known function. Here we report that MNL1 regulates weak acid stress responses. Deletion of MNL1 prevents the long-term adaptation of C. albicans cells to weak acid stresses and compromises their global transcriptional response under these conditions. The promoters of Mnl1-dependent genes contain a novel STRE-like element (SLE) that imposes Mnl1-dependent, weak acid stress-induced transcription upon a lacZ reporter in C. albicans. The SLE (HHYYCCCCTTYTY) is related to the Nrg1 response element (NRE) element recognized by the transcriptional repressor Nrg1. Deletion of NRG1 partially restores the ability of C. albicans mnl1 cells to adapt to weak acid stress, indicating that Mnl1 and Nrg1 act antagonistically to regulate this response. Molecular, microarray, and proteomic analyses revealed that Mnl1-dependent adaptation does not occur in cells exposed to proapoptotic or pronecrotic doses of weak acid, suggesting that Ras-pathway activation might suppress the Mnl1-dependent weak acid response in dying cells. Our work defines a role for this YER130c orthologue in stress adaptation and cell death.

Critical to the success of human corneal transplants is prevention of corneal endothelial rejection, yet little is known about the endothelial infiltrate. To examine the endothelium, a method for removal and processing this layer as a flat sheet was used and the infiltrate was compared with stroma and epithelium. LEW or PVG strain rat corneas were transplanted to PVG strain recipients. Clinical changes after transplantation were monitored by slit lamp and animals sacrificed at a range of time points during rejection. Clinically defined rejection, accompanied by an epithelial rejection line and endothelial cell infiltration, occurred between days 10 and 15. There was some infiltration of leukocytes in the stroma of isografts at these time points, but significantly more in allografts (p<0.003 for all subsets). There was no infiltration of isograft endothelium at any time and no infiltration of allograft endothelium on day 10. On day 15, there were similar numbers of all major subsets except B cells in the stroma, while on the endothelium macrophages, MHC class II(+) cells and CD8(+) cells predominated (p<0.001 CD4(+) vs CD8(+) cells). T cells and NK cells predominated in the epithelial rejection line. While TNF-alpha and IFN-gamma-producing cells were numerous in stroma and epithelium, no IFN-gamma-producing cells were found on endothelium. Distinct differences in infiltrative profile within layers of the cornea suggest that the mechanisms of rejection may also differ. The restricted endothelial cell profile and lack of IFN-gamma suggests that the anti-endothelial response may be modulated by the anterior chamber environment.

Background: Second and subsequent corneal transplants in the same eye are more prone to rejection reactions and failure than first grafts. This may be a result of local changes or systemic sensitization to antigen shared by the first and second donors. Because HLA typing is not routine in corneal transplantation, a clear correlation between accelerated rejection and specific sensitization has not been established., Methods: PVG (RT1), Lewis (LEW; RT1), or AO (RT1) strain corneas were transplanted to PVG strain rats, followed by a LEW strain cornea in the ipsilateral or contralateral eye 6 weeks later. Graft survival was evaluated by slit lamp biomicroscopy. Proliferation of recipient lymph node cells was tested against allogeneic, syngeneic and third-party stimulator cells after the second transplantation., Results: A second allograft in the ipsilateral or contralateral eye was rejected in an accelerated fashion that was not donor MHC specific. Rejection was not significantly accelerated in the ipsilateral eye compared with the contralateral eye. There was a secondary lymphocyte proliferation response to third party (AO strain) in animals previously exposed only to the LEW strain., Conclusions: Systemic sensitization to donor antigens, rather than local changes induced by first transplantation, contributed to accelerated rejection of a second graft. Accelerated rejection is not dependent on MHC compatibility between the grafts. It could be caused by shared "public" MHC determinants, by minor antigens shared by the first and second donors, or by cross-reactivity of T cells to epitopes on AO and LEW grafts. HLA mismatching of first and second donors may not prolong second graft survival.

Aim: To investigate the development of lymphoid aggregates in the conjunctiva after corneal transplantation in rats., Methods: LEW or PVG strain corneas were transplanted orthotopically to PVG rats. Cornea and conjunctiva were examined clinically for up to 42 days. Eyes were removed with attached conjunctiva on days 10 and 15 after transplantation (before and during rejection), together with normal eyes, fixed, paraffin embedded, and examined immunohistochemically., Results: Clinically, the temporal half of the upper palpebral conjunctiva of recipients of 10/19 allografts and 1/10 isografts developed pronounced swelling, correlating with inflammation and rejection. Histologically, the swelling comprised leucocytic aggregates with an altered overlying epithelium. Aggregates contained granulocytes, macrophages, and cells expressing major histocompatibility complex (MHC) class II, CD4, and CD8, all more numerous in allograft associated conjunctiva. Class II+ cells were more abundant at the surface, whereas macrophages and T cells were more numerous in the deeper stroma. There were few B cells. There was greater CD54 expression by vascular endothelium in allograft associated aggregates. Cells expressing TNFalpha and IFNgamma but not IL1beta were present in stromal and superficial areas., Conclusions: Corneal transplantation in rats induces the development of organised conjunctival leucocytic aggregates in a fixed location that are significantly more pronounced in recipients of allografts compared with isografts and show characteristics of a Th1 type immune response. These aggregates have characteristics of conjunctiva associated lymphoid tissue and may be sites of presentation of graft antigens and lymphocyte proliferation at the ocular surface.

Purpose: To investigate clinical and histologic changes in the epithelium during corneal graft rejection in the rat., Methods: LEW (RT1(l)) or PVG (RT1(c)) strain corneas were transplanted to PVG strain recipients and examined by slit lamp for clinical signs of rejection. Recipients were killed, and corneal epithelial sheets were removed and examined by adenosine diphosphatase (ADPase) staining for Langerhans cells (LC) and by immunohistology for leukocytes and adhesion molecules (T cells, macrophages, granulocytes, major histocompatibility complex [MHC] class II, CD2 and CD54 intercellular adhesion molecule [ICAM]-1) at a range of time points before, during, and after rejection, depending on the cell type sought. Normal and contralateral eyes were examined for ADPase(+) and MHC class II(+) cells., Results: Clinical rejection, as defined by stromal opacity, occurred between days 10 and 15 after transplantation. In 94% of allografts, a curved clinical epithelial rejection line was observed in which ADPase(+)/MHC class II(+), CD4(+), or CD8(+) T cells were identified. There were significantly more infiltrating cells of all types in epithelia of allografts than in those of isografts. The most numerous cells were CD4(+) and CD8(+) T cells, suggesting preferential migration of these cells into the epithelium from underlying layers. Expression of MHC class II and ICAM-1 was induced on epithelial cells., Conclusions: Epithelial rejection in rats is clinically similar to that in humans and occurs simultaneously with stromal infiltration. It may be mediated by T cells rather than macrophages. In isolation, its recognition in humans may be a useful indication that the patient is at high risk of endothelial rejection.

Background: In human corneal transplantation the value of matching, particularly for MHC class II, is unclear and controversial. The contribution of the direct pathway to T cell activation is also uncertain. We have determined the relative contribution of class I, II and non-MHC antigens to graft rejection and of the direct and indirect pathways to T cell activation in a rat model mimicking human incompatibilities., Methods: DA (RT1a) strain recipients received fully mismatched PVG (RT1c) strain grafts or grafts from one of three recombinant strains bearing DA MHC genes on a PVG background. Graft survival was assessed and the specificity of T cells generated in the draining lymph nodes was determined in mixed lymphocyte (MLR) proliferation assays. To assess the contribution of the direct pathway, fully mismatched graft were performed and allospecific proliferation was measured after depletion of recipient APC from the MLR reaction., Results: There was no significant difference in survival of grafts between the four grades of mismatch, which ranged from a full mismatch to non-MHC mismatches alone (median survival 12.5, 11, 13 and 12.5 days respectively). In conformity with clinical results, strong secondary responses were generated against targets matched for MHC with the recipient. Depletion of recipient APC from a fully allogeneic secondary MLR did not fully abrogate donor-specific proliferation., Conclusions: Class II matching is of no benefit in this model. Strong indirect responses to non-MHC mismatches are sufficient to induce the rapid rejection, but the small numbers of class II+ cells in the donor appear sufficient to generate a direct response.

An improved method of removing rat corneal endothelial sheets for study of endothelial pathology is described. The method was validated by examining morphological changes and changes in expression of major histocompatibility complex (MHC) and intercellular adhesion molecule (ICAM)-1 on endothelium undergoing immunological rejection. PVG strain rats received LEW strain corneal transplants or corneal isografts. Just prior to and during graft rejection, animals were killed, together with a group of untreated animals. The corneal stroma was injected with dispase or PBS, the cornea was carefully removed, fixed in acetone and the endothelium was gently peeled off and flattened on to a glass slide. Morphological changes, together with MHC class I, class II and ICAM-1 expression were visualised by immuno-histochemical staining and quantified by image analysis. Near complete endothelial sheets were obtained by this method. Because of the thin cell layer, there was minimal background staining, permitting rejection-associated changes to be clearly seen. MHC class I expression on normal endothelium was low and not significantly increased on endothelial cells of allografts at the time of rejection compared with controls (P = 0.1). MHC class II and ICAM-1 were induced de novo, expression being significantly higher on allografts than on isografts (P = 0.004 for MHC class II and P = 0.01 for ICAM-1). MHC class I and II and ICAM-1 were expressed on many infiltrating cells. Thus, this preparation method permits clear identification of the distribution and morphology of infiltrating cells and other mediators of the immune response in the entire donor endothelium. It confirms that MHC class I expression is low during rejection, while MHC class II and ICAM-I are induced de novo and strongly expressed.

Aims/background: There are more reagents and information available for immunological studies in the mouse compared with other animals. Unfortunately, the mouse penetrating keratoplasty model is associated with high background inflammation which hinders study of the immune response to the graft. To mitigate this drawback, a murine orthotopic corneal interlamellar transplantation model with mild non-specific inflammation was developed., Methods: A 1.5 mm diameter full thickness donor corneal button was placed in a 2 mm diameter recipient corneal interlamellar pocket without placement of a suture. The clinical course of graft status was studied daily for 60 days in 30 allografts (donor strain CBA 101 (H-2k) to recipient NIH (H-2q) and 30 syngeneic grafts (NIH to NIH) by slit lamp biomicroscopy and scored for neovascularisation, opacity, oedema, and granularity. In another cohort of animals, histological observation was performed after 30 minutes and on days 10, 20, 30, and 40 after transplantation (four allografts and four syngeneic grafts per time point). Histological study was also performed on grafts without donor epithelium and on interlamellar pockets without grafts., Results: There was significantly more neovascularisation (NV), opacity, oedema, and granularity in 24/30 allografts (80%) than in syngeneic grafts. Such grafts were defined as rejected. The median time to rejection was 21 days (range 18 to > 60 days). By histology, some allografts showed moderate to heavy cell infiltration which correlated with clinical scores of NV (4-5), opacity (1-3), oedema (1-3), and granularity (1-3). Such infiltration was absent in other allografts and syngeneic grafts., Conclusion: Surgically, corneal interlamellar transplantation could be accomplished in the mouse and rejection could be clearly defined. The model can therefore be useful for in situ study of cell and molecular aspects of corneal graft rejection.

We have successfully developed a method for the immunohistochemical detection of interleukin 2 (IL-2), IL-4, IL-6, IL-10O, IFNgamma and TNFalpha using monoclonal antibodies (MAb), in sections of mouse tissue embedded in paraffin wax. The method involved fixation in periodate-lysine-paraformaldehyde (PLP), rapid dehydration and infiltration under vacuum with paraffin wax at 54 degrees C. Comparative observations demonstrated that the method gives equivalent or better results than formaldehyde fixed, frozen sections. Since reliable controls, both positive and negative, are paramount for interpretation of immunohistochemical staining, such controls were determined. The following tissues were shown to be suitable as positive controls when using paraffin-embedding: spleen for the detection of TNFalpha, small intestine for IL-2, IL-4 and IL-10, and HSV-1 infected eyes for IL-6 and IFNgamma. We conclude that PLP fixation and low temperature paraffin-embedding is a method which provides both preservation of excellent tissue morphology and reliable immunohistochemical identification of cytokines. These attributes will be invaluable in a wide variety of experimental situations.

Reactivation of latent herpes simplex virus type 1 (HSV-1) infection was induced by UV irradiation of the corneas of latently infected mice. On days 1-4 after stimulation, infectious virus was sought in nervous and ocular tissue. On days 4, 7 and 10, eyes with either recurrent epithelial or stromal disease and appropriate controls were stained to identify immune cells and HSV-1 antigens. The maximum incidence of infectious virus was on day 2 when 5/10 ophthalmic parts of the trigeminal ganglion yielded HSV. Thus in this mouse model, as in humans, reactivation of virus in the trigeminal ganglion is the likely source of virus producing recurrent disease and shedding in the tear film. On day 4, when virus antigens were still present, granulocytes were the predominant infiltrating cell in corneas with either type of disease. Small numbers of T cells, dendritic cells and cells expressing MHC class II were also present. In stromal disease, the granulocyte infiltrate persisted and T cells remained sparse. In contrast, in epithelial disease, granulocyte numbers rapidly declined and both CD4+ and CD8+ T cells (present at a ratio of 1:1) increased significantly. The secondary immune response to virus antigen is more rapid and vigorous than that during primary corneal infection. Granulocytes may play a role in the initial clearance of virus, however, the other types of cells present early on provide the potential for a local secondary immune response. The high proportion of CD8+ cells in epithelial disease compared with stromal disease suggests that they may be acting as suppressors.

Purpose: To ascertain the effect of trauma from surgery and rejection on the incidence and timing of recurrent herpes simplex virus (HSV) disease after corneal transplantation. To locate virus antigen and identify cells of the immune system infiltrating corneas with recurrent disease., Methods: PVG rats were inoculated on the cornea with HSV-1 McKrae. Recurrent disease was induced either by ultraviolet (UV)-irradiation of the cornea or by corneal transplantation. After corneal transplantation, animals shedding virus in the tear film were killed on days 1 to 4 of shedding. Eyes were fixed, embedded, sectioned, and stained for virus antigens, infiltrating cells, major histocompatibility complex class II, and adhesion molecule molecule expression., Results: In the first 15 days after corneal transplantation, 8 of 91 rats shed virus, and between days 16 and 30, an additional 3 of 60 rats shed virus (12% of total rats, comparable to the percent that shed after UV irradiation). Shedding sometimes was accompanied by punctate epithelial lesions in the recipient cornea and stromal opacity. The rejection process itself did not induce or exacerbate recurrent disease. In all corneas examined from eyes that shed virus, antigen was found in several locations at the graft-host junction, sometimes in the absence of clinical signs of disease, and frequently it extended through the stroma to the endothelium. Granulocytes were the main infiltrating cell in areas of virus antigen., Conclusions: Corneal transplantation trauma is a stimulus to recurrent disease of similar potency to UV irradiation. The graft-host junction is an area in which virus spreads easily and can reach the endothelium readily. In humans, the incidence of recurrent disease at this location may be greater than has been recognized.

Following inoculation of the mouse cornea with herpes simplex virus type 1 (HSV-1), the spread of virus was investigated and the types of immune cell infiltrating the trigeminal ganglion (TG) were identified in low temperature paraffin wax sections. Virus antigen was first found on day 3 and was absent after day 14. Early presentation of antigen to T cells may occur since increased expression of major histocompatibility complex (MHC) class II antigens, including de novo expression on satellite and Schwann cells, was detected in foci of such antigen on day 3. A second large peak of such expression was detected on day 10 together with increasing numbers of B and T cells. Large numbers of these lymphocytes and extensive expression of MHC class II were seen in the TG well into the phase of virus latency; the significance of this is discussed.

We describe a method for immunohistochemical localization of T-cells, CD4+ T-cells, CD8+ T-cells, B-cells, activated lymphocytes, major histocompatibility complex (MHC) class II antigens, macrophages, dendritic cells, and granulocytes in rat and mouse tissue fixed in periodate-lysine-paraformaldehyde (PLP) and embedded in paraffin. Rat and mouse spleen and eyes were fixed in PLP for 18-24 hr, rapidly dehydrated, infiltrated under vacuum with paraffin at 54 degrees C, sectioned, and stained with appropriate monoclonal antibodies (MAbs). Sections of PLP-fixed, paraffin-embedded spleen were compared with acetone-fixed frozen spleen sections with respect to morphology and staining quality. Nine of 10 MAbs to rat antigens and eight of nine MAbs to mouse antigens stained paraffin sections equally or more intensely than frozen sections. The two MAbs that showed weaker staining still gave good staining on paraffin sections. Paraffin-embedded rat and mouse eyes were easier to section serially than frozen eyes, showed superior morphology, and individually stained cells were readily identified. Therefore, a combination of PLP fixation and low-temperature paraffin embedding permits detection of the major types of immune cell in rat and mouse tissues while maintaining good morphology, particularly in diseased, damaged, or delicate tissues.

We have used a high responder rat model to examine the role that non-MHC antigens play in corneal graft rejection. Recipients were backcross animals derived from a cross between two inbred strains, which mimicked the human outbred population in that donor and recipient could be matched or mismatched for MHC antigens, while non-MHC mismatches were variable and unknown. All mismatched grafts and 87% of matched grafts were rejected (median survival 11 and 17 days respectively). The high incidence of rejection of matched grafts indicates that several independently segregating non-MHC genes play a role in rejection. Moreover, the immune response to matched grafts appeared resistant to immunosuppression, suggesting that matching does not permit reduced dosage of immunosuppressants. A mechanism is discussed whereby matching at the class II locus may enhance presentation of mismatched histocompatibility antigens or viral peptides derived from infected graft cells, thereby prejudicing graft survival.

Purpose: To assess the suitability of the rat for studies of ocular infection with herpes simplex virus (HSV)., Methods: LEW, AO, DA, PVG, and (DAxLEW)F1 x LEW backcross generation rats, 7 to 9 weeks of age, were inoculated with HSV-1 McKrae. The course of primary disease was assessed by clinical observation using a slit lamp. Infectious virus was assayed in ocular and nervous tissue, and the incidence of latent infection was determined., Results: LEW and AO strains were the most susceptible. All LEW rats died after an inoculum of 4 x 10(2) plaque-forming units (pfu) and developed severe corneal disease and uveitis. In contrast, all PVG rats survived 10(4) pfu, 60% survived 4 x 10(4) pfu, and eye disease was restricted to epithelial lesions, sometimes accompanied by mild stromal haze. This resolved, even in animals that developed central nervous system disease. The DA strain showed intermediate susceptibility. Resistance was dominant because disease in backcross generation (DA x LEW)F1 x LEW rats resembled that of the DA rather than the LEW strain. Resistance appeared to be linked to coat color (P < 0.001) rather than to major histocompatibility complex (MHC) type. Chronic stromal disease did not occur in survivors (DA, PVG, and hybrid strains only)., Conclusions: The susceptibility of rat strains to infection of the cornea with HSV varies, and, as with mice, resistance seems to be controlled by non-MHC genes. Rats may prove useful for immunologic studies. Virus reactivation will be the subject of a future report.

Tolerance to noninherited maternal antigens (NIMAs) of the MHC was investigated in a rat model involving both skin and corneal transplants. Recipient animals were obtained by backcrossing F1 hybrids to parental strain animals. In one group of experiments, crosses were (DA[RT1a] x LEW[RT1(1)]) female-to-LEW male and, in a second group, (DAxPVG[RT1c]) female-to-PVG male. Homozygous backcross offspring (RT1(1/1) or RT1c/c) were putatively tolerant to DA NIMAs if the mother was a hybrid animal, having been exposed to these antigens in utero. The equivalent offspring of hybrid fathers, i.e., LEW female x (DAxLEW) male or PVG female x (DAxPVG) male, served as putatively nontolerant controls. Hemagglutinating antibody levels were measured against the class I RT1Aa antigen on days 7 and 14 after up to three consecutive subcutaneous DA strain skin grafts. Significantly lower titers were found in the putatively tolerant group 7 days after the first skin graft in the RT1a-to-RT1(1) combination (P < 0.05). Levels were not significantly different at any other time point, or at any time point in the RT1a-to-RT1c combination. Tolerance to a corneal graft was not demonstrated in either the strongly rejecting RT1a-to-RT1(1) combination or weakly rejecting RT1a-to-RT1c, whether or not animals were presensitized to RT1a antigens with DA skin grafts. We conclude that tolerance to NIMAs is unimportant in this clinical rat model of transplantation.

1. Clinical corneal transplantation has been performed for over a century, but many elements leading to a successful outcome have yet to be identified. 2. Because there are limitless supplies of tissue, the supply of corneas need never fall short of demand. Nevertheless, retrieval rates vary widely among regions in the UK due to uneven organization of services. 3. Organ culture of corneas improves the quality of transplanted tissues because it allows time for substandard material to be discarded. The outcome appears to equal other storage methods. 4. Between 1987 and 1991, 4,560 corneal transplants were performed by 428 surgeons at 216 centers in the UK and were registered with CTFS. Of these, 3,213 were evaluable for graft survival, rejection, and other measures of visual outcome. 5. Unifactorial analysis revealed that the percentage of graft survival at one year was 89% and rejection-free survival was 87%. However, the hazard of rejection appeared to increase at or after the time of suture removal. 6. The percentage of recipients in whom CVA was 6/24 or better (able to read normal text with correction) improved from 16% preoperatively to 59% at 3 and 70% at 12 months postoperatively overall. In patients transplanted purely for visual reasons, improvement was 78% and 83% at 3 and 12 months, respectively. 7. Interim results of multifactorial analysis suggest that the risk of graft failure, rejection, and decreased CVA increased in association with the following factors: surgeons who reported fewer than 50 transplants to the study; recipients under 10 years of age; previously failed grafts (the more failed grafts, the greater the risk); grafting for nonvisual reasons; certain diagnoses; and vascularization of the corneal bed prior to transplantation. 8. Astigmatism was investigated in 880 cases at 3 months postoperatively. Preliminary analysis indicated that the risk of severe astigmatism was influenced by suturing technique and large differences between (> 0.25 mm) donor and recipient trephine size. 9. The effects of HLA matching were evaluated in 542 transplants. HLA-A and B matching reduced the risk of rejection during the first 450 days posttransplant, but HLA-DR matching appeared to increase the risk of rejection. 10. A rat model designed to simulate clinical corneal grafting was used to investigate the interaction between immunosuppression and matching. Whereas MHC mismatching could be overcome with topical dexamethasone, non-MHC mismatching appeared resistant.(ABSTRACT TRUNCATED AT 400 WORDS)

The importance of minor histocompatibility genes in corneal graft rejection was investigated using a model that simulates the major histocompatibility complex (MHC) and minor mismatches of the human allograft more accurately than previous animal models. DA(RT1a) x LEW(RT1(1]F1 hybrid rats were backcrossed to LEW, and the backcross generation were used as corneal graft recipients. Female DA(RT1a) strain animals were used as donors throughout. As in humans, the MHC disparity (a to 1) between each donor-recipient pair could be controlled; minor mismatches were variable and unknown. The MHC haplotype of each backcross individual (either homozygous l/l) or heterozygous a/l) was determined. Depending on this haplotype, the transplanted DA cornea was either matched or mismatched with the recipient for MHC antigens. The average proportion of minor disparate loci was 50%, although this was variable and unknown from recipient to recipient. Some animals of each MHC type were sensitized with three subcutaneous DA strain skin grafts at intervals of 2 weeks. Prior sensitization caused more rapid corneal graft rejection in both MHC mismatched (P less than 0.001) and matched (P less than 0.01) animals. All animals in the two MHC-mismatched groups (sensitized, 26; unsensitized, 17) and most in the MHC-matched groups (sensitized, 25 of 27; unsensitized, all 13) rejected their grafts. The MHC matching resulted in a greater range of survival times, although the difference in survival in unsensitized animals between matched and mismatched groups was not significant (unsensitized, P greater than 0.05; sensitized, P less than 0.001).(ABSTRACT TRUNCATED AT 250 WORDS)

Mice were inoculated with herpes simplex virus (HSV) type 1 in the skin of the neck. The extent of primary and latent infection in the second and third cervical ganglia was investigated. Immunoperoxidase staining of ganglia during primary infection demonstrated HSV antigens initially in a restricted area of the ganglion. By the 5th day after infection, antigen was more widespread. Such a change in the staining pattern is explicable in terms of the zosteriform spread of virus from neurons innervating the site of infection to others supplying other areas of the dermatome. A maximum of approximately 10% of neurons became infected. By the 7th day staining was limited to a few cells. During latent infection, enzymic disaggregation of ganglia followed by immunoperoxidase staining or infectious centre assay indicated that virus reactivation began within 30 h of removal of ganglia and occurred in approximately 1% of viable neurons.