Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation

SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.

Profiling Diuraphis noxia (Hemiptera: Aphididae) Transcript Expression of the Biotypes SA1 and SAM Feeding on Various Triticum aestivum Varieties

The intimate relationship between an aphid and its host is mediated by the composition of the secreted saliva. In the present study, aphid heads were sampled and transcript profiling conducted after aphids were fed on their preference host and transferred to a variety of preference and nonpreference hosts. It was found that the virulent Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae) biotype SAM was able to selectively up-regulate more transcripts when confronted with feeding on a variety of hosts, than was the case with the less virulent D. noxia biotype SA1, suggesting increased genomic regulation when coping with a stressful environment. Collectively, the observed transcriptomic changes are supported by previous findings that host changes induce significant changes in the proteome of phytophagous hemipterans, unlike in many other entomophagous generalist species. The current data suggest that highly specialized hemipterans may be able to counter plant defenses with inducible salivary transcripts with resulting protein biosynthesis, as demonstrated here.

Comparative ultrastructural characterization of African horse sickness virus-infected mammalian and insect cells reveals a novel potential virus release mechanism from insect cells

African horse sickness virus (AHSV) is an arbovirus capable of successfully replicating in both its mammalian host and insect vector. Where mammalian cells show a severe cytopathic effect (CPE) following AHSV infection, insect cells display no CPE. These differences in cell death could be linked to the method of viral release, i.e. lytic or non-lytic, that predominates in a specific cell type. Active release of AHSV, or any related orbivirus, has, however, not yet been documented from insect cells. We applied an integrated microscopy approach to compare the nanomechanical and morphological response of mammalian and insect cells to AHSV infection. Atomic force microscopy revealed plasma membrane destabilization, integrity loss and structural deformation of the entire surface of infected mammalian cells. Infected insect cells, in contrast, showed no morphological differences from mock-infected cells other than an increased incidence of circular cavities present on the cell surface. Transmission electron microscopy imaging identified a novel large vesicle-like compartment within infected insect cells, not present in mammalian cells, containing viral proteins and virus particles. Extracellular clusters of aggregated virus particles were visualized adjacent to infected insect cells with intact plasma membranes. We propose that foreign material is accumulated within these vesicles and that their subsequent fusion with the cell membrane releases entrapped viruses, thereby facilitating a non-lytic virus release mechanism different from the budding previously observed in mammalian cells. This insect cell-specific defence mechanism contributes to the lack of cell damage observed in AHSV-infected insect cells.

Limited endosymbiont variation in Diuraphis noxia (Hemiptera: Aphididae) biotypes from the United States and South Africa

Symbiosis allows an insect access to imbalanced food sources on which other organisms cannot survive. A bacterial endosymbiont, Buchnera aphidicola, gives aphids the ability to feed on phloem depleted of certain essential amino acids by producing those required. Pseudogenes and lower plasmid copy numbers of essential amino acid genes in B. aphidicola, endosymbiont of the Russian wheat aphid, Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae), suggest that this symbiotic relationship is degenerating. The complete endosymbiont assemblages, copy numbers of plasmids (important in essential amino acid production), and sequence variation in B. aphidicola, from 10 Russian wheat aphid biotypes, were investigated. B. aphidicola was found to be monosymbiotic in the Russian wheat aphid biotypes and other Diuraphis species examined. An insert, occurring in an inverted repeat region on the leucine plasmid, was the only variation found in the approximately 10-kb B. aphidicola sequence analyzed from each Russian wheat aphid biotype. This inverted repeat was shown previously to be conserved within the family Aphididae. The insert occurred in B. aphidicola sequences isolated from four Russian wheat aphid biotypes. Copy numbers of the leucine plasmid differ between the South African and U.S. biotypes and were similar to previously reported values for biotypes from the same geographic regions. These results suggest that B. aphidicola may still contribute to Russian wheat aphid fitness when the aphid feeds on a variety of hosts.

Alternative approaches for regional ulnar nerve blockade: a cadaveric study

Wrist blockade is a safe and effective alternative to general anesthesia in surgery of hand injuries. With regard to the ulnar nerve, the volar approach is used, where the needle passes through or medial to the flexor carpi ulnaris tendon; however, the ulnar artery is at risk because the needle may accidentally penetrate it, causing profuse bleeding. Alternatively, the wrist may be approached medially, the ulnar approach, and the needle tip placed posterior to the flexor carpi ulnaris tendon. To determine which of these methods may be preferable for avoiding ulnar artery injury, needles were inserted into the wrist area of cadaver hands (n = 57) using the volar and ulnar approaches; detailed dissection of the region around the inserted needles was subsequently carried out. The position of the ulnar nerve relative to the ulnar artery and injury to the artery was documented. Damage to the ulnar artery using the volar approach was 36.8% (21/57 cases) compared to no (0%) injury observed using the ulnar approach. At the level of the wrist crease just proximal to the pisiform bone, the ulnar nerve was medial to the artery in 92.9% (53/57) of cases, medial and posterior in 5.3% (3/57), and anterior to the artery in 1.8% (1/57) of cases. This study suggests that in cases where ulnar artery pulsation is not reliable, the ulnar approach may be preferable for ulnar nerve blockade due to an increased incidence of ulnar artery penetration with the volar approach.

A comparison of the vector competence of the biting midges, Culicoides (Avaritia) bolitinos and C. (A.) imicola, for the Bryanston serotype of equine encephalosis virus

Equine encephalosis virus (EEV) is widespread and prevalent in southern Africa. In this study, the oral susceptibility of Culicoides (Avaritia) imicola Kieffer (Diptera: Ceratopogonidae) to EEV was confirmed. In addition, C. (A.) bolitinos Meiswinkel, collected in the high-lying eastern Free State, South Africa, was systemically infected with the Bryanston serotype of EEV after feeding through a membrane on artificially infected equine blood containing 4.7 log10 PFU/mL of EEV. The mean infectivity of Bryanston virus in C. bolitinos increased from 1.2 log10 PFU/midge, in midges assayed for virus immediately after feeding on the blood-virus mixture, to 3.1 log10 PFU/midge in midges assayed after 10 days' incubation at 23.5 degrees C. Elevated virus infectivity titres, found in individual infected C. bolitinos, suggested that this Culicoides species is a vector of EEV. This bovine dung-breeding Culicoides species may play an important role in transmitting EEV in the cooler parts of southern Africa, where it can be the most abundant Culicoides species collected near livestock. In the present study the prevalence of infection obtained for C. bolitinos (2.2%) with the Bryanston serotype of EEV was significantly lower than that of C. imicola (18.4%). After incubation, the Bryanston serotype of EEV was also isolated from one of 110 C. onderstepoortensis Fiedler assayed. However, the virus titre in this midge was 1.2 log10 PFU/midge, which is not different from the titre that would be expected immediately after feeding on the blood-virus mixture. Culicoides species that survived the incubation period and that were negative for the presence of Bryanston virus were C. magnus Colaço (96), C. bedfordi Ingram & Macfie (95) and C. pycnostictus Ingram & Macfie (45).

The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Silicosis and tuberculosis: a proposed radiographic classification of tuberculosis to accompany the ILO international classification of radiographs of pneumoconioses

A significant proportion of workers exposed to silica dust are at risk of developing tuberculosis (TB). The higher the International Labor Organization (ILO) category of silicosis, the greater the TB risk. Subtle radiographic presentations of TB may be the initial manifestation of TB, particularly in the absence of sputum identification of TB bacilli. A proposed TB x-ray-reading form in addition to the ILO categorization of silicosis is offered. The implementation of a standardized TB x-ray-reading approach should alert the clinician to indolent TB lesions.

The genome sequence of Drosophila melanogaster

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

Expression of the histone H3 gene in benign, semi-malignant and malignant lesions of the head and neck: a reliable proliferation marker

To search for a reliable proliferation marker in epithelial head and neck lesions, we have analysed the expression of the histone H3 gene by in situ hybridisation and compared this with the immunoreactivity of the widely used monoclonal antibody Ki-67. In many lesions, the Ki-67 staining failed to delineate proliferation. In contrast, the H3 hybridisation signals were in accordance with the histopathology of the biopsies: in hyperplastic epithelia, significant H3 mRNA levels were only seen in areas with inflammation. Dysplastic cells showed distinctly elevated H3 expression. Benign and semi-malignant tumours, i.e. basal cell carcinomas, showed moderate H3 signals at the periphery. In squamous cell carcinomas, H3 expression was always high at the expanding zone of the tumour and was most extensive in undifferentiated carcinomas. Thus, the expression of the histone H3 gene closely reflected the dynamics of neoplastic growth within and around head and neck tumours.