Genome-first detection of emerging resistance to novel therapeutic agents for SARS-CoV-2

Some COVID-19 patients are unable to clear their infection or are at risk of severe disease, requiring treatment with neutralising monoclonal antibodies (nmAb) and/or antivirals. The rapid roll-out of novel therapeutics means there is limited understanding of the likely genetic barrier to drug resistance. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to the detection of emerging drug resistance. Here we report the accrual of mutations in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively. Mutations occur within the epitopes of the respective nmAbs. For casirivimab+imdevimab these are present on contiguous raw reads, simultaneously affecting both components. Using surface plasmon resonance and pseudoviral neutralisation assays we demonstrate these mutations reduce or completely abrogate antibody affinity and neutralising activity, suggesting they are driven by immune evasion. In addition, we show that some mutations also reduce the neutralising activity of vaccine-induced serum.

Further antibody escape by Omicron BA.4 and BA.5 from vaccine and BA.1 serum

The Omicron lineage of SARS-CoV-2, first described in November 2021, spread rapidly to become globally dominant and has split into a number of sub-lineages. BA.1 dominated the initial wave but has been replaced by BA.2 in many countries. Recent sequencing from South Africas Gauteng region uncovered two new sub-lineages, BA.4 and BA.5 which are taking over locally, driving a new wave. BA.4 and BA.5 contain identical spike sequences and, although closely related to BA.2, contain further mutations in the receptor binding domain of spike. Here, we study the neutralization of BA.4/5 using a range of vaccine and naturally immune serum and panels of monoclonal antibodies. BA.4/5 shows reduced neutralization by serum from triple AstraZeneca or Pfizer vaccinated individuals compared to BA.1 and BA.2. Furthermore, using serum from BA.1 vaccine breakthrough infections there are likewise, significant reductions in the neutralization of BA.4/5, raising the possibility of repeat Omicron infections.

Construction of a prediction model for prognosis of severe pneumonia patients combined with sepsis / 中华临床感染病杂志

Objective:To construct a prediction model for prognosis of severe pneumonia patients combined with sepsis.Methods:Clinical data of 318 severe pneumonia patients combined with sepsis admitted at Taizhou People’s Hospital affiliated to Nanjing Medical University from March 2019 to March 2022 were retrospectively analyzed. Patients were randomized into a modeling set ( n=233) and a validation set ( n=85) with a 3∶1 ratio. In the modeling set there were 180 survival cases and 53 fatal cases according to the clinical outcomes within 30 days of admission. Multivariate Cox regression analysis was used to evaluate the independent prognostic factors for patients in the modeling set. A nomogram prediction model was constructed by R based on these prognostic factors and further verified using the data of the validation set with receiver operating curve (ROC), decision curve analysis (DCA), and calibrated with calibration curve analyses. Results:Multivariate Cox regression analysis suggested that septic shock ( HR=2.32, 95% CI 1.37-3.89, P=0.013) and neutrophil/lymphocyte ratio (NLR) ( HR=2.52, 95% CI 1.23-5.61, P=0.017) were independent risk factors for mortality in severe pneumonia patients combined with sepsis within 30 days of admission, while albumin/fibrinogen ratio (AFR) ( HR=0.64, 95% CI 0.41-0.83, P=0.011) and prognostic nutritional index (PNI) ( HR=0.68, 95% CI 0.57-0.83, P=0.009) were independent protective factors. The area under ROC curve (AUC) of the nomogram model based on these four indicators in the modeling and validation sets were 0.875 and 0.880, respectively. The DCA curve analysis indicated that the clinical benefit of this model was better than "All" or "None" curves in both the modeling and verification sets.The calibrate curve analysis indicated that the actual and corrected curves fitted well and were close to the ideal curve. Conclusion:The constructed nomogram model based on septic shock, AFR, NLR and PNI has a well prognostic value in severe pneumonia patients combined with sepsis.

Receptor binding and escape from Beta antibody responses drive Omicron-B.1.1.529 evolution

On the 24th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.

The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer

Large trimeric Spikes decorate SARS-CoV-2 and bind host cells via receptor binding domains (RBDs). We report a conformation in which the trimer is locked into a compact well-ordered form. This differs from previous structures where the RBD can flip up to recognise the receptor. In the locked form regions associated with fusion transitions are stabilised and the RBD harbours curved lipids. The acyl chains bind a hydrophobic pocket in one RBD whilst the polar headgroups attach to an adjacent RBD of the trimer. By functional analogy with enteroviral pocket factors loss of the lipid would destabilise the locked form facilitating receptor attachment, conversion to the postfusion state and virus infection. The nature of lipids available at the site of infection might affect the antigenicity/pathogenicity of released virus. These results reveal a potentially druggable pocket and suggest that the natural prefusion state occludes neutralising RBD epitopes, achieving conformational shielding from antibodies. HighlightsO_LISARS-CoV-2 Spike can adopt a locked conformation with all receptor binding domains (RBDs) down, likely to represent the prefusion resting state C_LIO_LIThis locked conformation is compact and stable, braced by lipid bound within a potentially druggable pocket C_LIO_LIKey neutralization epitopes are shielded in the locked form C_LIO_LILoss of lipid may trigger a cascade of events that lead to cell entry analogous to the role of lipids in enterovirus cell entry C_LI

Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient

The COVID-19 pandemic has had unprecedented health and economic impact, but currently there are no approved therapies. We have isolated an antibody, EY6A, from a late-stage COVID-19 patient and show it neutralises SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds tightly (KD of 2 nM) the receptor binding domain (RBD) of the viral Spike glycoprotein and a 2.6[A] crystal structure of an RBD/EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues of this epitope are key to stabilising the pre-fusion Spike. Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19.

Neutralization of SARS-CoV-2 by destruction of the prefusion Spike

There are as yet no licenced therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 [A] of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilising, CR3022 epitope is inaccessible in the prefusion Spike, suggesting that CR3022 binding would facilitate conversion to the fusion-incompetent post-fusion state. Cryo-EM analysis confirms that incubation of Spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope may be useful therapeutically, possibly in synergy with an antibody blocking receptor attachment. HighlightsO_LICR3022 neutralises SARS-CoV-2 C_LIO_LINeutralisation is by destroying the prefusion SPIKE conformation C_LIO_LIThis antibody may have therapeutic potential alone or with one blocking receptor attachment C_LI

A single nucleotide polymorphism in the interferon-γ gene (IFNG +874 T/A) is associated with susceptibility to tuberculosis.

Interferon-γ (Interferon gamma, IFNG) is an important cytokine involved in providing resistance to mycobacterial diseases. Common variants of IFNG, such as IFNG +874 T/A(rs2430561), may be related to tuberculosis susceptibility, but this association has not been consistently observed. We performed an updated meta-analysis to evaluate the association between the IFNG +874 T/A (rs2430561) polymorphism and tuberculosis susceptibility. PubMed and SinoMed databases were searched up to October 2016, and odds ratios (OR) and 95% confidence intervals (CI) were used to assess the association strength. Based on search criteria for manuscripts reporting tuberculosis susceptibility and its relationship with the IFNG +874 T/A(rs2430561)polymorphism, 42 case-control studies from 39 different articles were retrieved. Significantly positive, decreased, and protective associations were found between the IFNG +874 T/A(rs2430561)polymorphism and tuberculosis risk in five genetic models. Moreover, in the stratified subgroup analysis, a protective relationship was detected in four different ethnicities and sources of the control groups. Furthermore, the IFNG +874 T/A(rs2430561)polymorphism played an important role in protecting individuals from both pulmonary tuberculosis and extra-pulmonary tuberculosis. Our meta-analysis suggests that the IFNG +874 T/A(rs2430561)polymorphism is potentially associated with tuberculosis susceptibility and may be used as a predictive biomarker. Further studies with larger sample sizes and consideration of gene-environment interactions should be conducted to elucidate the role of IFNG +874 T/A(rs2430561) polymorphism in tuberculosis susceptibility.

ERCC1 expression and prognosis in non-small cell lung cancer / 实用肿瘤学杂志

Objective To explore the expression of Excision repair cross -completion 1 in non-small cell lung cancer and to analyze its clinical significance .Methods ERCC1 protein expression was detected by IHC method in 160 cases of non-small cell lung cancer tissue .We analyzed relationship between the ERCC 1 ex-pression and clinicopathological parameters of non -small cell lung cancer ,as well as its correlation between ER-CC1 expression and the prognosis .At the same time ,160 cases of intraoperative specimens were primarily cul-tured.The relationship between ERCC1 expression and the drug sensitivity of DDP was analyzed .Results ER-CC1 protein was mainly expressed in the nucleus .ERCC1 protein expression in lung cancer tissue showed no rela-tionship with age,gender,tumor size and pathological types .ERCC1 protein expression was associated with TNM stages and lymph node metastases .High expression of ERCC1was significantly correlated with poor prognosis in pa-tients,indicating that ERCC1 is the independent factor of NSCLC patients .MTT results showed that the positive ex-pression rate of ERCC1 in DDP sensitive groups was higher than in DDP resistant groups .Conclusion ERCC1 is an independent factor influencing the prognosis of non -small cell lung cancer ,and associated with DDP resistance .

Clinical observation of IMRT therapy combined with astragalus polysaccharide injection on cervicoce-rebral tumor treatment / 实用医学杂志

Objective To observe the effect of IMRT combined with astragalus polysaccharide (ASP) injection on cervicocerebral tumor,radiation side effects and its influence on immune function. Methods 61 head and neck tumor patients were randomly divided into two groups.One groups received the IMRT combined with Astragalus Polysaccharide (ASP) injection (n=30) while the other group only received the IMRT(n=31). The recent effect, immune function and the side effects of radiotherapy between the 2 groups were observed and compared , changes of T-lymphocyte subsets, natural killer (NK) cell activity and the dermatitis,oral mucosa reaction,thirsty condition on patients in intraoperative or postoperative period were also observed and compared. Results The total effective rate in experimental group and the control group were 83.0% and 80.6% respectively.The cell viability of peripheral blood lymphocyte and NK cell as well as the T3、T4、NK cell value increased in IMRT-ASP group (P<0.05) after treatment. While T3、T4、NK cell value in peripheral blood decreased (P<0.05). Mucosa,dermatitis and salivary gland damage showed in IMRT-ASP group were significantly better than in control group after 3 weeks treatment (P<0.05). Conclusion ASP can improve immune function effect in head and neck tumor patients during RT, and can also eliminate the side effects of radiotherapy.

Syndrome of inappropriate anti-diuretic hormone in lung-cancer patients:six cases / 中国肿瘤临床

Objective:To investigate the clinical characteristics, treatment, and evaluation of the prognosis of syndrome of inap-propriate anti-diuretic hormone (SIADH) in lung-cancer patients. Methods:We review the clinical data of six lung cancer cases, includ-ing four small cell lung cancer, one adenocarcinoma, and one squamous cell carcinoma, with SIADH complication. All six cases were treated in our hospital over the past three years. Results:Patients with various serum sodium levels were provided different therapeutic regimens. Symptoms of fatigue and nervous system disorders, plasma sodium, urine sodium, and plasma osmotic pressure were alleviat-ed. Conclusion:SIADH is a common complication of lung cancer, particularly in small lung cancer cases. Electrolyte disturbances indi-cate poor prognosis, high mortality rate, and delay in treatment because of clinical interest. After a final diagnosis has been made and ap-propriate treatment has been administered, clinical symptoms were relieved and blood sodium levels were quickly and significantly im-proved in these patients.

Dynamic study of cerebral spinal fluid markers in patients with tuberculous meningitis / 重庆医科大学学报

Objective:To discuss the value for earlier diagnosis and curative effect evaluation of tuberculosis meningitis(TBM)by detecting the cerebrospinal fluid(CSF)routine,biochemistry and cytology check.Methods:Dynamic Analysis of cerebrospinal fluid routine,biochemistry and cytology variation have been performed on 80 cases with TBM between prior-treatment and post-treatment.Results:There is a obviously rise performed in the cerebrospinal fluid for the pressure,biochemistry index singularity ratio and neutrophil proportion prior treatment,while a progressive decline was observed in post treatment with a significant difference.The typical TBM in forepart showed intermix cytology reaction which had most granulocytes.During the middle period of the treatment,granulocytes reduced,more over immune cells and active hyaline leukocytes increased.During the later period of the treatment,active lymphocytes reaction was the most obvious.Cerebrospinal fluid cytology was back to normal when TBM had been cured.Conclusion:The cerebrospinal fluid cytology check is a significant index in earlier diagnosis of TBM;Dynamic observation on cerebrospinal fluid cytology is helpful for earlier diagnosis of TBM.Furthermore the method has some value in judging the prognosis of the patients suffened TBM.