Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features

In the ENSEMBLE randomized, placebo-controlled phase 3 trial (NCT04505722), estimated single-dose Ad26.COV2.S vaccine efficacy (VE) was 56% against moderate to severe-critical COVID-19. SARS-CoV-2 Spike sequences were determined from 484 vaccine and 1,067 placebo recipients who acquired COVID-19. In this set of prespecified analyses, we show that in Latin America, VE was significantly lower against Lambda vs. Reference and against Lambda vs. non-Lambda [family-wise error rate (FWER) p < 0.05]. VE differed by residue match vs. mismatch to the vaccine-insert at 16 amino acid positions (4 FWER p < 0.05; 12 q-value ≤ 0.20); significantly decreased with physicochemical-weighted Hamming distance to the vaccine-strain sequence for Spike, receptor-binding domain, N-terminal domain, and S1 (FWER p < 0.001); differed (FWER ≤ 0.05) by distance to the vaccine strain measured by 9 antibody-epitope escape scores and 4 NTD neutralization-impacting features; and decreased (p = 0.011) with neutralization resistance level to vaccinee sera. VE against severe-critical COVID-19 was stable across most sequence features but lower against the most distant viruses.

Prevention efficacy of the broadly neutralizing antibody VRC01 depends on HIV-1 envelope sequence features

In the Antibody Mediated Prevention (AMP) trials (HVTN 704/HPTN 085 and HVTN 703/HPTN 081), prevention efficacy (PE) of the monoclonal broadly neutralizing antibody (bnAb) VRC01 (vs. placebo) against HIV-1 acquisition diagnosis varied according to the HIV-1 Envelope (Env) neutralization sensitivity to VRC01, as measured by 80% inhibitory concentration (IC80). Here, we performed a genotypic sieve analysis, a complementary approach to gaining insight into correlates of protection that assesses how PE varies with HIV-1 sequence features. We analyzed HIV-1 Env amino acid (AA) sequences from the earliest available HIV-1 RNA-positive plasma samples from AMP participants diagnosed with HIV-1 and identified Env sequence features that associated with PE. The strongest Env AA sequence correlate in both trials was VRC01 epitope distance that quantifies the divergence of the VRC01 epitope in an acquired HIV-1 isolate from the VRC01 epitope of reference HIV-1 strains that were most sensitive to VRC01-mediated neutralization. In HVTN 704/HPTN 085, the Env sequence-based predicted probability that VRC01 IC80 against the acquired isolate exceeded 1 µg/mL also significantly associated with PE. In HVTN 703/HPTN 081, a physicochemical-weighted Hamming distance across 50 VRC01 binding-associated Env AA positions of the acquired isolate from the most VRC01-sensitive HIV-1 strain significantly associated with PE. These results suggest that incorporating mutation scoring by BLOSUM62 and weighting by the strength of interactions at AA positions in the epitope:VRC01 interface can optimize performance of an Env sequence-based biomarker of VRC01 prevention efficacy. Future work could determine whether these results extend to other bnAbs and bnAb combinations.

Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases

Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that plays a crucial role in normal development and disease. To study the nature and extent of somatic mosaicism in autism spectrum disorder, bipolar disorder, focal cortical dysplasia, schizophrenia, and Tourette syndrome, a multi-institutional consortium called the Brain Somatic Mosaicism Network (BSMN) was formed through the National Institute of Mental Health (NIMH). In addition to genomic data of affected and neurotypical brains, the BSMN also developed and validated a best practices somatic single nucleotide variant calling workflow through the analysis of reference brain tissue. These resources, which include >400 terabytes of data from 1087 subjects, are now available to the research community via the NIMH Data Archive (NDA) and are described here.

Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features

It is of interest to pinpoint SARS-CoV-2 sequence features defining vaccine resistance. In the ENSEMBLE randomized, placebo-controlled phase 3 trial, estimated single-dose Ad26.COV2.S vaccine efficacy (VE) was 56% against moderate to severe-critical COVID-19. SARS-CoV-2 Spike sequences were measured from 484 vaccine and 1,067 placebo recipients who acquired COVID-19 during the trial. In Latin America, where Spike diversity was greatest, VE was significantly lower against Lambda than against Reference and against all non-Lambda variants [family-wise error rate (FWER) p < 0.05]. VE also differed by residue match vs. mismatch to the vaccine-strain residue at 16 amino acid positions (4 FWER p < 0.05; 12 q-value ≤ 0.20). VE significantly decreased with physicochemical-weighted Hamming distance to the vaccine-strain sequence for Spike, receptor-binding domain, N-terminal domain, and S1 (FWER p < 0.001); differed (FWER ≤ 0.05) by distance to the vaccine strain measured by 9 different antibody-epitope escape scores and by 4 NTD neutralization-impacting features; and decreased (p = 0.011) with neutralization resistance level to vaccine recipient sera. VE against severe-critical COVID-19 was stable across most sequence features but lower against viruses with greatest distances. These results help map antigenic specificity of in vivo vaccine protection.

CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances

SUMMARY

In recent years, the ability to generate genomic data has increased dramatically along with the demand for easily personalized and customizable genome browsers for effective visualization of diverse types of data. Despite the large number of web-based genome browsers available nowadays, none of the existing tools provides means for creating multiple visualization instances without manual set up on the deployment server side. The Cranfield Genome Browser (CRAMER) is an open-source, lightweight and highly customizable web application for interactive visualization of genomic data. Once deployed, CRAMER supports seamless creation of multiple visualization instances in parallel while allowing users to control and customize multiple tracks. The application is deployed on a Node.js server and is supported by a MongoDB database which stored all customizations made by the users allowing quick navigation between instances. Currently, the browser supports visualizing a large number of file formats for genome annotation, variant calling, reads coverage and gene expression. Additionally, the browser supports direct Javascript coding for personalized tracks, providing a whole new level of customization both functionally and visually. Tracks can be added via direct file upload or processed in real-time via links to files stored remotely on an FTP repository. Furthermore, additional tracks can be added by users via simple drag and drop to an existing visualization instance.

AVAILABILITY AND IMPLEMENTATION

CRAMER is implemented in JavaScript and is publicly available on GitHub on https://github.com/FadyMohareb/cramer. The application is released under an MIT licence and can be deployed on any server running Linux or Mac OS.

CONTACT

f.mohareb@cranfield.ac.uk.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Vaccination with recombinant vaccinia viruses expressing ICP27 induces protective immunity against herpes simplex virus through CD4+ Th1+ T cells

This study was designed to evaluate the efficacy and mechanisms of protection mediated by recombinant vaccinia viruses encoding immediate-early (IE) proteins of herpes simplex virus type 2 (HSV-2). Three mouse strains were immunized against the IE proteins ICP27, ICP0, and ICP4, and mice were challenged intracutaneously in the zosteriform model with HSV-2 strain MS. Protection was observed only following immunization with the ICP27 construct and then only in the BALB/c mouse strain. Protection in BALB/c mice was ablated by CD4+ T-cell suppression but remained intact in animals depleted of CD8+ T cells. Moreover, protection could be afforded to SCID nude recipients with CD4+ but not CD8+ T cells from ICP27-immunized mice. Only BALB/c mice developed a delayed-type hypersensitivity reaction to HSV-2, and in vitro measurements of humoral and cell-mediated immunity revealed response patterns to ICP27 and HSV that differed between protected BALB/c and unprotected mouse strains. Accordingly, BALB/c responses showed antigen-induced cytokine profiles dominated by type 1 cytokines, whereas C57BL/6 and C3H/HeN mice generated cytokine responses mainly of the type 2 variety. Our results may indicate that protection against zosterification is mainly mediated by CD4+ T cells that express a type 1 cytokine profile and that protective vaccines against HSV which effectively induce such T-cell responses should be chosen.

Induction of Plasmodium falciparum sporozoite-neutralizing antibodies upon vaccination with recombinant Pfs16 vaccinia virus and/or recombinant Pfs16 protein produced in yeast

Pfs16 is a sexual stage/sporozoite-specific antigen of Plasmodium falciparum and is a potential candidate for a sporozoite-neutralizing vaccine. To obtain more information on the function of Pfs16 and to investigate its role during transmission and hepatocyte invasion, immunization experiments were performed with both a Pfs16-specific recombinant vaccinia virus and virus-like particles produced in yeast composed of the hepatitis B surface antigen (HBsAg) and antigen Pfs16 fused to HBsAg. Upon transformation of yeast cells, harbouring a genomic copy of the HBsAg gene, with a plasmid carrying the fusion gene Pfs16-HBsAg (Pfs16-S) virus-like hybrid particles composed of HBsAg and Pfs16-S were formed of a size similar to those present in human sera after infection with the hepatitis B virus. Cells infected with recombinant Pfs16 vaccinia virus synthesized a polypeptide of approx. 16 kDa that reacted with a Pfs16-specific polyclonal antibody. Animals vaccinated with the yeast hybrid particles and/or recombinant vaccinia virus both produced Pfs16-specific antibodies. These antibodies showed no transmission-blocking activity, but they efficiently diminished or abolished in vitro invasion of sporozoites into human hepatoma cells (HepG2-A16) and primary human hepatocytes.

Hepatitis B virus-specific cytotoxic T lymphocyte responses in patients with acute and chronic hepatitis B virus infection

An in vitro model was developed that allowed the analysis of hepatitis B virus-specific cytotoxic T lymphocyte responses in patients suffering from acute and chronic hepatitis B virus infections. Since virus-specific cytotoxic T lymphocytes recognize endogenously synthesized and processed antigen only when it is presented in the context of autologous HLA class I molecules and since hepatitis B virus does not infect human cells in vitro, a panel of recombinant vaccinia viruses was constructed to induce the expression of hepatitis B virus envelope and nucleocapsid proteins in cultured primary cells or cell lines derived from the patients to be studied. In order for a cytotoxic T lymphocyte response to be detectable with the currently available techniques, a sufficient number of activated cytotoxic T lymphocytes is required. To meet this requirement, lymphocytes freshly isolated from venous blood were stimulated in vitro with recombinant vaccinia-infected and formaldehyde-fixed autologous T lymphoblasts. The presence of hepatitis B virus-specific cytotoxic T lymphocytes, amplified and activated during this induction culture, was demonstrated in a microcytotoxicity assay using 51Cr-labeled, recombinant vaccinia-infected Epstein-Barr virus-immortalized, autologous B lymphocytes as target cells. Using this in vitro model, we were able to demonstrate the presence of hepatitis B virus envelope- and nucleocapsid-specific cytotoxic T lymphocytes in venous blood from one subject who had recently recovered from an acute hepatitis B virus infection and in three patients suffering from chronic hepatitis B virus infections. No hepatitis B virus-specific cytotoxic T lymphocytes activity was discernible in the venous blood from two vaccine recipients.(ABSTRACT TRUNCATED AT 250 WORDS)

Hand involvement in multiple hereditary exostosis

In summary, patients with multiple hereditary exostosis often inherit hand involvement but rarely show hand deformity. The principal area of involvement appears to be around the MCP joint but the PIP joint is the most common area of deformity. Metacarpal shortening usually does not cause functional problems and need not be treated. Angular deformity, though rare, does cause problems and needs surgical treatment. Unfortunately, there is no evidence that prevention of deformity is possible by early excision of osteochondromas. Treatment, therefore, requires both osteochondroma excision and closing-wedge corrective osteotomy.

Nucleotide sequence of the gene encoding the active-site serine beta-lactamase from Actinomadura R39

The gene encoding the extracellular, active-site serine beta-lactamase of Actinomadura R39, previously cloned into Streptomyces lividans, has the information for the synthesis of a 304 amino acid protein, the amino terminal region of which has the characteristic features of a signal peptide. The Actinomadura R39 beta-lactamase is another member of the class A beta-lactamases. In particular, it shows high homology with the beta-lactamase of Bacillus licheniformis.

Cloning and amplified expression in Streptomyces lividans of the gene encoding the extracellular beta-lactamase of Actinomadura R39

By using the promoter-probe plasmid pIJ424, genomic DNA fragments of Actinomadura R39 were shown to have promoter activity in Streptomyces lividans. The same 100-200-copy-number plasmid was used to clone in S. lividans TK24, the gene that encodes the Actinomadura R39 beta-lactamase. Gene cloning resulted in an amplified expression of the beta-lactamase when compared with the amounts of enzyme produced by the original strain (1 mg versus 0.008 mg.litre of culture-1).

Several antigenic determinants exposed on the gp120 moiety of HIV-1 gp160 are hidden on the mature gp120

Mouse mAb reactive to the HIV-1 envelope glycoprotein precursor gp160 of the HTLVIII(B) isolate were characterized in radioimmunoprecipitation and immunoblot tests with the use of HTLVIII(B) isolate as Ag. The reactivities of these mAb were also measured in a capture enzyme immunoassay and in radioimmunoprecipitation assay by using gp160 and gp120 expressed as vaccinia recombinants. Striking differences in exposure of specific epitopes were noted between the gp120 component of the gp160 precursor and the fully processed gp120 in both tests. These conformational rearrangements affecting the gp120 moiety of the HIV-1 envelope glycoprotein might have important implications on its immunogenicity.

Several antigenic determinants exposed on the gp120 moiety of HIV-1 gp160 are hidden on the mature gp120

Mouse mAb reactive to the HIV-1 envelope glycoprotein precursor gp160 of the HTLVIII(B) isolate were characterized in radioimmunoprecipitation and immunoblot tests with the use of HTLVIII(B) isolate as Ag. The reactivities of these mAb were also measured in a capture enzyme immunoassay and in radioimmunoprecipitation assay by using gp160 and gp120 expressed as vaccinia recombinants. Striking differences in exposure of specific epitopes were noted between the gp120 component of the gp160 precursor and the fully processed gp120 in both tests. These conformational rearrangements affecting the gp120 moiety of the HIV-1 envelope glycoprotein might have important implications on its immunogenicity.