Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants

Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and XBB-derived variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose-vaccinated and bivalent-vaccinated healthcare workers, XBB.1.5-wave-infected first responders, and monoclonal antibody (mAb) S309. We assessed the biology of the variant spikes by measuring viral infectivity and membrane fusogenicity. BA.2.86 is less immune evasive compared to FLip and other XBB variants, consistent with antigenic distances. Importantly, distinct from XBB variants, mAb S309 was unable to neutralize BA.2.86, likely due to a D339H mutation based on modeling. BA.2.86 had relatively high fusogenicity and infectivity in CaLu-3 cells but low fusion and infectivity in 293T-ACE2 cells compared to some XBB variants, suggesting a potentially different conformational stability of BA.2.86 spike. Overall, our study underscores the importance of SARS-CoV-2 variant surveillance and the need for updated COVID-19 vaccines.

Immune evasion and membrane fusion of SARS-CoV-2 XBB subvariants EG.5.1 and XBB.2.3

Immune evasion by SARS-CoV-2 paired with immune imprinting from monovalent mRNA vaccines has resulted in attenuated neutralizing antibody responses against Omicron subvariants. In this study, we characterized two new XBB variants rising in circulation - EG.5.1 and XBB.2.3, for their neutralization and syncytia formation. We determined the neutralizing antibody titers in sera of individuals that received a bivalent mRNA vaccine booster, BA.4/5-wave infection, or XBB.1.5-wave infection. Bivalent vaccination-induced antibodies neutralized ancestral D614G efficiently, but to a much less extent, two new EG.5.1 and XBB.2.3 variants. In fact, the enhanced neutralization escape of EG.5.1 appeared to be driven by its key defining mutation XBB.1.5-F456L. Notably, infection by BA.4/5 or XBB.1.5 afforded little, if any, neutralization against EG.5.1, XBB.2.3 and previous XBB variants - especially in unvaccinated individuals, with average neutralizing antibody titers near the limit of detection. Additionally, we investigated the infectivity, fusion activity, and processing of variant spikes for EG.5.1 and XBB.2.3 in HEK293T-ACE2 and CaLu-3 cells but found no significant differences compared to earlier XBB variants. Overall, our findings highlight the continued immune evasion of new Omicron subvariants and, more importantly, the need to reformulate mRNA vaccines to include XBB spikes for better protection.

Immune Evasion, Infectivity, and Fusogenicity of SARS-CoV-2 Omicron BA.2.86 and FLip Variants

Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and the XBB-lineage variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose vaccinated and bivalent vaccinated healthcare workers, XBB.1.5-wave infected first responders, and monoclonal antibody (mAb) S309. We assessed the biology of the variant Spikes by measuring viral infectivity and membrane fusogenicity. BA.2.86 is less immune evasive compared to FLip and other XBB variants, consistent with antigenic distances. Importantly, distinct from XBB variants, mAb S309 was unable to neutralize BA.2.86, likely due to a D339H mutation based on modeling. BA.2.86 had relatively high fusogenicity and infectivity in CaLu-3 cells but low fusion and infectivity in 293T-ACE2 cells compared to some XBB variants, suggesting a potentially differences conformational stability of BA.2.86 Spike. Overall, our study underscores the importance of SARS-CoV-2 variant surveillance and the need for updated COVID-19 vaccines.

Neural transcriptomic signature of chronic wasting disease in white-tailed deer

Background

The increasing prevalence and expanding geographical range of the chronic wasting disease (CWD) panzootic in cervids is threatening human, animal, environmental and economic health. The pathogenesis of CWD in cervids is, however, not well understood. We used RNA sequencing (RNA-seq) to compare the brain transcriptome from white-tailed deer (WTD; Odocoileus virginianus) clinically affected with CWD (n = 3) to WTD that tested negative (n = 8) for CWD. In addition, one preclinical CWD+ brain sample was analyzed by RNA-seq.

Results

We found 255 genes that were significantly deregulated by CWD, 197 of which were upregulated. There was a high degree of overlap in differentially expressed genes (DEGs) identified when using either/both the reference genome assembly of WTD for mapping sequenced reads to or the better characterized genome assembly of a closely related model species, Bos taurus. Quantitative PCR of a subset of the DEGs confirmed the RNA-seq data. Gene ontology term enrichment analysis found a majority of genes involved in immune activation, consistent with the neuroinflammatory pathogenesis of prion diseases. A metagenomic analysis of the RNA-seq data was conducted to look for the presence of spiroplasma and other bacteria in CWD infected deer brain tissue.

Conclusions

The gene expression changes identified highlight the role of innate immunity in prion infection, potential disease associated biomarkers and potential targets for therapeutic agents. An association between CWD and spiroplasma infection was not found.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08306-0.

P–061 Protective effect of melatonin against bleomycin, etoposide, and cisplatin (BEP) chemotherapy-induced testicular toxicity in Wistar rats: A biochemical, immunohistochemical and apoptotic genes based evidence

Study question

Does exogenous melatonin (MLT) attenuate BEP-induced damage in testicular cells and spermatogenesis in a dose-dependent manner?

Summary answer

Melatonin protected the testes against BEP-induced testis damage through ameliorating nitro-oxidative stress, apoptosis, and inflammation. However, there was no significant difference between melatonin-treated groups.

What is known already

Recently, the prevalence of testicular cancer (TC), accounting for the most common cancer among young people of reproductive age (15–40 years), has risen internationally. BEP chemotherapy has increased the 5-year survival rate of TC patients at all stages of testicular germ cell tumors to 90–95%. However, BEP creates a high incidence of male infertility and even long-term genotoxic effects, which emerges as a critical health issue. Melatonin is a well-known potent antioxidant with widespread clinical applications that recently has been giving increasing attention to its role in male sub/infertility.

Study design, size, duration

60 Adult male Wistar rats were randomly assigned to six groups (n = 10/group). Group 1, 3, and 4 were injected with vehicle, 10 and 20 mg/kg of melatonin, respectively. Other groups received one cycle of bleomycin, etoposide, and cisplatin for a total of 3 weeks with or without melatonin. Melatonin administration started daily one week before BEP initiation continued on days 2, 9, and 16; and one week after the completion of the BEP cycle.

Participants/materials, setting, methods

Bodyweight, testes weight, Sperm parameters (count, motility, viability, and morphology), testosterone hormone level, testicular histopathology, stereological parameters, testicular level of malondialdehyde (MDA), nitric oxide (NO), and total antioxidant capacity (TAC), the expression of Bcl–2, Bax, Caspase–3, p53, and TNF-α (Real-time PCR and immunohistochemistry) were evaluated at the end of the study (day 35).

Main results and the role of chance

Our findings showed that melatonin restores the BEP-induced reduction in the body and testes weight (P<.05). the evaluation of quantitative analysis of the testes stereological procedures, QRT-PCR examination and immunohistochemical (IHC) staining revealed that melatonin reverses the BEP-induced impaired spermatogenesis (P<.05). Furthermore, melatonin rectifies BEP-induced disturbance on sperm count, motility, viability, and morphology. The testosterone level in the BEP-treated group was decreased significantly by comparison with the control group (P<.01). By contrast, co-administration of 10 and 20 mg/kg of melatonin could enhance the serum testosterone level significantly (P<.05). Moreover, melatonin enhanced the antioxidant status of the testis by elevating TAC and ameliorating MDA and NO levels. More notably, QRT-PCR examination indicated that melatonin therapy suppressed BEP-induced apoptosis by modulating apoptosis-associated genes such as Bcl–2, Bax, Caspase–3, p53 in the testis (P<.01). Besides, Co-administration of 10 and 20 mg/kg of melatonin with BEP regimen decreased significantly the population of p53 (54.21 ±6.18% and 51.83±8.45, respectively) and TNF-α positive cells (42.91±9.92% and 33.57±2.97, respectively) by comparison to the BEP group. Also, melatonin with low and high doses could enhance the expression of Bcl–2 protein in spermatogenic cells line (59.19±10.18%, 63.08±5.23, respectively) compared to the BEP-treated group.

Limitations, reasons for caution

Owing to limited laboratory facilities we were not able to perform further studies to verify the mechanism of melatonin in the specific targets by using transfection technique and transgenic.

Wider implications of the findings: These findings can draw attention to the clinical application of melatonin and also suggest that melatonin may be an attractive agent for attenuating chemotherapy-associated male sub/infertility. This indolamine also may shorten the fertility recovery period in patients undergoing chemotherapy with the BEP regimen.

Trial registration number

N/A

Histological characterisation of the skin of the Paraechinus hypomelas, Brandt, 1836 (Erinaceidae: Eulipotyphla)

BACKGROUND

The current study represents the first description of the histological characterisations of the normal skin of Brandt's hedgehog (paraechinus hypomelas).

MATERIALS AND METHODS

Skin samples were collected from abdomen, back, nostril and cloacal regions.

RESULTS

The skin consisted of 3 layers including epidermis, dermis and hypodermis. The epidermis was covered by a layer of keratinised squamous epithelium mainly in the back region, but the skin keratinisation was present with a little amount or may was absent in other regions. Histologically, the total thickness of skin was maximum on the back and minimum on the cloacal regions. The epidermis consisted of 4 layers and stratum lucidum was absent in all regions. Beneath the epidermis, the dermis layer was constituted of dense connective tissue in which the hair follicles, sweat glands, sebaceous glands, arrector pilli muscles and blood vessels were present. The sweat and sebaceous glands were more populated in the nostril region. The hair follicles were located in the epidermal and dermal regions. Vibrissae were only in the nostrils region and characterised from other hairs by their large and well innervated hair follicle which was surrounded by the blood sinus.

CONCLUSIONS

The present findings show that in Brandt's hedgehog (paraechinus hypomelas) the back and cloacal regions have thickest and thinnest skin respectively as compared to the nostril and abdominal regions. In addition, sebaceous and sweat glands were mainly populated in the nostril region.

Morpholoical Study of the Brandt’s Hedgehog, Paraechinus hypomelas (Eulipotyphla, Erinaceidae), Tongue

The morphology and histological structure of two adult Brandt’s hedgehog, Paraechinus hypomelas, (Brandt, 1836) tongue were examined by light and scanning electron microscopy. On the dorsal surface of the tongue, three types of papillae were observed: filiform, fungiform and vallate papillae. Apex and corpus of the tongue as well as the lateral surface of the corpus were covered with numerous filiform papillae with bifurcated tip, while the epithelium lining the ventral lingual surface was free from papillae. Discoid shape fungiform papillae were scattered over the entire surface of the lingual apex, corpus and lateral surface uniformly between the filiform ones without regional variation in number and size. Three elliptical or oval vallate papillae in an inverted triangle form were found on the root of the tongue. Each papilla had a lobulated and very irregular dorsal surface. Both fungiform and vallate papillae contain taste buds. The foliate papillae was absent. Overall, the present findings reveal that despite some similarities, the lingual papillae of the Brandt’s hedgehog as an omnivore animal has spices-specific characteristics compare to the Erinaceous auritus as an insectivore species. This finding provides a set of basic data about the morphology of tongue and its lingual papillae in Brandt’s hedgehog.

Insights Into Non-Thermal Recovery of Heavy Oil

Abstract

Many heavy oil reservoirs contain oil that has some limited mobility under reservoir conditions. In these reservoirs, a small fraction of the oil-in-place can be recovered using the internal reservoir energy through heavy oil solution gas drive (primary production). An integral part of this process is the so-called 'foamy oil mechanism', whereby oil is produced as a gas-in-oil dispersion. At the end of primary production, the bulk of the oil is still in place, while the natural energy of the reservoir has been depleted. This remaining oil is still mostly continuous and presents a valuable target for further recovery. Many of these reservoirs are relatively small or thin, or may be contacted by overlying gas or underlying water. As such, they are poor candidates for thermal oil recovery methods, so any additional oil recovery after primary production must be non-thermal. In this work, we present experimental results of foamy oil depletion at two different length scales and varying depletion rates. Tests were conducted in the absence of sand production, and the results from the depletion experiments are interpreted in terms of viscous forces. At the conclusion of primary recovery, the potential for further non-thermal exploitation of these reservoirs is explored. Results for waterflooding and chemical flooding are presented, demonstrating the viability of these techniques for heavy oil EOR. Several displacement mechanisms are identified through the secondary and tertiary processes that contribute to significant (although potentially slow) incremental recovery of heavy oil.

Introduction

Many countries have heavy oil reservoirs. Canada and Venezuela in particular contain some of the largest heavy oil and bitumen resources in the world. Rising energy demands, coupled with a decline in conventional oil reserves, has led to increased interest in heavy oil recovery in recent years. The size of these heavy oil deposits is considerable, and with volatile crude oil prices making it difficult to produce from some higher viscosity bitumen reservoirs, production of heavy oil could potentially be very important in years to come. Understanding the mechanisms by which heavy oil can be displaced in reservoirs is crucial to the successful recovery of this resource base.

Heavy oil can be defined as a class of oils with viscosity ranging from 50 mPa.s up to around 50,000 mPa.s. This oil has limited mobility under reservoir temperature and pressure, and Darcy's Law predicts that the oil can flow slowly under high applied pressure gradients. However, it has been observed that in these reservoirs, solution gas drive leads to significantly higher rates and recoveries than what was expected by conventional understanding of gas-oil relative permeability behaviour(1). This behaviour, first reported in Canadian heavy oil, has since been observed in many other reservoirs around the world including South America, China and Albania. Investigations into the causes of this abnormal, but fortuitous, primary production response have been the focus of many publications in the past 25 years.

The recovery from primary production in heavy oil reservoirs may be as high as 20%(2), but is usually lower.