HIV-1 Gag, Pol, and Env diversified with limited adaptation since the 1980s

Knowledge of HIV-1 global sequence diversity is critical for developing an effective prophylactic against HIV-1 infection. We developed the Hervé platform to analyze and visualize trends in HIV-1 diversification. Using Hervé, we analyzed 4,830 Env, 4,407 Gag, and 3,002 Pol publicly available independent sequences corresponding to subtypes A1, A6, B, C, D, F1, and G and circulating recombinant forms (CRFs) 01_AE, 02_AG, and 07_BC; sequences were sampled between 1980 and 2020 from 82 countries. HIV-1 diversified with a median of 1.82 amino acid substitutions per year in Env, 0.297 in Gag, and 0.779 in Pol. Yet, Env subtype B diversification plateaued post-2000. Pairwise diversity within subtypes and CRFs increased by 41.82% (range = 24.85%-54.41%) in Env, 56.93% (15.38%-89.16%) in Gag, and 46.12% (11.70%-70.57%) in Pol. Consensus sequences based on sequences sampled in each decade remained relatively stable over time. Similarly, at antibody epitope sites, only 0-8 residues that were minority variants became consensus over time in any subtype/CRF and only one known drug resistance mutation site differed from the reference (subtype G). The apparent contradiction between the fast diversification of HIV-1 and its limited adaptation illustrates that HIV-1 evolution is not directional and its consensus is at the intersection of millions of within-host selective processes occurring in a star-like manner. While a consensus sequence is a better representation of HIV-1 diversity than any individual sequence, consensus sequences have progressively become more distant from the circulating sequences they represent.

IMPORTANCE

Global surveillance of HIV-1 sequences is critical for designing relevant prophylactic and therapeutic interventions to infection. We designed an open-source platform, Hervé, for analyzing and visualizing the diversification dynamics of HIV-1 protein sequences. We characterized the evolution of over 12,000 HIV-1 Env, Gag, and Pol protein sequences from 1980-2020 and found that, despite a steady increase in intra-subtype and circulating recombinant form diversity, the most frequent residue at each site, i.e., the consensus, has varied only moderately.

Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features

In the ENSEMBLE randomized, placebo-controlled phase 3 trial (NCT04505722), estimated single-dose Ad26.COV2.S vaccine efficacy (VE) was 56% against moderate to severe-critical COVID-19. SARS-CoV-2 Spike sequences were determined from 484 vaccine and 1,067 placebo recipients who acquired COVID-19. In this set of prespecified analyses, we show that in Latin America, VE was significantly lower against Lambda vs. Reference and against Lambda vs. non-Lambda [family-wise error rate (FWER) p < 0.05]. VE differed by residue match vs. mismatch to the vaccine-insert at 16 amino acid positions (4 FWER p < 0.05; 12 q-value ≤ 0.20); significantly decreased with physicochemical-weighted Hamming distance to the vaccine-strain sequence for Spike, receptor-binding domain, N-terminal domain, and S1 (FWER p < 0.001); differed (FWER ≤ 0.05) by distance to the vaccine strain measured by 9 antibody-epitope escape scores and 4 NTD neutralization-impacting features; and decreased (p = 0.011) with neutralization resistance level to vaccinee sera. VE against severe-critical COVID-19 was stable across most sequence features but lower against the most distant viruses.

Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain

Given the continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs), immunotherapeutics that target conserved epitopes on the spike (S) glycoprotein have therapeutic advantages. Here, we report the crystal structure of the SARS-CoV-2 S receptor-binding domain (RBD) at 1.95 Å and describe flexibility and distinct conformations of the angiotensin-converting enzyme 2 (ACE2)-binding site. We identify a set of SARS-CoV-2-reactive monoclonal antibodies (mAbs) with broad RBD cross-reactivity including SARS-CoV-2 Omicron subvariants, SARS-CoV-1, and other sarbecoviruses and determine the crystal structures of mAb-RBD complexes with Ab246 and CR3022 mAbs targeting the class IV site, WRAIR-2134, which binds the recently designated class V epitope, and WRAIR-2123, the class I ACE2-binding site. The broad reactivity of class IV and V mAbs to conserved regions of SARS-CoV-2 VoCs and other sarbecovirus provides a framework for long-term immunotherapeutic development strategies.

Prevention efficacy of the broadly neutralizing antibody VRC01 depends on HIV-1 envelope sequence features

In the Antibody Mediated Prevention (AMP) trials (HVTN 704/HPTN 085 and HVTN 703/HPTN 081), prevention efficacy (PE) of the monoclonal broadly neutralizing antibody (bnAb) VRC01 (vs. placebo) against HIV-1 acquisition diagnosis varied according to the HIV-1 Envelope (Env) neutralization sensitivity to VRC01, as measured by 80% inhibitory concentration (IC80). Here, we performed a genotypic sieve analysis, a complementary approach to gaining insight into correlates of protection that assesses how PE varies with HIV-1 sequence features. We analyzed HIV-1 Env amino acid (AA) sequences from the earliest available HIV-1 RNA-positive plasma samples from AMP participants diagnosed with HIV-1 and identified Env sequence features that associated with PE. The strongest Env AA sequence correlate in both trials was VRC01 epitope distance that quantifies the divergence of the VRC01 epitope in an acquired HIV-1 isolate from the VRC01 epitope of reference HIV-1 strains that were most sensitive to VRC01-mediated neutralization. In HVTN 704/HPTN 085, the Env sequence-based predicted probability that VRC01 IC80 against the acquired isolate exceeded 1 µg/mL also significantly associated with PE. In HVTN 703/HPTN 081, a physicochemical-weighted Hamming distance across 50 VRC01 binding-associated Env AA positions of the acquired isolate from the most VRC01-sensitive HIV-1 strain significantly associated with PE. These results suggest that incorporating mutation scoring by BLOSUM62 and weighting by the strength of interactions at AA positions in the epitope:VRC01 interface can optimize performance of an Env sequence-based biomarker of VRC01 prevention efficacy. Future work could determine whether these results extend to other bnAbs and bnAb combinations.

Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques

The repeat emergence of SARS-CoV-2 variants of concern (VoC) with decreased susceptibility to vaccine-elicited antibodies highlights the need to develop next-generation vaccine candidates that confer broad protection. Here we describe the antibody response induced by the SARS-CoV-2 Spike Ferritin Nanoparticle (SpFN) vaccine candidate adjuvanted with the Army Liposomal Formulation including QS21 (ALFQ) in non-human primates. By isolating and characterizing several monoclonal antibodies directed against the Spike Receptor Binding Domain (RBD), N-Terminal Domain (NTD), or the S2 Domain, we define the molecular recognition of vaccine-elicited cross-reactive monoclonal antibodies (mAbs) elicited by SpFN. We identify six neutralizing antibodies with broad sarbecovirus cross-reactivity that recapitulate serum polyclonal antibody responses. In particular, RBD mAb WRAIR-5001 binds to the conserved cryptic region with high affinity to sarbecovirus clades 1 and 2, including Omicron variants, while mAb WRAIR-5021 offers complete protection from B.1.617.2 (Delta) in a murine challenge study. Our data further highlight the ability of SpFN vaccination to stimulate cross-reactive B cells targeting conserved regions of the Spike with activity against SARS CoV-1 and SARS-CoV-2 variants.

Zika-specific neutralizing antibodies targeting inter-dimer envelope epitopes

Zika virus (ZIKV) is an emerging pathogen that causes devastating congenital defects. The overlapping epidemiology and immunologic cross-reactivity between ZIKV and dengue virus (DENV) pose complex challenges to vaccine design, given the potential for antibody-dependent enhancement of disease. Therefore, classification of ZIKV-specific antibody targets is of notable value. From a ZIKV-infected rhesus macaque, we identify ZIKV-reactive B cells and isolate potent neutralizing monoclonal antibodies (mAbs) with no cross-reactivity to DENV. We group these mAbs into four distinct antigenic groups targeting ZIKV-specific cross-protomer epitopes on the envelope glycoprotein. Co-crystal structures of representative mAbs in complex with ZIKV envelope glycoprotein reveal envelope-dimer epitope and unique dimer-dimer epitope targeting. All four specificities are serologically identified in convalescent humans following ZIKV infection, and representative mAbs from all four groups protect against ZIKV replication in mice. These results provide key insights into ZIKV-specific antigenicity and have implications for ZIKV vaccine, diagnostic, and therapeutic development.

Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity

Novel therapeutic monoclonal antibodies (MAbs) must accommodate comprehensive breadth of activity against diverse sarbecoviruses and high neutralization potency to overcome emerging variants. Here, we report the crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD) in complex with MAb WRAIR-2063, a moderate-potency neutralizing antibody with exceptional sarbecovirus breadth, that targets the highly conserved cryptic class V epitope. This epitope overlaps substantially with the spike protein N-terminal domain (NTD) -interacting region and is exposed only when the spike is in the open conformation, with one or more RBDs accessible. WRAIR-2063 binds the RBD of SARS-CoV-2 WA-1, all variants of concern (VoCs), and clade 1 to 4 sarbecoviruses with high affinity, demonstrating the conservation of this epitope and potential resiliency against variation. We compare structural features of additional class V antibodies with their reported neutralization capacity to further explore the utility of the class V epitope as a pan-sarbecovirus vaccine and therapeutic target. IMPORTANCE Characterization of MAbs against SARS-CoV-2, elicited through vaccination or natural infection, has provided vital immunotherapeutic options for curbing the COVID-19 pandemic and has supplied critical insights into SARS-CoV-2 escape, transmissibility, and mechanisms of viral inactivation. Neutralizing MAbs that target the RBD but do not block ACE2 binding are of particular interest because the epitopes are well conserved within sarbecoviruses and MAbs targeting this area demonstrate cross-reactivity. The class V RBD-targeted MAbs localize to an invariant site of vulnerability, provide a range of neutralization potency, and exhibit considerable breadth against divergent sarbecoviruses, with implications for vaccine and therapeutic development.

Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features

It is of interest to pinpoint SARS-CoV-2 sequence features defining vaccine resistance. In the ENSEMBLE randomized, placebo-controlled phase 3 trial, estimated single-dose Ad26.COV2.S vaccine efficacy (VE) was 56% against moderate to severe-critical COVID-19. SARS-CoV-2 Spike sequences were measured from 484 vaccine and 1,067 placebo recipients who acquired COVID-19 during the trial. In Latin America, where Spike diversity was greatest, VE was significantly lower against Lambda than against Reference and against all non-Lambda variants [family-wise error rate (FWER) p < 0.05]. VE also differed by residue match vs. mismatch to the vaccine-strain residue at 16 amino acid positions (4 FWER p < 0.05; 12 q-value ≤ 0.20). VE significantly decreased with physicochemical-weighted Hamming distance to the vaccine-strain sequence for Spike, receptor-binding domain, N-terminal domain, and S1 (FWER p < 0.001); differed (FWER ≤ 0.05) by distance to the vaccine strain measured by 9 different antibody-epitope escape scores and by 4 NTD neutralization-impacting features; and decreased (p = 0.011) with neutralization resistance level to vaccine recipient sera. VE against severe-critical COVID-19 was stable across most sequence features but lower against viruses with greatest distances. These results help map antigenic specificity of in vivo vaccine protection.

Efficient Spin-to-Charge Conversion via Altermagnetic Spin Splitting Effect in Antiferromagnet RuO_{2}

The relativistic spin Hall effect and inverse spin Hall effect enable the efficient generation and detection of spin current. Recently, a nonrelativistic altermagnetic spin splitting effect (ASSE) has been theoretically and experimentally reported to generate time-reversal-odd spin current with controllable spin polarization in antiferromagnet RuO_{2}. The inverse effect, electrical detection of spin current via ASSE, still remains elusive. Here we show the spin-to-charge conversion stemming from ASSE in RuO_{2} by the spin Seebeck effect measurements. Unconventionally, the spin Seebeck voltage can be detected even when the injected spin current is polarized along the directions of either the voltage channel or the thermal gradient, indicating the successful conversion of x- and z-spin polarizations into the charge current. The crystal axes-dependent conversion efficiency further demonstrates that the nontrivial spin-to-charge conversion in RuO_{2} is ascribed to ASSE, which is distinct from the magnetic or antiferromagnetic inverse spin Hall effects. Our finding not only advances the emerging research landscape of altermagnetism, but also provides a promising pathway for the spin detection.

Design of a pan-betacoronavirus vaccine candidate through a phylogenetically informed approach

Coronaviruses are a diverse family of viruses that crossed over into humans at least seven times, precipitating mild to catastrophic outcomes. The severe acute respiratory syndrome coronavirus 2 pandemic renewed efforts to identify strains with zoonotic potential and to develop pan-coronavirus vaccines. The analysis of 2181 coronavirus genomes (from 102 host species) confirmed the limited sequence conservation across genera (alpha-, beta-, delta-, and gammacoronavirus) and proteins. A phylogenetically informed pan-coronavirus vaccine was not feasible because of high genetic heterogeneity across genera. We focused on betacoronaviruses and identified nonhuman-infecting receptor binding domain (RBD) sequences that were more genetically similar to human coronaviruses than expected given their phylogenetic divergence. These human-like RBDs defined three phylogenetic clusters. A vaccine candidate based on a representative sequence for each cluster covers the diversity estimated to protect against existing and future human-infecting betacoronaviruses. Our findings emphasize the potential value of conceptualizing prophylaxis against zoonoses in terms of genetic, rather than species, diversity.

Association between CYP2E1 C-1054T and 96-bp I/D genetic variations and the risk of polycystic ovary syndrome in Chinese women

PURPOSE

To investigate the association of cytochrome P450 2E1 (CYP2E1) C-1054T (rs2031920) and 96-bp I/D genetic variations with the risk of polycystic ovary syndrome (PCOS), and to estimate the effects of genotypes on the clinical, metabolic, hormonal, and oxidative stress indicators.

METHODS

This case-control study included 762 control women and 1034 patients with PCOS. Genotypes were determined using polymerase chain reaction and/or restriction fragment length polymorphism analysis. Clinical and biochemical parameters were also analyzed.

RESULTS

Frequencies of the TT + CT genotype (35.4 vs. 28.9%) and T allele (19.6 vs. 16.0%) of the CYP2E1 C-1054T polymorphism were significantly higher in the PCOS group than in the control group (OR = 1.350, 95% CI 1.103-1.652, P = 0.004 for the dominant model). Genotype TT + CT remained a significant predictor of PCOS in a logistic regression model including age, body mass index (BMI), and recruitment year of participants (OR = 1.345, 95% CI 1.071-1.688, P = 0.011). No statistical differences were found in the genotype and allele frequencies of CYP2E1 96-bp I/D polymorphism. However, the combined genotype DD/TT + CT was related to an increased risk of PCOS when the DD/CC wild-type combined genotype was used as a reference. Patients with the I allele of 96-bp I/D polymorphism had a lower BMI but higher plasma apolipoprotein B and oxidized low-density lipoprotein cholesterol levels than those with the DD genotype.

CONCLUSION

CYP2E1 C-1054T, but not 96-bp I/D, genetic polymorphism is associated with an increased risk of PCOS in Chinese women.

Investigating the mechanism of interactive regulation of B-cell lymphoma-2/Beclin 1 through electroacupuncture intervention during reperfusion in myocardial ischemia-reperfusion injury in a rat model

To observe the regulation of B-cell lymphoma-2 (Bcl-2)/Beclin 1 interaction through electroacupuncture (EA) intervention during reperfusion and to investigate the EA mechanism of apoptosis-autophagy interactive regulation against myocardial ischemia-reperfusion injury (MIRI). A total of 48 adult Sprague Dawley (SD) rats were randomly divided into the sham-operated group (group Sham), the model group (group Model), the EA group (group EA), and the JNK inhibitor (SP600125) group (group JNK), with 12 rats in each group. Biospecimens were collected randomly from six rats in each group four hours after reperfusion. Evans Blue and triphenyl tetrazolium chloride double-staining were applied to observe each group's myocardial damage area and risk area. We collected 4 ml of blood by abdominal aortic method to detect serum troponin cTnI level by enzyme-linked immunosorbent assay (ELISA). For the remaining six in each group, a part of myocardial tissue below the ligation line was stored in 4% paraformaldehyde for immunohistochemistry and TUNEL staining; the other amount of myocardial tissue was detected by Western blotting to determine the expression levels of Bcl-2, Beclin1, and the phosphorylation levels of Thr69, Ser70, and Ser87 in Bcl-2. In results: electroacupuncture (EA) intervention during reperfusion significantly reduced the myocardial infarction area, cTnI level, and myocardial apoptosis, upregulated Bcl-2 expression, downregulated Beclin 1 expression and inhibited phosphorylation levels of Thr69, Ser70, and Ser87 in Bcl-2. We concluded that EA effectively inhibited apoptosis by upregulating Bcl-2 expression and inhibiting the phosphorylation of Thr69, Ser70, and Ser87 in Bcl-2. This reduced the separation of Bcl-2 and Beclin 1, restrains excessive autophagy, alleviates MIRI, and has a protective effect on myocardial tissue.

Bone mineral density, osteopenia and osteoporosis among US adults with cancer

BACKGROUND

Bone mineral deficits are one of the most common complications in cancer survivors. However, there are no studies evaluating bone mineral density (BMD) and the prevalence of osteopenia and osteoporosis among patients with different types of cancers.

AIM

The objective was to assess BMD and evaluate the prevalence of osteopenia and osteoporosis among US adults with cancer.

DESIGN

A cross-section propensity score matching study.

METHODS

We extracted data from National Health and Nutrition Examination Survey database from 2005 to 2018. We compared BMD in participants with and without cancer which was further analyzed according to cancer type. We conducted logistic regression to evaluate adjusted odds ratios of osteopenia and osteoporosis and determine risk factors for their development.

RESULTS

We found that BMD was significantly higher in participants without cancer than cancer patients. Furthermore, the median BMD of patients with breast cancer or skin cancer (including melanoma) was significantly lower than participants without cancer. People with breast, lung, genitourinary and skin cancers were more likely to incur osteopenia/osteoporosis than those without cancer.

CONCLUSIONS

BMD differs depending upon type in survivors. Individuals with a history of cancer have a poor understanding of osteoporosis and its risk factors. Understanding risk factors in patients with cancers identified in our study may be helpful for preventing osteoporosis and fractures and the development of screening guidelines.

Robust deep learning-based protein sequence design using ProteinMPNN

Although deep learning has revolutionized protein structure prediction, almost all experimentally characterized de novo protein designs have been generated using physically based approaches such as Rosetta. Here, we describe a deep learning-based protein sequence design method, ProteinMPNN, that has outstanding performance in both in silico and experimental tests. On native protein backbones, ProteinMPNN has a sequence recovery of 52.4% compared with 32.9% for Rosetta. The amino acid sequence at different positions can be coupled between single or multiple chains, enabling application to a wide range of current protein design challenges. We demonstrate the broad utility and high accuracy of ProteinMPNN using x-ray crystallography, cryo-electron microscopy, and functional studies by rescuing previously failed designs, which were made using Rosetta or AlphaFold, of protein monomers, cyclic homo-oligomers, tetrahedral nanoparticles, and target-binding proteins.

[Influence of age on advanced neoplasia detection in colorectal cancer screening in population at high risk]

Objective: To compare the detection rate of advanced neoplasia and the number of people needing endoscopy in colorectal cancer screening giving at different starting age in population at high risk. Methods: Based on the screening project of early diagnosis and treatment of colorectal cancer in Jiashan county, Zhejiang province, two rounds of colorectal cancer screening were conducted between January 2007 and December 2020. After excluding participants who were not at high risk or had incomplete information, 27 130 participants and 31 205 participants were finally enrolled in round one and in round two, respectively. The spline analysis based on the generalized additive model was used to describe the trend of detection rate of advanced neoplasia with age. The detection rate and number of people needing endoscopy for the groups with starting age at 50, 45 and 40 years were calculated, and the differences in the detection rate were tested by χ² goodness of fit test. Results: A total of 21 077 (77.69%) participants in round one and 25 249 (80.91%) participants in round two received endoscopy, in whom 1 097 (detection rate=52.05‰) and 1 151 (detection rate=45.59‰) had advanced neoplasia (cancers and advanced adenomas), respectively. The detection rate increased significantly with age, and the detection rate in round one were significantly higher than that in round two (P<0.05). The overall detection rates of advanced neoplasia for the groups with starting age at 50, 45 and 40 years were 61.11‰, 56.14‰ and 52.05‰ in round one, and 49.10‰, 46.75‰ and 45.59‰ in round two, respectively. The rates were significantly higher for the group with starting age at 50 years than that with starting age at 40 years in both round one and round two (P<0.05). The numbers of people needing endoscopy of advanced neoplasia for the groups with starting age at 50, 45 and 40 years were 17, 18, and 20 in round one, and 21, 22 and 22 in round two. Conclusions: The detection rate of advanced neoplasia increased with age. Starting screening at lower age might contribute to decreased detection rate and increased number of people needing endoscopy. However, the difference was limited.

[Influence of age on advanced neoplasia detection in colorectal cancer screening in population at high risk]

Objective: To compare the detection rate of advanced neoplasia and the number of people needing endoscopy in colorectal cancer screening giving at different starting age in population at high risk. Methods: Based on the screening project of early diagnosis and treatment of colorectal cancer in Jiashan county, Zhejiang province, two rounds of colorectal cancer screening were conducted between January 2007 and December 2020. After excluding participants who were not at high risk or had incomplete information, 27 130 participants and 31 205 participants were finally enrolled in round one and in round two, respectively. The spline analysis based on the generalized additive model was used to describe the trend of detection rate of advanced neoplasia with age. The detection rate and number of people needing endoscopy for the groups with starting age at 50, 45 and 40 years were calculated, and the differences in the detection rate were tested by χ² goodness of fit test. Results: A total of 21 077 (77.69%) participants in round one and 25 249 (80.91%) participants in round two received endoscopy, in whom 1 097 (detection rate=52.05‰) and 1 151 (detection rate=45.59‰) had advanced neoplasia (cancers and advanced adenomas), respectively. The detection rate increased significantly with age, and the detection rate in round one were significantly higher than that in round two (P<0.05). The overall detection rates of advanced neoplasia for the groups with starting age at 50, 45 and 40 years were 61.11‰, 56.14‰ and 52.05‰ in round one, and 49.10‰, 46.75‰ and 45.59‰ in round two, respectively. The rates were significantly higher for the group with starting age at 50 years than that with starting age at 40 years in both round one and round two (P<0.05). The numbers of people needing endoscopy of advanced neoplasia for the groups with starting age at 50, 45 and 40 years were 17, 18, and 20 in round one, and 21, 22 and 22 in round two. Conclusions: The detection rate of advanced neoplasia increased with age. Starting screening at lower age might contribute to decreased detection rate and increased number of people needing endoscopy. However, the difference was limited.

Effects of residual feed intake divergence on growth performance, carcass traits, meat quality, and blood biochemical parameters in small-sized meat ducks

Feed efficiency (FE) is a major economic trait of meat duck. This study aimed to evaluate the effects of residual feed intake (RFI) divergence on growth performance, carcass traits, meat quality, and blood biochemical parameters in small-sized meat ducks. A total of 500 healthy 21-day-old male ducks were housed in individual cages until slaughter at 63 d of age. The growth performance was determined for all the ducks. The carcass yield, meat quality, and blood biochemical parameters were determined for the selected 30 high-RFI (HRFI) and 30 low-RFI (LRFI) ducks. In terms of growth performance, the RFI, feed conversion ratio (FCR), and average daily feed intake (ADFI) were found to be significantly lower in the LRFI group (P < 0.01), whereas no differences were observed in the BW and body weight gain (P > 0.05). For slaughter performance, no differences were observed in the carcass traits between the LRFI and HRFI groups (P > 0.05). For meat quality, the shear force of breast muscle was significantly lower in the LRFI group (P < 0.05), while the other meat quality traits of breast and thigh muscles demonstrated no differences (P > 0.05). For blood biochemical parameters, the serum concentrations of triglycerides (TG) and glucose (GLU) were significantly lower in the LRFI group (P < 0.05), while the other parameters showed no differences (P > 0.05). The correlation analysis demonstrated a high positive correlation between RFI, FCR, and ADFI (P < 0.01). The RFI demonstrated a negative effect on the breast muscle and lean meat yields, but a positive effect on the shear force of breast muscle (P < 0.05). Further, the RFI demonstrated a positive effect on the TG and GLU levels (P < 0.05). These results indicate that the selection for low RFI could improve the FE of small-sized meat ducks without affecting the production performance. This study provides valuable insight into the biological processes underlying the variations in FE in small-sized meat ducks.

Observation of Spin Splitting Torque in a Collinear Antiferromagnet RuO_{2}

Current-induced spin torques provide efficient data writing approaches for magnetic memories. Recently, the spin splitting torque (SST) was theoretically predicted, which combines advantages of conventional spin transfer torque (STT) and spin-orbit torque (SOT) as well as enables controllable spin polarization. Here we provide the experimental evidence of SST in collinear antiferromagnet RuO_{2} films. The spin current direction is found to be correlated to the crystal orientation of RuO_{2} and the spin polarization direction is dependent on (parallel to) the Néel vector. These features are quite characteristic for the predicted SST. Our finding not only presents a new member for the spin torques besides traditional STT and SOT, but also proposes a promising spin source RuO_{2} for spintronics.

[Progress in pulmonary enteric adenocarcinoma]

Pulmonary enteric adenocarcinoma (PEAC), as a rare histologic subtype of primary lung adenocarcinoma, is defined as an adenocarcinoma in which the enteric component exceeds 50%. It is named after its shared morphological and immunohistochemical features with colorectal cancer. While with such similarity, the differential diagnosis of PEAC and lung metastatic colorectal cancer is a great challenge in the clinic. PEAC may originate from the intestinal metaplasia of respiratory basal cells stimulated by risk factors such as smoking. Current studies have found that KRAS is a relatively high-frequency mutation gene, and other driver gene mutations are rare. In terms of immunohistochemistry, in pulmonary enteric adenocarcinoma, the positive rate was 88.2% (149/169) for CK7, 78.1% (132/169) for CDX2, 48.2% (82/170) for CK20 and 38.8% (66/170) for TTF1. As for clinical features, the average age of onset for pulmonary enteric adenocarcinoma was 62 years, male patients accounted for 56.5% (35/62), smokers accounted for 78.8% (41/52), and 41.4% (24/58) of the primary lesion was located in the upper lobe of the right lung. In terms of treatment, conventional non-small cell lung cancer (NSCLC) regimens rather than colorectal cancer regimens are now recommended. There is still an urgent need for more basic and clinical research, in-depth exploration of its molecular feature and pathogenesis from the level of omics and other aspects, to help diagnosis and differential diagnosis, and find the optimal chemotherapy regimen, possibly effective targeted therapy and even immunotherapy.

HIV-1 infections with multiple founders associate with the development of neutralization breadth

Eliciting broadly neutralizing antibodies (bnAbs) is a cornerstone of HIV-1 vaccine strategies. Comparing HIV-1 envelope (env) sequences from the first weeks of infection to the breadth of antibody responses observed several years after infection can help define viral features critical to vaccine design. We investigated the relationship between HIV-1 env genetics and the development of neutralization breadth in 70 individuals enrolled in a prospective acute HIV-1 cohort. Half of the individuals who developed bnAbs were infected with multiple HIV-1 founder variants, whereas all individuals with limited neutralization breadth had been infected with single HIV-1 founders. Accordingly, at HIV-1 diagnosis, env diversity was significantly higher in participants who later developed bnAbs compared to those with limited breadth (p = 0.012). This association between founder multiplicity and the subsequent development of neutralization breadth was also observed in 56 placebo recipients in the RV144 vaccine efficacy trial. In addition, we found no evidence that neutralization breath was heritable when analyzing env sequences from the 126 participants. These results demonstrate that the presence of slightly different HIV-1 variants in acute infection could promote the induction of bnAbs, suggesting a novel vaccine strategy, whereby an initial immunization with a cocktail of minimally distant antigens would be able to initiate bnAb development towards breadth.

Vaccines against viral pathogens protect through the induction of broadly neutralizing antibodies (bnAbs). No HIV-1 vaccine has successfully elicited bnAbs, and a successful HIV-1 vaccine will need to accelerate the process of development of a broadly neutralizing response that typically takes a couple of years to develop in natural infection. We studied diversity in the HIV-1 envelope gene from initial infection to several years out in 126 individuals from two cohorts. We showed that the development of bnAbs at 2–3 years was not due to transmissible viral genetics, but rather associated with diversity during the first month of infection. We propose that designing a vaccine that mimics an infection with multiple, minimally distant founder variants may successfully elicit the development of bnAbs and provide effective prophylaxis against HIV-1.

RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection

The scale of the HIV-1 epidemic underscores the need for a vaccine. The multitude of circulating HIV-1 strains together with HIV-1’s high evolvability hints that HIV-1 could adapt to a future vaccine. Here, we wanted to investigate the effect of vaccination on the evolution of the virus post-breakthrough infection. We analyzed 2,635 HIV-1 env sequences sampled up to a year post-diagnosis from 110 vaccine and placebo participants who became infected in the RV144 vaccine efficacy trial. We showed that the Env signature sites that were previously identified to distinguish vaccine and placebo participants were maintained over time. In addition, fewer sites were under diversifying selection in the vaccine group than in the placebo group. These results indicate that HIV-1 would possibly adapt to a vaccine upon its roll-out.

Alcohol intake and the risk of chronic kidney disease: results from a systematic review and dose-response meta-analysis

Many prospective cohort studies have investigated the association between the consumption of alcohol and CKD risk and have revealed inconsistent results. In the present study, we aimed to perform a meta-analysis of these studies to assess this association.We searched the PubMed and Embase databases up to 2020 and reviewed the reference lists of relevant articles to identify appropriate studies. We calculated the pooled relative risks with 95% CIs using random effects models, and then performed subgroup and meta-regression analyses. Dose-response meta-analyses were performed by sex separately. We identified 25 eligible prospective cohort studies, including 514,148 participants and 35,585 incident CKD cases. Compared with the category of minimal alcohol intake, light (RR = 0.90, I2 = 49%), moderate (RR = 0.86, I2 = 40%), and heavy (RR = 0.85, I2 = 51%) alcohol intake were associated with a lower risk of CKD. Subgroup meta-analysis by sex indicated that light (RR = 0.92, I2 = 0%), moderate (RR = 0.83, I2 = 39%) and heavy (RR = 0.76, I2 = 40%), alcohol consumption were inversely associated with CKD risk in male. Dose-response meta-analyses detected a nonlinear inverse association between alcohol consumption and the risk of CKD in all participants and linear inverse association in female participants. This meta-analysis shows that light (<12 g/day), moderate (12-24 g/day), and heavy (>24 g/day) alcohol consumption are protective against chronic kidney disease in adult participants especially in males.

Neutralizing antibody VRC01 failed to select for HIV-1 mutations upon viral rebound

Infusion of the broadly neutralizing antibody VRC01 has been evaluated in individuals chronically infected with HIV-1. Here, we studied how VRC01 infusions affected viral rebound after cessation of antiretroviral therapy (ART) in 18 acutely treated and durably suppressed individuals. Viral rebound occurred in all individuals, yet VRC01 infusions modestly delayed rebound and participants who showed a faster decay of VRC01 in serum rebounded more rapidly. Participants with strains most sensitive to VRC01 or with VRC01 epitope motifs similar to known VRC01-susceptible strains rebounded later. Upon rebound, HIV-1 sequences were indistinguishable from those sampled at diagnosis. Across the cohort, participant-derived Env showed different sensitivity to VRC01 neutralization (including 2 resistant viruses), yet neutralization sensitivity was similar at diagnosis and after rebound, indicating the lack of selection for VRC01 resistance during treatment interruption. Our results showed that viremia rebounded despite the absence of HIV-1 adaptation to VRC01 and an average VRC01 trough of 221 μg/mL. Although VRC01 levels were insufficient to prevent a resurgent infection, knowledge that they did not mediate Env mutations in acute-like viruses is relevant for antibody-based strategies in acute infection.

[Aldo-keto reductase family 1 B10 participates in the regulation of hepatoma cell cycle through p27/p-Rb signaling pathway]

Objective: Aldo-keto reductase family 1 member B10 (AKR1B10) pathogenesis, early diagnosis and prognosis are closely related with hepatoma. Therefore, this study explores the effect and mechanism of AKR1B10 on cell cycle in hepatoma cells. Methods: HepG2 cells were infected with lentivirus LV-AKR1B10-shRNA or treated with epalrestat, an AKR1B10 inhibitor. The expression level of AKR1B10 was detected by Western blot assay and real-time fluorescence quantitative PCR (RT-qPCR). Decreased AKR1B10 activity was detected by reduced coenzyme II (NADPH) absorbance at 340 nm. The low expression of AKR1B10 and the effect of different concentrations of epalrestat on cell proliferation and cell cycle were detected by CCK-8 method and flow cytometry. The protein expression levels of p-rb, cyclin D1, E1, p27 in HepG2 cells were detected by Western blot. The mean of the two samples was tested using independent sample t-test. Results: AKR1B10 expression level in hepatoma cells was significantly increased compared to normal liver cells, and the relative expression level of AKR1B10 protein in HepG2 cells was 6.71 ± 1.11 (P = 0.012). Epalrestat was significantly inhibited with the enzymatic activity of AKR1B10 in a dose-dependent manner. AKR1B10 gene in HepG2 cells was effectively silenced. HepG2 cells treated with different concentrations of epalrestat (AKR1B10 inhibitor) for 24, 48 and 72 h had inhibited cell proliferation, promoted G0/G1 cell cycle arrest, reduced the expression of p-Rb, cyclin D1, and cyclin E1 and increased the expression of cyclin dependent kinase inhibitor p27 expression. Conclusion: AKR1B10 inhibitory expression and activity can promote G0/G1 cell cycle arrest in HepG2 cells through the p27 / p-Rb pathway.

[Thyroid disruptor p, p'-DDE inhibited the expression of LHX4 and DIS3L protein in Nthy-ori-3-1 cells]

Objective: To observe the changes of LHX4 and DIS3L mRNA and protein expression in Nthy-ori-3-1 cells after the treatment of thyroid disruptor p, p'-DDE. Methods: Nthy-ori-3-1 cells in logarithmic growth phase were treated with 0, 0.5, 1.0, 2.0 and 5.0 μg/ml p, p'-DDE solution. The growth state and morphology of the cells were observed by microscope. The mRNA levels of LHX4 and DIS3L were detected by real-time fluorescent quantitative PCR, and the protein expression levels of LHX4 and DIS3L were detected by Western blot. Results: when the concentrations of p, p'-DDE were 0, 0.5, 1.0 and 2.0 μg/ml, Nthy-ori-3-1 cells grew normally. There were 33 differential genes in 2.0 μg/ml group, among which 13 genes were down regulated and 20 genes were up-regulated. Compared with the control group, the protein expression levels of LHX4 and DIS3L in 1.0 and 2.0 μg/ml groups were significantly decreased (P<0.05) , and the relative expression levels of LHX4 and DIS3L protein mRNA in 1.0 μg/ml group were significantly decreased (P<0.05) . Conclusion: p, p'-DDE can affect the protein expression of LHX4 and dis3l in nthy-ori-3-1 cells.

[Efficacy and safety of generic azacitidine in Chinese patients with higher-risk myelodysplastic syndromes: a multicenter, prospective, single-arm study]

Objective: To evaluate the efficacy, safety, and pharmacokinetics of the generic azacitidine in Chinese patients with higher-risk myelodysplastic syndromes(MDS). Methods: Between October 2013 and 2016, 72 patients were eligible for enrollment at 9 sites from China received generic subcutaneous azacitidine 75 mg·m(-2)·d(-1) for 7 days per 28-day cycle, for ≥6 cycles. Pharmacokinetic blood samples were collected on day 1 of a single-dose. Results: For each patient at cycle 6 or at the time of study discontinuation, whichever came first, the overall response rate, which included complete remission (CR)and partial remission(PR), was 6.9%(5/72), the rate of patients who had the best effect with CR or PR during the treatment was 12.5%(9/72). Patients who were dependent on red-blood-cell transfusions and platelet transfusions at baseline became transfusion independent were 46.3%(19/41)and 41.2% (7/17), respectively. The median time of treatment was 6 cycles, and the median OS was 16.1 months (95%CI 10.9-20.6 months). For 36 patients(50%)received treatment at ≥6 cycles, and the median OS was 22.3 months(95%CI 16.1- not evaluative). Most common grade Ⅲ-Ⅳ hematologic treatment-emergent adverse events were neutropenia(55%), leukopenia(47%), and thrombocytopenia(61%). Pharmacokinetic profiles were similar for generic and original azacitidine in Chinese patients. Conclusion: Generic azacitidine treatment was favorable and safe and can be used as a standard treatment for patients with higher-risk MDS.

A high-throughput multiplex assay to characterize flavivirus-specific immunoglobulins

Genus Flavivirus, which includes 53 virus species, is the leading cause of arthropod-borne diseases in humans. Diagnosis of these viral diseases is complicated by their overlapping epidemiology and clinical manifestations, and the fact that cross-reactive antibody responses are frequently elicited by individuals in response to infection. We developed a bead-based immunoassay to concomitantly profile the isotype and subclass of antibody responses (five isotypes and four subclasses) in parallel with specificity against multiple antigens. Our panel included 22 envelope (E) and non-structural 1 (NS1) proteins of different flaviviruses (Zika (ZIKV), Dengue (DENV), Yellow Fever (YFV), West Nile (WNV), Japanese Encephalitis (JEV) and Tick-Borne Encephalitis (TBEV)) and the envelope protein of Chikungunya virus (CHIKV). Using 54 samples from 40 individuals with ZIKV infection that had been pre-characterized, we identified 1) stronger ZIKV responses in individuals previously exposed to flavivirus compared to flavivirus-naïve individuals; 2) different antibody isotypes depending on the stage of infection: acute, convalescent and late convalescent; 3) cross-reactive responses; and 4) a potential CHIKV infection. The assay had a broad dynamic range (>5 logs) and has the potential to distinguish antigen-specific responses induced by ZIKV infection from cross-reactive responses. The multidimensional data provided by this high-throughput antibody-profiling platform can advance our understanding of the human immune response to flaviviruses as they expand their global reach.

A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants

The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by neutralizing antibodies and plays a key role in viral entry. Here we investigate the diversity seen in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences and compare it to the sequence on which most vaccine candidates are based. Using 18,514 sequences, we perform phylogenetic, population genetics, and structural bioinformatics analyses. We find limited diversity across SARS-CoV-2 genomes: Only 11 sites show polymorphisms in >5% of sequences; yet two mutations, including the D614G mutation in Spike, have already become consensus. Because SARS-CoV-2 is being transmitted more rapidly than it evolves, the viral population is becoming more homogeneous, with a median of seven nucleotide substitutions between genomes. There is evidence of purifying selection but little evidence of diversifying selection, with substitution rates comparable across structural versus nonstructural genes. Finally, the Wuhan-Hu-1 reference sequence for the Spike protein, which is the basis for different vaccine candidates, matches optimized vaccine inserts, being identical to an ancestral sequence and one mutation away from the consensus. While the rapid spread of the D614G mutation warrants further study, our results indicate that drift and bottleneck events can explain the minimal diversity found among SARS-CoV-2 sequences. These findings suggest that a single vaccine candidate should be efficacious against currently circulating lineages.

[Quick community survey on the impact of COVID-19 outbreak for the healthcare of people living with HIV]

Objective: To collect the current status and healthcare needs of people living with HIV (PLHIV) in China during the COVID-19 outbreak to inform quick response from government and communities. Methods: During February 5(th) to 10(th), 2020, a national anonymous survey was conducted using an online questionnaire among PLHIV at least 18 years of age and had started antiretroviral treatment (ART) to collect the information on COVID-19 prevention, HIV-related health services and the needs on psychosocial support. Current status and needs of people living with HIV were analyzed in Hubei and other regions. Results: A total of 1 014 valid questionnaires were collected, with PLHIV respondents cross the country. The survey revealed that 93.79% of the respondents could obtain information regarding the prevention of COVID-19 from their communities or villages. Respondents were concerned with HIV-specific protective measures and personal protective equipment shortage. 32.64% of all respondents were not carrying sufficient antiretroviral medicines (ARVs) to meet the needs under traffic and travel restrictions, and some could face stock-outs in the coming month. In Hubei province where 53 respondents needed ARV refill, 64.15% reported difficulty accessing ARV due to the "blockage" . 28.93% respondents were in need of sociopsychological support, and 85.31% anticipated further improvement of the out-of-town ARV refill process from the government. Conclusion: PLHIV wants to know HIV-specific protective measures against COVID-19 outbreak. PLHIV who returned to their home-towns and affected by the lock-downs reported challenges with refills. We should undertake a more systematic study on impacts of the COVID-19 on PLHIV to develop preparedness capacity for future public health emergency.

Short communication: Menaquinone-4 (vitamin K2) induces proliferation responses in bovine peripheral blood mononuclear cells

The effects of vitamin K (VK) on immune cells in ruminants are yet to be fully investigated. The objective of this study was to examine the effects of VK on peripheral blood mononuclear cells (PBMC) in Holstein dairy cows. A cell proliferation assay was performed to evaluate the effect of menaquinone-4 (MK-4, the biologically active form of VK) on immune response of PBMC. The proliferation of PBMC stimulated by MK-4 was significantly higher than that of nonstimulated controls. The expression of T cell-related genes in PBMC, stimulated with MK-4, was assessed by quantitative PCR. No significant changes were observed in the mRNA expression levels of both CD4 and CD8 as helper T cell and cytotoxic T cell markers, respectively. The present study demonstrated that MK-4 positively influenced cow PBMC proliferation and suggested the possibility of bovine-specific immune cell activation. The present study lays a foundation for understanding the physiological role of VK in cattle.

[Individualized treatment recommendations for lung cancer patients at different stages of treatment during the outbreak of 2019 novel coronavirus disease]

In order to achieve the overall victory over 2019 novel coronavirus disease epidemic, especially to prevent the disease recurrence from rebounding during the resumption of labor, the government has not loosened any control of personnel mobility, which has obviously affected the normal examination and treatment of lung cancer patients under the influence of this epidemic. During the epidemic period, cancer patients with low immunity levels face the double ordeals of disease and epidemic situation. Compared with the general population, they are more likely to be infected with the new coronavirus. Among the infected cancer patients, lung cancer is the most common type. It is necessary to provide more appropriate individualized treatment recommendations for patients with lung cancer based on the epidemic situation of the patient's location and in combination with the patient's own condition. Through active prevention of infection, timely conversion of treatment strategies, online and offline joint control, and positive psychological counseling, we do our best to help patients with lung cancer to survive this difficult period.

A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein

SARS-CoV-2 is a zoonotic virus that has caused a pandemic of severe respiratory disease-COVID-19-within several months of its initial identification. Comparable to the first SARS-CoV, this novel coronavirus's surface Spike (S) glycoprotein mediates cell entry via the human ACE-2 receptor, and, thus, is the principal target for the development of vaccines and immunotherapeutics. Molecular information on the SARS-CoV-2 S glycoprotein remains limited. Here we report the crystal structure of the SARS-CoV-2 S receptor-binding-domain (RBD) at a the highest resolution to date, of 1.95 Å. We identified a set of SARS-reactive monoclonal antibodies with cross-reactivity to SARS-CoV-2 RBD and other betacoronavirus S glycoproteins. One of these antibodies, CR3022, was previously shown to synergize with antibodies that target the ACE-2 binding site on the SARS-CoV RBD and reduce viral escape capacity. We determined the structure of CR3022, in complex with the SARS-CoV-2 RBD, and defined a broadly reactive epitope that is highly conserved across betacoronaviruses. This epitope is inaccessible in the "closed" prefusion S structure, but is accessible in "open" conformations. This first-ever resolution of a human antibody in complex with SARS-CoV-2 and the broad reactivity of this set of antibodies to a conserved betacoronavirus epitope will allow antigenic assessment of vaccine candidates, and provide a framework for accelerated vaccine, immunotherapeutic and diagnostic strategies against SARS-CoV-2 and related betacoronaviruses.