Selective adaptation of SARS-CoV-2 Omicron under booster vaccine pressure: a multicentre observational study

BACKGROUND

High rates of vaccination and natural infection drive immunity and redirect selective viral adaptation. Updated boosters are installed to cope with drifted viruses, yet data on adaptive evolution under increasing immune pressure in a real-world situation are lacking.

METHODS

Cross-sectional study to characterise SARS-CoV-2 mutational dynamics and selective adaptation over >1 year in relation to vaccine status, viral phylogenetics, and associated clinical and demographic variables.

FINDINGS

The study of >5400 SARS-CoV-2 infections between July 2021 and August 2022 in metropolitan New York portrayed the evolutionary transition from Delta to Omicron BA.1-BA.5 variants. Booster vaccinations were implemented during the Delta wave, yet booster breakthrough infections and SARS-CoV-2 re-infections were almost exclusive to Omicron. In adjusted logistic regression analyses, BA.1, BA.2, and BA.5 had a significant growth advantage over co-occurring lineages in the boosted population, unlike BA.2.12.1 or BA.4. Selection pressure by booster shots translated into diffuse adaptive evolution in Delta spike, contrasting with strong, receptor-binding motif-focused adaptive evolution in BA.2-BA.5 spike (Fisher Exact tests; non-synonymous/synonymous mutation rates per site). Convergent evolution has become common in Omicron, engaging spike positions crucial for immune escape, receptor binding, or cleavage.

INTERPRETATION

Booster shots are required to cope with gaps in immunity. Their discriminative immune pressure contributes to their effectiveness but also requires monitoring of selective viral adaptation processes. Omicron BA.2 and BA.5 had a selective advantage under booster vaccination pressure, contributing to the evolution of BA.2 and BA.5 sublineages and recombinant forms that predominate in 2023.

FUNDING

The study was supported by NYU institutional funds and partly by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center.

The impact of COVID-19 monoclonal antibodies on clinical outcomes: A retrospective cohort study

DISCLAIMER

In an effort to expedite the publication of articles, AJHP is posting manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time.

PURPOSE

Despite progress in the treatment of coronavirus disease 2019 (COVID-19), including the development of monoclonal antibodies (mAbs), more clinical data to support the use of mAbs in outpatients with COVID-19 is needed. This study is designed to determine the impact of bamlanivimab, bamlanivimab/etesevimab, or casirivimab/imdevimab on clinical outcomes within 30 days of COVID-19 diagnosis.

METHODS

A retrospective cohort study was conducted at a single academic medical center with 3 campuses in Manhattan, Brooklyn, and Long Island, NY. Patients 12 years of age or older who tested positive for COVID-19 or were treated with a COVID-19-specific therapy, including COVID-19 mAb therapies, at the study site between November 24, 2020, and May 15, 2021, were included. The primary outcomes included rates of emergency department (ED) visit, inpatient admission, intensive care unit (ICU) admission, or death within 30 days from the date of COVID-19 diagnosis.

RESULTS

A total of 1,344 mAb-treated patients were propensity matched to 1,344 patients with COVID-19 patients who were not treated with mAb therapy. Within 30 days of diagnosis, among the patients who received mAb therapy, 101 (7.5%) presented to the ED and 79 (5.9%) were admitted. Among the patients who did not receive mAb therapy, 165 (12.3%) presented to the ED and 156 (11.6%) were admitted (relative risk [RR], 0.61 [95% CI, 0.50-0.75] and 0.51 [95% CI, 0.40-0.64], respectively). Four mAb patients (0.3%) and 2.64 control patients (0.2%) were admitted to the ICU (RR, 01.51; 95% CI, 0.45-5.09). Six mAb-treated patients (0.4%) and 3.37 controls (0.3%) died and/or were admitted to hospice (RR, 1.61; 95% CI, 0.54-4.83). mAb therapy in ambulatory patients with COVID-19 decreases the risk of ED presentation and hospital admission within 30 days of diagnosis.

Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York

In 2021, Delta has become the predominant SARS-CoV-2 variant worldwide. While vaccines effectively prevent COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occur. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contribute to increased rates of breakthrough infections compared to unvaccinated controls. Here, we show a steep and near complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25, its spike mutation S112L, and nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthroughs increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. Our data indicate a limited impact of vaccine escape in favor of Delta's increased epidemic growth in times of waning vaccine protection.

Prevention of trauma-induced cochlear fibrosis using intracochlear application of anti-inflammatory and antiproliferative drugs

Cochlear fibrosis is a common finding following cochlear implantation. Evidence suggests that cochlear fibrosis could be triggered by inflammation and epithelial-to-mesenchymal cell transition (EMT). In this study, we investigate the mechanisms of cochlear fibrosis and the risk/benefit ratio of local administration of the anti-inflammatory drug dexamethasone (DEX) and antimitotic drug aracytine (Ara-C). Cochlear fibrosis was evaluated in cochlear fibrosis models of rat cochlear slices in vitro and in KLH-induced immune labyrinthitis and platinum wire cochlear implantation-induced fibrosis in vivo. Cochleae were invaded with tissue containing fibroblastic cells expressing α-SMA (alpha smooth muscle actin), which along with collagen I, fibronectin, and laminin in the extracellular matrix, suggests the involvement of a fibrotic process triggered by EMT in vitro and in vivo. After perilymphatic injection of an adenoviral vector expressing GFP in vivo, we demonstrated that the fibroblastic cells derived from the mesothelial cells of the scalae tympani and vestibuli. Activation of inflammatory and EMT pathways was further assessed by ELISA analysis of the expression of IL-1β and TGF-β1. Both markers were elevated in vitro and in vivo, and DEX and Ara-C were able to reduce IL-1β and TGF-β1 production. After 5days of culture in vitro, quantification of calcein-positive cells revealed that Ara-C was 30-fold more efficient in preventing fibrosis, and provoked less sensory hair cell loss, than DEX. In KLH-induced immune labyrinthitis and platinum wire-implanted models, Ara-C was more efficient in preventing proliferation of fibrosis with less side effects on hair cells and neurons than DEX. In conclusion, DEX and Ara-C both prevent fibrosis in the cochlea. Analysis of the risk/benefit ratio favors the use of Ara-C for preventing cochlear fibrosis.

Helicobacter pylori and overweight status in the United States: data from the Third National Health and Nutrition Examination Survey

Obesity is an important public health problem in the United States. Because of its potential effects on gastric leptin homeostasis, Helicobacter pylori may play a role in regulating body weight. The authors' aim in this study was to examine the association between H. pylori colonization and overweight status. Nonpregnant participants in the Third National Health and Nutrition Examination Survey (1988-1994) aged > or = 20 years who had had H. pylori testing performed and body mass index (weight (kg)/height (m2)) measured were studied. Overweight was defined as a body mass index greater than or equal to 25. On the basis of serologic results, the participants were categorized into three H. pylori status groups: H. pylori-positive and cytotoxin-associated gene A (cagA)-positive (H. pylori+ cagA+), H. pylori-positive and cagA-negative (H. pylori+ cagA-), and H. pylori-negative (H. pylori-). Of the 7,003 subjects with complete body mass index and H. pylori data, 2,634 (weighted percentage, 22.9%) were H. pylori+ cagA+, 1,385 (15.1%) were H. pylori+ cagA-, and 2,984 (62.0%) were H. pylori-. The adjusted odds of being overweight were 1.17 (95% confidence interval: 0.98, 1.39; p = 0.075) for the H. pylori+ cagA+ group and 0.99 (95% confidence interval: 0.80, 1.22; p = 0.92) for the H. pylori+ cagA- group in comparison with H. pylori- subjects. Serum leptin levels did not differ significantly between the three H. pylori groups. In this US population-based study, there was no significant association between H. pylori colonization, cagA+ strains of H. pylori, and being overweight.

Alternative identification test relying upon sexual reproductive abilities of Candida lusitaniae strains isolated from hospitalized patients

The in vitro mating ability of Candida lusitaniae (teleomorph Clavispora lusitaniae) clinical isolates has been investigated. Studying the effects of culture conditions, we showed that ammonium ion depletion in the medium is a major trigger of the sexual cycle. Moreover, a solid support is required for mating, suggesting a role for adhesion factors in addition to the mating type gene recognition function. Monitoring of mating and meiosis efficiency with auxotrophic strains showed great variations in ascospore yields, which appeared to be strain and temperature dependent, with an optimal range of 18 to 28 degrees C. The morphogenetic events taking place from mating to ascospore release were studied by scanning and electron microscopy, and the ultrastructure of the conjugation canal, through which intercellular nuclear exchanges occur, was revealed. Labeling experiments with a lectin-fluorochrome system revealed that the nuclear transfer was predominantly polarized, thus allowing a distinction between the nucleus donor and the nucleus acceptor strains. The direction of the transfer depended on the strain combination used, rather than on the genotypes of the strains, and did not appear to be controlled by the mating type genes. Finally, we demonstrated that all of the 76 clinical isolates used in this study were able to reproduce sexually when mated with an opposite mating type strain, and we identified a 1:1 MATa/MATalpha ratio in the collection. These results support the idea that there is no anamorph state in C. lusitaniae. Accordingly, the mating type test, which is easy to use and can usually be completed within 48 h, is a reliable alternative identification system for C. lusitaniae.

[Peri-aortic fibrosis: unusual case of jaundice]

Periaortic fibrosis is defined as the development of aortic perianeuvrysmal fibrosis either resulting from a focal inflammatory reaction or a self-perpetuating process. Compression of neighboring organs is a possible complication. Bile duct obstruction is exceptional.

A population of PC12 cells that is initiating apoptosis can be rescued by nerve growth factor

Programmed cell death, or apoptosis, occurs asynchronously in neuronal cells. To overcome this asynchrony, rat pheochromocytoma (PC12) cells were separated at different stages of apoptosis on the basis of cell density. Live cells that exhibited no apoptotic features floated to the top of density gradients. The most dense cells showed extensive loss of cytochrome c from mitochondria, caspase activation, chromatin condensation, and DNA fragmentation. These cells were committed to apoptosis and could not be rescued by reculturing in with nerve growth factor (NGF). Cells of intermediate density displayed no DNA fragmentation, but had begun to show cytochrome c loss, caspase activation, and chromatin condensation. This population displayed upregulation of the prodeath factor, c-Jun, and downregulation of prosurvival kinase, Akt. Importantly, apoptosis was reversible by NGF in this population. These studies suggest that increased cell density correlates with an initial step in the apoptosis mechanism that precedes irreversible commitment to suicide.

[ A registry of ischaemic cardiopathies among active workers at Electricité de France-Gaz de France. Program development and first results]

BACKGROUND

The social security department of the French national electric and gas company has established an ischemic heart disease register among a population of about 140 000 employees based on sick leaves as well as deaths recorded with their medical cause.

METHODS

History of the illness, medical tests and treatments were known retrospectively from the consulting physicians of the company. Acute coronary events recorded were: inaugural angina pectoris, myocardial infarction, sudden coronary death and fortuitous discovery of coronary disease.

RESULTS

A first study conducted on employees during the 1993-1995 period showed infarction incidence age rates similar to those estimated from the French MONICA registers for France as a whole. Regional discrepancies were observed for myocardial infarction rates: Nord-Pas de Calais, Champagne-Ardennes, Lorraine, Franche-Comté and Limousin were at the most elevated risk (SIR=131, 155, 169, 125 and 178 resp). Large variations according to socio-economic status were observed.

CONCLUSION

This register will permit studies on the links between socio-economic status at different professional career points and the occurrence of ischemic heart disease and the evaluation of the impact of psychosocial factors such as previous depressive disorders.

CREB is cleaved by caspases during neural cell apoptosis

Programmed cell death, or apoptosis, is a tightly regulated process mediated by selective cleavage of proteins by caspases, resulting in ordered destruction of the cell. In addition to structural proteins, proteins that mediate anti-apoptotic signal transduction are also substrates; their destruction eliminates potential futile attempts to escape execution. We asked whether cAMP response element binding protein (CREB), a transcription factor that mediates nerve growth factor (NGF) survival signals, is a target for caspases during apoptosis. CREB was specifically cleaved by caspases in neuroblastoma extracts, and in cells induced to undergo apoptosis by staurosporine. The destruction of CREB eliminates a key factor that could reverse apoptosis.

Phosphorylation-dependent Akt cleavage in neural cell in vitro reconstitution of apoptosis

Neuronal apoptotic execution uses a cytochrome c-dependent caspase activation mechanism that is conserved in other cell types. Phosphatidylinositol 3-kinase and its downstream effector, Akt/protein kinase B, appear to control this mechanism and govern the life/death decision. We have developed a cell-free system using cytosol from human neuroblastoma (SY5Y) cells that reconstitutes biochemical features of neuronal apoptosis. In the presence of cytochrome c and ATP, caspase-9 and -3 were activated, which initiated chromatin condensation and DNA cleavage in rat pheochromocytoma (PC12) nuclei. Akt was cleaved in reactions where caspase-3 was activated and its cleavage was prevented by the caspase inhibitor DEVD-aldehyde. The phosphatase inhibitors orthovanadate and okadaic acid prevented catalytic processing and activation of caspase-3 and digestion of Akt and partially inhibited cleavage of caspase-9. Caspase-dependent destruction of Akt irreversibly inactivates this key mediator of survival signaling, ensuring that the execution pathway will prevail.

Reporter cell lines to study the estrogenic effects of xenoestrogens

In order to characterize the estrogenic activity of chemicals, we established complementary in vitro recombinant receptor-reporter gene assays in stably transfected MCF-7 and HeLa cells. MCF-7 cells which express the endogenous estrogen receptor alpha (ER alpha) were stably transfected with only an estrogen-regulated luciferase gene. These cells enable the detection of compounds which bind to ER alpha or interfere with the induction of ER alpha mediated gene expression. Furthermore, HeLa cells, which do not express endogenous ERs, were transfected with an ER alpha or an ER beta construct together with an estrogen-regulated luciferase gene, or a chimeric GAL4-ER alpha receptor and the corresponding luciferase reporter gene. Finally, we tested these four cellular models as tools to check the estrogenic activities of several potential xenoestrogens and to detect estrogenic activity in wastewater sewage treatment effluents. In all of the models, nonylphenol mixture (NPm), 4n-nonylphenol (4nNP), 2,4'-DDE, 4,4'-DDE and wastewater sewage treatment effluent were active, while PCB mixture (Aroclor 1254), PCB 77, atrazine and lindane (gamma hexachlorocyclohexane) were inactive. Dioxin partially activates the estrogen receptor in MCF-7 cells while in HeLa-derived cell lines, it decreased the estrogenic-induced expression of luciferase.

Superior mesenteric arteriovenous fistula after ileal resection

Postoperative superior mesenteric arteriovenous fistula is very rare. We report the case of a 55-year-old woman in whom the discovery of an abdominal bruit led to the diagnosis of superior mesenteric arteriovenous fistula seven years after ileal resection. The clinical and pathophysiological aspects, as well as the therapeutic modalities, of this rare lesion are reviewed.

[Coronary surgery in patients aged 70 years and older. 65 cases]

Out of 428 patients operated upon for coronary disease between December 1984 and November 1989, sixty-five (15.18 percent) were 70 to 80 years' old. All were suffering from a more or less invalidating stage II, III or IV angina. Coronary arteriography showed severe lesions of two or three main vessels (24.6 and 60 percent respectively). Each patient underwent 2.06 bypasses on average. Perioperative mortality was 7.7 percent, and late mortality 1.53 percent. The postoperative myocardial infarction rate was 4.61 percent, and 83 percent of these patients became asymptomatic. There was no deterioration. These satisfactory results are the consequences of numerous technical advances in cardiovascular surgery, anaesthesia and intensive care. As more and more elderly patients undergo coronary surgery, the desire of other elderly patients to be operated upon and their comfort after coronary surgery, the desire of other elderly patients to be operated upon and their comfort after coronary bypass are two additional reasons to opt for surgery. In spite of new vascular recanalization techniques, coronary surgery remains of considerable value. Close cooperation between surgical and medical teams should clarify the respective indications for coronary angioplasty and direct coronary bypass, thereby making these two procedures complementary and no longer competitive.

Conservative treatment of prosthetic aortic graft infection with irrigation

An infected prosthetic aortic graft is usually treated by ablation of the graft associated with extraanatomic bypass. In spite of this aggressive attitude, mortality and morbidity remain high, especially due to secondary rupture of the aortic stump. We report the case of a patient who incurred periprosthetic purulent collection four weeks after insertion of an inlay aortobiiliac prosthetic graft for aneurysm, who was treated by debridement, irrigation, and omental transposition. Recovery has been maintained for four years. Conservative treatment of infection can control infection and obviate the need of complex resection and revascularization procedures.

Femorofemoral crossover bypass for noninfective complications of aortoiliac surgery

Between 1973 and 1989, 39 femorofemoral crossover bypasses were performed to treat unilateral noninfective complications of aortoiliac surgery. The initial revascularization procedure, performed an average of 79.5 months previously, was an aortobifemoral bypass in 29 cases, an aorto- or iliofemoral bypass in six cases, an inlay graft for abdominal aortic aneurysm and aortoiliac endarterectomy in two cases each. The indications for femorofemoral crossover bypass included prosthetic occlusion in 35 cases, thrombosed false aneurysm in two, and further degradation after endarterectomy (iliac stenosis and occlusion in one case each). There was no operative mortality. One patient with acute ischemia upon admission and another with distal gangrene required below-knee and forefoot amputations, respectively. No amputations were required during the rest of the follow-up period. Three repeat aortobifemoral bypasses were performed because of occurrence of aortic or inflow vessel lesions. Primary and secondary actuarial five year patency rates for femorofemoral crossover bypasses were 59.7% and 78.4%, respectively. Femorofemoral crossover bypass can extend the benefits derived from direct aortoiliac surgery with low mortality and morbidity in the absence of associated aortic pathology (false aneurysm at the aortic implantation site or severe obstructive lesions).

[Role of x-ray computed tomography in the preoperative evaluation of aneurysm of the abdominal aorta]

The authors have studied the files of 50 consecutive patients (1987-89) operated for abdominal aortic aneurysm (AAA) and examined with CT. The criteria for inclusion were surgical features. CT can be made more accurate for the study of AAA: Thus the location of the neck of the aneurysm relative to the renal arteries was defined in 94% of all cases. In addition, CT yields information about the wall of the aneurysm, whether it be thickened (3 inflammatory aneurysms were properly diagnosed) or, mor importantly, weakened (solution of continuity in the wall in the "prior-to-rupture" appearance). Owing to the quality of its performances and to its noninvasive character, the authors regard CT with contrast injection as an essential technique for the preoperative assessment of abdominal aortic aneurysm in most cases. The examination must be carried out strictly, especially for the contiguous sections of the renal arteries and their extension to the crural arch. As it demonstrates weakened areas more easily, a more accurate study of the aneurysmal wall with CT might increase the surgical indications for some smaller aneurysms, the potential evolution of which does not seem to be associated with their diameter only.