Genomic perspectives on the emerging SARS-CoV-2 Omicron variant

A new variant of concern for SARS-CoV-2, Omicron (B.1.1.529), was designated by the World Health Organization on November 26, 2021. This study analyzed the viral genome sequencing data of 108 samples collected from patients infected with Omicron. First, we found that the enrichment efficiency of viral nucleic acids was reduced due to mutations in the region where the primers anneal to. Second, the Omicron variant possesses an excessive number of mutations compared to other variants circulating at the same time (62 vs. 45), especially in the Spike gene. Mutations in the Spike gene confer alterations in 32 amino acid residues, which was more than those observed in other SARS-CoV-2 variants. Moreover, a large number of nonsynonymous mutations occur in the codons for the amino acid residues located on the surface of the Spike protein, which could potentially affect the replication, infectivity, and antigenicity of SARS-CoV-2. Third, there are 53 mutations between the Omicron variant and its closest sequences available in public databases. Many of those mutations were rarely observed in the public database and had a low mutation rate. In addition, the linkage disequilibrium between these mutations were low, with a limited number of mutations (6) concurrently observed in the same genome, suggesting that the Omicron variant would be in a different evolutionary branch from the currently prevalent variants. To improve our ability to detect and track the source of new variants rapidly, it is imperative to further strengthen genomic surveillance and data sharing globally in a timely manner.

Neutralization of recombinant RBD-subunit vaccine ZF2001-elicited antisera to SARS-CoV-2 variants including Delta

SARS-CoV-2 variants brought new waves of infection worldwide. In particular, Delta variant (B.1.617.2 lineage) has become predominant in many countries. These variants raised the concern for their potential immune escape to the currently approved vaccines. ZF2001 is a subunit vaccine received emergency use authorization (EUA) in both China and Uzbekistan, with more than 100-million doses administrated with a three-dose regimen. The tandem-repeat dimer of SARS-CoV-2 spike protein receptor binding domain (RBD) was used as the antigen. In this work, we evaluated the neutralization of ZF2001-elicited antisera to SARS-CoV-2 variants including all four variants of concern (Alpha, Beta, Gamma and Delta) and other three variants of interest (Epsilon, Eta and Kappa) by pseudovirus-based assay. We found antisera preserved majority of the neutralizing activity against these variants. E484K/Q substitution is the key mutation to reduce the RBD-elicited sera neutralization. Moreover, ZF2001-elicited sera with a prolonged intervals between the second and third dose enhanced the neutralizing titers and resilience to SARS-CoV-2 variants.

Emerging SARS-CoV-2 mutation hotspots associated with clinical outcomes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Understanding the influence of mutations in the SARS-CoV-2 gene on clinical outcomes and related factors is critical for treatment and prevention. Here, we analyzed 209,551 high-coverage complete virus sequences and 321 RNA-seq samples to mine the mutations associated with clinical outcome in the SARS-CoV-2 genome. Several important hotspot variants were found to be associated with severe clinical outcomes. Q57H variant in ORF3a protein were found to be associated with higher mortality rate, and was high proportion in severe cases (39.36%) and 501Y.V2 strains (100%) but poorly proportional to asymptomatic cases (10.04%). T265I could change nsp2 structure and mitochondrial permeability, and evidently higher in severe cases (20.12%) and 501Y.V2 strains (100%) but lower in asymptomatic cases (1.43%). Additionally, R203K and G204R could decrease the flexibility and immunogenic property of N protein with high frequency among severe cases, VUI 202012/01 and 484K.V2 strains. Interestingly, the SARS-CoV-2 genome was more susceptible to mutation because of the high frequency of nt14408 mutation (which located in RNA polymerase) and the high expression levels of ADAR and APOBEC in severe clinical outcomes. In conclusion, several important mutation hotspots in the SARS-CoV-2 genome associated with clinical outcomes was found in our study, and that might correlate with different SARS-CoV-2 mortality rates.

A non-competing pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2

Neutralizing antibodies could be antivirals against COVID-19 pandemics. Here, we report the isolation of four human-origin monoclonal antibodies from a convalescent patient in China. All of these isolated antibodies display neutralization abilities in vitro. Two of them (B38 and H4) block the binding between RBD and vial cellular receptor ACE2. Further competition assay indicates that B38 and H4 recognize different epitopes on the RBD, which is ideal for a virus-targeting mAb-pair to avoid immune escape in the future clinical applications. Moreover, therapeutic study on the mouse model validated that these two antibodies can reduce virus titers in the infected mouse lungs. Structure of RBD-B38 complex revealed that most residues on the epitope are overlapped with the RBD-ACE2 binding interface, which explained the blocking efficacy and neutralizing capacity. Our results highlight the promise of antibody-based therapeutics and provide the structural basis of rational vaccine design. One Sentence SummaryA pair of human neutralizing monoclonal antibodies against COVID-19 compete cellular receptor binding but with different epitopes, and with post-exposure viral load reduction activity.

Antimicrobial Resistance of Staphylococcus aureus in Our Hospital over the Last 10 Years / 中国医科大学学报

Objective To retrospectively analyze the clinical distribution and changes in antimicrobial resistance profiles of Staphylococcus aureus (S. aureus). Methods We collected clinical specimens of S. aureus from The First Hospital of China Medical University. The Vitek-2 and BD Phoenix 100 were performed for bacterial identification and drug sensitivity tests,and WHONET 5.6 was used to analyze the data. Results From 2007 to 2016,there were 3 377 unrepeatable strains of S. aureus,including 1 705 that were methicillin resistant S. aureus (MRSA). The isolation rate of S. aureus was 9.4 ％ and of these,50.5 ％ were MRSA. There were 776 S. aureus specimens from outpatients or the emergency department,including 16.8 ％ MRSA,and 2 011 S. aureus from inpatient departments,including 60.2 ％ MRSA. The main sources of specimens were sputum (41.8 ％),pus (17.9 ％),and body secretions (17.5 ％). The average resistance rates of MRSA for erythromycin,ofloxacin,ciprofloxacin,gentamycin,and tetracycline were higher than 75.0 ％. The average resistance rate of methicillin sensitive S. aureus (MSSA) for erythromycin was up to 76.8 ％,and for tetracycline,gentamycin,ciprofloxacin,and ofloxacin,were less than 25.0 ％. In 10 years,the average resistance rates of MRSA and MSSA for 11 kinds of common antibiotics had no obvious change. Conclusion The constituent rate of MRSA was high in The First Hospital of China Medical University,especially from the areas that were not sterile,suggesting that clinicians should pay attention to the identification of infection and sources for MRSA,which were from such areas. Hospital infection control should be focused on at the same time,in order to reduce the incidence of MRSA.

Influence of Progesterone and Vitamin D on the Cell Proliferation of Hormone-dependent Breast Cancer and the Interaction / 中国医科大学学报

Objective To study the influence of progesterone on the cell proliferation of hormone?dependent breast cancer and observe the co?effect of vitamin D and progesterone of different levels on the proliferation of the cell line T?47D in hormone?dependent breast cancer and the interaction be?tween vitamin D and progesterone. Methods The cultured T?47D cells were divided into the high and the low progesterone mono?treated groups to observe the effects of different levels of progesterone on the cell proliferation of hormone?dependent breast cancer cell line(T?47D). The high and the low vitamin D mono?treated groups were set to observe the effects of different levels of vitamin D on the cell proliferation. Groups treated by differ?ent levels of progesterone combined with vitamin D were set to observe the interaction between them. Normal breast cancer cells were set as the con?trol group. The two?factor two?level parallel factorial experiment was conducted to observe the co?effect of different levels of progesterone and vitamin D on the proliferation of T?47D. The growth and apoptosis of cells was observed through detection of absorbance in each group by MTT. Results The cell concentration in high and low progesterone treated groups was increased than that in the control group,and was increased in the low proges?terone treated group compared with the high progesterone treated group(P<0.05). The cell concentration in dual?low level treated group was de?creased than that in the other three groups which were two?factor treated and the control group(P<0.05). Conclusion Progesterone stimulates the cell proliferation of hormone?dependent breast cancer. The concentration?based interaction between vitamin D and progesterone indicates that the bi?directional effect of progesterone on breast cancer cells may be related to the concentration of progesterone and other factors,but the specific interac?tion and the mechanism is unclear.

Crystal structures of the two membrane-proximal Ig-like domains (D3D4) of LILRB1/B2: alternative models for their involvement in peptide-HLA binding

Leukocyte immunoglobulin-like receptors (LILRs), also called CD85s, ILTs, or LIRs, are important mediators of immune activation and tolerance that contain tandem immunoglobulin (Ig)-like folds. There are 11 (in addition to two pseudogenes) LILRs in total, two with two Ig-like domains (D1D2) and the remaining nine with four Ig-like domains (D1D2D3D4). Thus far, the structural features of the D1D2 domains of LILR proteins are well defined, but no structures for the D3D4 domains have been reported. This is a very important field to be studied as it relates to the unknown functions of the D3D4 domains, as well as their relative orientation to the D1D2 domains on the cell surface. Here, we report the crystal structures of the D3D4 domains of both LILRB1 and LILRB2. The two Ig-like domains of both LILRB1-D3D4 and LILRB2-D3D4 are arranged at an acute angle (∼60°) to form a bent structure, resembling the structures of natural killer inhibitory receptors. Based on these two D3D4 domain structures and previously reported D1D2/HLA I complex structures, two alternative models of full-length (four Ig-like domains) LILR molecules bound to HLA I are proposed.

A novel xeno-free and feeder-cell-free system for human pluripotent stem cell culture

While human induced pluripotent stem cells (hiPSCs) have promising applications in regenerative medicine, most of the hiPSC lines available today are not suitable for clinical applications due to contamination with nonhuman materials, such as sialic acid, and potential pathogens from animal-product-containing cell culture systems. Although several xeno-free cell culture systems have been established recently, their use of human fibroblasts as feeders reduces the clinical potential of hiPSCs due to batch-to-batch variation in the feeders and time-consuming preparation processes. In this study, we have developed a xeno-free and feeder-cell-free human embryonic stem cell (hESC)/hiPSC culture system using human plasma and human placenta extracts. The system maintains the self-renewing capacity and pluripotency of hESCs for more than 40 passages. Human iPSCs were also derived from human dermal fibroblasts using this culture system by overexpressing three transcription factors-Oct4, Sox2 and Nanog. The culture system developed here is inexpensive and suitable for large scale production.

The clinical significance of urinary B-type natriuretic peptide assay for the diagnosis of chronic heart failure / 中华检验医学杂志

ObjectiveTo investigate the value of urinary BNP for diagnosis of chronic heart failure (CHF). MethodsThe levels of Urinary BNP and plasma BNP were measured by microparticle enzyme immunoassay (MEIA) in 83 patients with CHF and 30 control subjects. The heart function was classified according totheNYHAcriteria. Leftventricularejectionfractions(LVEF)weremeasuredby echocardiology. ResultsThe level of urinary BNP in patients with CHF was[90. 0(38. 3 -209. 5 )]ng/L and the level of plasma BNP was[680. 0 ( 289. 7 - 1543.5)]ng/L, both of them were much higher than those in healthy subjects,[17. 0 ( 13.0 - 33. 0)]ng/L and[84. 5 ( 56. 0 - 158.0 )]ng/L, respectively (P＜0. 01 ). The concentrations of urinary BNP increased gradually with more severe symptoms ( NYHA cl ass Ⅰ -ⅣV ). The level of urinary BNP was positively correlated with NYHA class ( r = 0. 742, P ＜ 0. 01 )and the level of plasma BNP (r =0. 842,P ＜0. 01 ) while negatively related with LVEF (r = -0. 801 ,P ＜0. 01 ). The level of urinary BNP in patients with LVEF ＜ 40％ was[143.0 ( 85. 0 - 258.0)]ng/L , which was much higher than that in patients with LVEF≥40％ ,[31.5( 17.3 -38. 8)]ng/L, (P ＜0. 01 ). At a decision threshold of 36. 5 ng/L, the urine BNP assay demonstrated a clinical sensitivity and specificity of 84％ and 80％ ,respectively. In this study,the area under the curve(AUC) was 0. 905. ConclusionUrinary BNP is a new candidate marker for the diagnosis of CHF,it provides a similar accuracy with plasma BNP.