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BackgroundPeople living with HIV (PLWH) are more vulnerable to SARS-CoV-2. However, evidence on the immunogenicity of coronavirus disease 2019 (COVID-19) vaccines in this population is insufficient. The objective of this study is to assess the immunogenicity and safety of the two-dose schedule of Sinovac CoronaVac for 6 months postvaccination in PLWH.MethodsWe conducted a multicenter prospective cohort study among PLWH and HIV-negative adults in China. Participants who received two doses of CoronaVac prior to the recruitment were allocated into two groups and followed up for 6 months. The neutralizing antibodies (nAbs), immunoglobulin G against the receptor-binding domain of the spike protein (S-IgG), and gamma-interferon (IFN-γ) were measured to assess the associations among CoronaVac immunogenicity and related factors. Adverse reactions were collected to evaluate the safety profile of vaccination.ResultsA total of 203 PLWH and 100 HIV-negative individuals were enrolled. A small portion of participants reported mild or moderate adverse reactions without serious adverse events. Median nAbs level in PLWH (31.96 IU/mL, IQR: 12.34-76.40) was lower than that in the control group (46.52 IU/mL, IQR: 29.08-77.30) at the 2-4 weeks postvaccination (P=0.002), and the same trend was presented for median S-IgG titer (37.09 vs. 60.02 IU/ml) (both P <0.05). The nAbs seroconversion rate in the PLWH group was also lower than in the control group (75.86% vs. 89.00%). After then, the immune responses reduced over time in term of only 23.04% of PLWH and 36.00% of HIV-negative individuals had a positive seroconversion for nAbs at 6-month. The multivariable generalized estimating equation analysis showed that PLWH with CD4+T count≥350 cells/µL presented higher immune response than PLWH with CD4+T count ConclusionThe Sinovac CoronaVac was generally safe and immunogenic in PLWH, but the immunity response was inferior and the antibodies vanished faster compared to HIV-negative individuals. This study suggested a shorter than 6-month interval of prime-boost vaccination for PLWH to ensure a better protection.

Antiretroviral therapy (ART) regimens containing integrase strand transfer inhibitors (INSTIs) have become the recommended treatment for human immunodeficiency virus type 1 (HIV-1)-infected patients in the updated guidelines in China. In this study, we investigated the prevalence of acquired and transmitted INSTI-associated resistance of HIV-1 strains in the Henan Province (China) to provide guidance on the implementation of routine INSTI-associated HIV-1 genotypic resistance testing. Serum samples from HIV-1-infected patients seeking treatment in our hospital from August 2018 to December 2020 were collected and the HIV-1 integrase gene coding sequence was amplified, sequenced and analyzed for INSTI resistance. We obtained integrase sequence data from a total of 999 HIV-1-infected patients, including 474 ART-naive patients, 438 ART-treated patients, and 87 patients with unknown treatment history. We detected INSTI resistance in 12 patients (1.2%, 12/999) of the study group, which included 9 ART-treated patients (2.05%, 9/438), with 6 being INSTI-treated (14.63%, 6/41) and 3 INSTI-naive (0.76%, 3/397) and 3 ART-naive (0.63%, 3/474) patients. The most common major resistance mutation was E138AK (0.5%, 5/999), while the most common accessory resistance mutation was E157Q (1.8%, 18/999). Phylogenetic analysis based on the HIV-1 integrase gene indicated that INSTI resistance was primarily detected in patients infected with HIV-1 subtype B. In conclusion, our study reveals that INSTI resistance is observed in INSTI-treated patients, as expected, and the prevalence of INSTI resistance in ART-naive patients in Henan Province is low. However, baseline INSTI resistance testing should be considered, as the prescription of INSTI-based regimens is anticipated to increase considerably in the near future.

Norovirus (NoV) infection is a leading cause of non-bacterial gastroenteritis worldwide and there are currently no effective therapeutics available to target the virus. The norovirus major capsid protein VP1 is a potential candidate for the development of vaccines due to the similar morphology and immunogenicity of its assembled virus-like particles (VLPs) compared to native virions. In this study, we explored the effects of N- and C-terminal sequence additions to the VP1 of a GII.4 NoV during its assembly into VLPs. A series of sequences of different lengths derived from the minor capsid protein VP2 of the GII.4 NoV were added to the N- and C-terminus of VP1. The fusion proteins were expressed using a recombinant baculovirus expression system and the assembly of the expressed fusion proteins was subsequently observed under electron microscopy (EM). Our results indicated that all constructed fusion proteins were successfully expressed with different degrees of enzyme cleavage at the N-terminus. Electron microscopy revealed the successful assembly of VLPs of different sizes for all fusion proteins. An in vitro binding assay for VLP-histo-blood group antigens (HBGAs) indicated that all fusion proteins exhibited similar binding patterns compared with their wild-type VP1. Our results demonstrate that (Xi et al., 1990) [1] NoV VP1 can tolerate foreign sequences at its N- or C-terminus without affecting its ability to assemble into VLPs, and (Jiang et al., 1992) [2] that the cleavage pattern and effects of foreign sequences on the sizes of assembled VLPs observed in this study might represent important experimental data that can be used to elucidate VP1 self-assembly.

In this study, we determined the near-complete and partial genome sequences of ten SaV isolates. Phylogenetic analysis based on full-length VP1 and RdRp nucleotide sequences indicated that nine isolates were of GI.1 and one was GII.3. Evolutionary dynamics analysis indicated that GI.1 and GII.3 SaVs evolved at different rates, the latter evolving more rapidly. Cluster analysis indicated that distantly related GI.1 SaVs were more similar in their amino acid compositions than were GII.3 SaVs. The data provided in this study may facilitate studies on SaV genomic diversity and epidemiological patterns in China and worldwide.

Genogroup II, genotype 4 noroviruses (GII.4 NoVs) are a leading cause of epidemic and sporadic acute non-bacterial gastroenteritis worldwide. In this study, we isolated a GII.4 NoV strain (designated 2015HN08) from a kid presenting with acute gastroenteritis and determined its near-complete genome sequence. We then performed sequence analysis by comparing this strain with the prototypical GII.4 strain. Virus-like particles (VLPs) derived from the major capsid protein (VP1) were expressed by using a recombinant-baculovirus expression system, and monoclonal antibodies (mAbs) were produced to compare changes in antigenic or histo-blood group antigens (HBGAs) binding sites with the previously characterized GII.4 NoV strain (JZ403). The genome of 2015HN08 was 7559 nucleotides (nt) long, excluding the poly(A) tail. Genotyping analysis indicated that this strain was a Sydney 2012 variant. In comparison with the prototype Sydney 2012 strain, there were 74, 35, and 16 differences in nucleotide sequences in ORF1, OFR2, and OFR3, causing 7, 10, and 6 amino acid (aa) changes, respectively. Expression of VP1 led to successful assembly of VLPs, as demonstrated by electron microscopy. Screening of hybridoma cell supernatants with an in vitro VLP-HBGAs binding blockade assay led to the identification of a cell clone 3G10 that exhibited HBGA-blocking effects. This mAb also exhibited blocking effects against JZ403 strain, suggesting maintenance of the antigenic site and/or HBGAs binding sites between the two strains. In summary, we determined the near-complete genome sequence of a GII.4 Sydney 2012 variant and produced an mAb with blocking effects that might be useful in evaluating the evolution of current Sydney 2012 NoV strains.

In this study, the prevalence and genotype distribution of human papillomavirus (HPV) in 49,793 women aged 25-64 years were determined by fluorescent real-time polymerase chain reaction (PCR) assay. HPV was detected in 6,020 women, giving a prevalence of 12.09% (6020/49,793). Single and multiple infections accounted for 71.81% (4323/6020) and 28.19% (1697/6020) of total infections, respectively. The most commonly found genotypes were HPV52 (19.90%, 1198/6020) and HPV16 (19.17%, 1154/6020), followed by HPV58 (13.11%, 789/6020), HPV81 (10.10%, 608/6020) and HPV56 (9.00%, 542/6020). The prevalence of HPV increased with age and was highest in the 54- to 64-year-old age group. The genotypes covered by the nonavalent HPV vaccine accounted for 39.32% (2367/6020) and 22.81% (1373/6020) of the total monoinfections and polyinfections, respectively. This study indicates a high HPV infection rate in women in the city of Zhengzhou and a large percentage of women are infected with single or multiple high-risk HPV genotypes that cannot be prevented using the current nonavalent HPV vaccine. Vaccines incorporating more HPV genotypes and extended age coverage for the current nonavalent vaccine might be necessary to better prevent HPV-related cervical cancer.

The fundamental goal of artificial intelligence (AI) is to mimic the core cognitive activities of human. Despite tremendous success in the AI research, most of existing methods have only single-cognitive ability. To overcome this limitation and take a solid step towards artificial general intelligence (AGI), we develop a foundation model pre-trained with huge multimodal data, which can be quickly adapted for various downstream cognitive tasks. To achieve this goal, we propose to pre-train our foundation model by self-supervised learning with weak semantic correlation data crawled from the Internet and show that promising results can be obtained on a wide range of downstream tasks. Particularly, with the developed model-interpretability tools, we demonstrate that strong imagination ability is now possessed by our foundation model. We believe that our work makes a transformative stride towards AGI, from our common practice of "weak or narrow AI" to that of "strong or generalized AI"., Published by Nature Communications, see https://www.nature.com/articles/s41467-022-30761-2

The surface-exposed loop regions of the protruding domain of the norovirus (NoV) major capsid protein VP1 can tolerate the insertion of foreign antigens without affecting its assembly into subviral particles. In this study, we investigated the tolerance of the surface-exposed loop region of the GII.4 NoV VP1 by replacing it with homologous or heterologous sequences. We designed a panel of constructs in which the amino acid sequence from position 298-305 of the GII.4 NoV VP1 was replaced by sequences derived from the same region of GI.3, GII.3, GII.6, and GII.17 NoVs as well as neutralizing epitopes of enterovirus type 71 and varicella-zoster virus. The constructs were synthesized and expressed using a recombinant baculovirus expression system. The expression of target proteins was measured by indirect enzyme-linked immunosorbent assay (ELISA), and the assembly of virus-like particles (VLPs) was confirmed by electron microscopy. Our results showed that all of the constructs expressed high levels of target chimeric proteins, and all of the chimeric proteins successfully assembled into VLPs or subviral particles. An in vitro VLP-histo-blood group antigen (HBGA) binding assay revealed that chimeric-protein-containing VLPs did not bind or showed reduced binding to salivary HBGAs, a ligand for NoV particles. The results of an in vitro VLP-HBGA binding blockade assay indicated that the predicted surface-exposed loop region of the GII.6 NoV VP1 may comprise a blockade epitope. In summary, the surface-exposed loop region of the GII.4 NoV VP1 can be replaced by foreign sequences of a certain length. Using this strategy, we found that the predicted surface-exposed loop region of GII.6 NoV VP1 might contain a blockade epitope.

This paper proposes a novel pretext task for self-supervised video representation learning by exploiting spatiotemporal continuity in videos. It is motivated by the fact that videos are spatiotemporal by nature and a representation learned to detect spatiotemporal continuity/discontinuity is thus beneficial for downstream video content analysis tasks. A natural choice of such a pretext task is to construct spatiotemporal (3D) jigsaw puzzles and learn to solve them. However, this task turns out to be intractable. We thus propose Constrained Spatiotemporal Jigsaw (CSJ) whereby the 3D jigsaws are formed in a constrained manner to ensure that large continuous spatiotemporal cuboids exist in a shuffled clip to provide sufficient cues for the model to reason about the continuity. With the constrained jigsaw puzzles, instead of solving them directly, which could still be extremely hard, we carefully design four surrogate tasks that are more solvable but meanwhile still ensure that the learned representation is sensitive to spatiotemporal continuity at both the local and global levels. Extensive experiments show that our CSJ achieves state-of-the-art on two downstream tasks across various benchmarks.

Complex action segmentation aims to detect what actions and when they happen in fine-grained level from long videos. Despite the fact that videos are often stored in a compressed format (e.g., MPEG-4), most existing approaches are proposed to directly model raw RGB videos: when only compressed videos are accessible, they have to first decode these videos, which is very time-consuming. In this paper, by explicitly leveraging the ‘compressed’ characteristic of compressed videos, we are the first to address the challenging task of complex action segmentation in compressed videos. To extract meaningful representations for complex action segmentation, we introduce the GOP-Level Compressed features (Golec), which can be obtained directly from compressed videos without video decompression. Importantly, by taking GOPs as the atomic units of actions, our Golec representation is intrinsically suitable for fine-grained action segmentation. Moreover, to remedy the coarser motion vectors (compared with optical flows which are computed from raw frames) used in our Golec representation for capturing the temporal context, we propose a new Bi-path knowledge distillation strategy. Extensive experiments show the effectiveness of our Golec representation and the Bi-path strategy. Importantly, our proposed model for complex action detection not only runs 5.2 times faster but also achieves significantly better results than the state-of-the-art alternatives using raw videos.

Large-scale pre-trained models (PTMs) such as BERT and GPT have recently achieved great success and become a milestone in the field of artificial intelligence (AI). Owing to sophisticated pre-training objectives and huge model parameters, large-scale PTMs can effectively capture knowledge from massive labeled and unlabeled data. By storing knowledge into huge parameters and fine-tuning on specific tasks, the rich knowledge implicitly encoded in huge parameters can benefit a variety of downstream tasks, which has been extensively demonstrated via experimental verification and empirical analysis. It is now the consensus of the AI community to adopt PTMs as backbone for downstream tasks rather than learning models from scratch. In this paper, we take a deep look into the history of pre-training, especially its special relation with transfer learning and self-supervised learning, to reveal the crucial position of PTMs in the AI development spectrum. Further, we comprehensively review the latest breakthroughs of PTMs. These breakthroughs are driven by the surge of computational power and the increasing availability of data, towards four important directions: designing effective architectures, utilizing rich contexts, improving computational efficiency, and conducting interpretation and theoretical analysis. Finally, we discuss a series of open problems and research directions of PTMs, and hope our view can inspire and advance the future study of PTMs.

Rabies remains a public health threat in China, and most transmissions are dog-mediated. In this study, we studied 31 clinically diagnosed human rabies patients that had been scratched or bitten by dogs. Real-time reverse transcription polymerase chain reaction (RT-qPCR) and nested RT-PCR were performed on saliva samples or cerebrospinal fluid, and samples from 28 patients tested positive for rabies virus. A total of one near-complete genome sequence, 15 complete glycoprotein (G) gene sequences, and five partial G gene sequences were determined. Phylogenetic analysis was performed, based on complete G gene sequences, using the maximum-likelihood method. The results indicated that the isolates belonged to the lyssavirus genotype I lineage and China I lineage. The Chinese rabies virus can be divided into six major lineages. The China I lineage was the dominant clade and could be divided into four subclades. Isolates 17HN19, 17HN75, and 18HN162 fell within clade IC subgroup, and the other isolates were assigned to the clade IA subgroup. This study provides epidemiological and genetic information on rabies incidence in humans.

Noroviruses are leading cause of acute gastroenteritis worldwide. In our previous study, we established an in vitro histo-blood group antigens (HBGAs) binding blockade assay against GII.3 Norovirus virus like particles (VLPs) with trypsin digestion. In this study, we characterized the blocking antibody binding site and epitope type (linear or conformational) by using hyperimmune sera produced against different antigens. VP1 from Jingzhou402 (GII.3, JZ402) strain was expressed by using pGEX-6p-1 expression vector and the insoluble proteins were purified for immunization in rabbit. Previously characterized chimeric VP1-assembled VLPs (GII.4-VP1/GII.3-P2) were used to immunize guinea pig. Peptides reactive with hyperimmune serum against VLPs derived from the VP1 of JZ402 strain were conjugated with BSA and used to immunize rabbits. Hyperimmune sera against above antigens and JZ402 and JZ403 strain-derived VLPs were used to compare their HBGAs blocking effects. Rabbit anti-GST-VP1 and BSA-peptide conjugated hyperimmune sera demonstrated no blocking effects against the binding of GII.3 and GII.4 NoV VLPs to salivary HBGAs. Guinea pig anti-GII.4-VP1/GII.3-P2 hyperimmune serum blocked the binding of trypsin cleaved GII.3 VLPs to salivary HBGAs with no or very weak blocking effects against the binding of GII.4 VLPs to salivary HBGAs. Our data indicated that HBGAs blocking antibodies primarily bound the P2 domain of GII.3 NoV VP1 and their binding epitopes were most probably conformation-dependent.

Routine vaccination has proven to be highly effective in reducing the incidence of mumps. However, sporadic cases and/or mumps outbreaks have been reported in children and adolescents younger than 15 years of age, particularly among those aged 5-9 years. To explore the characteristics of such outbreaks in the Henan Province, clinical data of patients infected with mumps virus (MuV) were collected, and the isolated strains were phylogenetically analyzed. Of the total 426 samples analyzed, MuV RNA targeting the small hydrophobic (SH) gene was detected in 153 samples. MuV-positive cases in age groups

Noroviruses (NoVs) are a major cause of acute non-bacterial gastroenteritis worldwide. In this study, we report the isolation, near-complete genome sequencing, and expression and biological characterization of the major capsid protein (VP1) of a GI.3 NoV isolated from a child presenting acute gastroenteritis. The genome of the GI.3 NoV is 7746 bp in length, not including the poly-adenylation tail. Phylogenetic analysis based on the complete VP1 nucleotide sequences indicates that GI.3 NoVs could be divided into four clusters, with 4.6%, 5.3%, 6.6%, 1.9% intracluster variations in nucleotide and 4.8%, 3.8%, 6.1%, 1.7% intracluster variations in amino acid sequences, respectively. A Bayesian evolutionary analysis showed that GI.3 NoVs evolved at 2.44 × 10−3, 2.78 × 10−3, and 3.04 × 10−3 nucleotide substitutions/site/year using a strict clock model, an uncorrelated log-normal model (UCLN), and an uncorrelated exponential derivation model (UCED), respectively. VP1 protein expression using a recombinant baculovirus expression system leads to the successful assembly of virus-like particles (VLPs). In vitro VLP-Histo-blood group antigen (HBGA) binding assay indicates that GI.3 NoV VLPs strongly bind to blood type A salivary HBGAs, moderately bind to blood type O salivary HBGAs, and weakly bind or do not bind to blood type B and AB salivary HBGAs. In vitro VLP-HBGA binding blockade assay indicated that the binding of GI.3 NoV VLPs to blood type A salivary HBGAs could only be blocked by anti-GI.3 NoV VLPs serum but not non-GI.3 NoV genotype-specific hyperimmune sera (GI.2, GI.7, GII.4, GII.6, GII.7, and GII.17). The detailed characterization of GI.3 NoV in this study provides evidence that GI.3 NoV undergoes rapid evolution and exhibits no cross-blocking effects, suggesting that GI.3 NoV may potentially be utilized in the development of multivalent NoV vaccines.

Coxsackievirus A16 (CVA16) is one of the major etiological agents of hand, foot and mouth disease (HFMD), a common acute infectious disease affecting infants and young children. Severe symptoms of the central nervous system may develop and even lead to death. Here, a plaque-purified CVA16 strain, L731-P1 (P1), was serially passaged in Vero cells for six times and passage 6 (P6) stock became highly attenuated in newborn mice. Genomic sequencing of the P1 and P6 revealed seven nucleotide substitutions at positions 1434 (C to U), 2744 (A to G), 2747 (A to G), 3161 (G to A), 3182 (A to G), 4968 (C to U), and 6064 (C to U). Six of these substitutions resulted in amino acid changes at VP2-T161 M, VP1–N102D, VP1-T103A, VP1-E241K, VP1-T248A, and 2C–S297F, respectively. P1-based infectious cDNA was generated to further investigate these virulent determinants. Independent reverse transcription-polymerase chain reaction (RT-PCR) amplifications for mutant constructions and plaque-purification of the P6 for isolation of variants were performed to determine dominant mutations and strains more related to attenuation. The virulent P1, attenuated P6, as well as a plaque purified strain (PP) and other four recombinant mutants, were inoculated into one-day-old BALB/c mice and the 50% lethal dose of each strain was determined. Comparison of virulence among these strains indicated that amino acid changes of VP1–N102D, VP1-E241K and 2C–S297F might be associated more closely with a high level attenuation of CVA16-L731-P6 than other mutations. Identification of novel residues associated with virulence may contribute to understanding of molecular basis of virulence of CVA16 and other enteroviruses.

Most existing action recognition models are large convolutional neural networks that work only with raw RGB frames as input. However, practical applications require lightweight models that directly process compressed videos. In this work, for the first time, such a model is developed, which is lightweight enough to run in real-time on embedded AI devices without sacrifices in recognition accuracy. A new Aligned Temporal Trilinear Pooling (ATTP) module is formulated to fuse three modalities in a compressed video. To remedy the weaker motion vectors (compared to optical flow computed from raw RGB streams) for representing dynamic content, we introduce a temporal fusion method to explicitly induce the temporal context, as well as knowledge distillation from a model trained with optical flows via feature alignment. Compared to existing compressed video action recognition models, it is much more compact and faster thanks to adopting a lightweight CNN backbone.

3D object detection from a single image without LiDAR is a challenging task due to the lack of accurate depth information. Conventional 2D convolutions are unsuitable for this task because they fail to capture local object and its scale information, which are vital for 3D object detection. To better represent 3D structure, prior arts typically transform depth maps estimated from 2D images into a pseudo-LiDAR representation, and then apply existing 3D point-cloud based object detectors. However, their results depend heavily on the accuracy of the estimated depth maps, resulting in suboptimal performance. In this work, instead of using pseudo-LiDAR representation, we improve the fundamental 2D fully convolutions by proposing a new local convolutional network (LCN), termed Depth-guided Dynamic-Depthwise-Dilated LCN (D$^4$LCN), where the filters and their receptive fields can be automatically learned from image-based depth maps, making different pixels of different images have different filters. D$^4$LCN overcomes the limitation of conventional 2D convolutions and narrows the gap between image representation and 3D point cloud representation. Extensive experiments show that D$^4$LCN outperforms existing works by large margins. For example, the relative improvement of D$^4$LCN against the state-of-the-art on KITTI is 9.1\% in the moderate setting. The code is available at https://github.com/dingmyu/D4LCN., 12 pages, 8 figures, modify email and add code

Context We observed a special type of bug reopen that has no direct impact on the user experience or the normal operation of the system being developed. We refer to these as non-negative bug reopens. Objective Non-negative bug reopens are novel and somewhat contradictory to popular conceptions. Therefore, we thoroughly explored these phenomena in this study. Method We begin with a novel approach that preliminarily characterizes non-negative bug reopens. Based on bug reports extracted from Eclipse Bugzilla, we then examined a case study to compare non-negative and regular bug reopens using the Wilcoxon-Mann-Whitney test. Results The results show that non-negative bug reopens are statistically significantly different than regular bug reopens, based on their survival times and the number of developers involved in the entire debugging process. Conclusion Taking into account the significant differences, we suggest that the effects of non-negative bug reopens should be considered in future research in related areas, such as bug triage and reopened bug prediction.

Norovirus (NoV) virus like particles (VLPs) produced in Spodoptera frugiperda (Sf9) cells have been tested in human volunteers as vaccine candidate and were shown to be protective against NoV induced acute gastroenteritis. In this study, prevailing Sydney-2012-like NoV major capsid protein gene with or without N-terminal deletions (N26 and N38, 26 and 38 amino acids deleted from N terminus，respectively) were sub-cloned into prokaryotic expression vector, pCold III and pCold IV. Soluble and insoluble proteins were detected for both vectors after induction and higher levels of protein expression were observed for constructs pCold III-N26 and pCold III-N38. Electron microscopy observation of unpurified and purified lysates indicated in vivo assembly of VLPs with two sizes in accordance with those observed in Sf9 cells. In vitro salivary HBGA-VLP binding assay demonstrated that VLPs assembled in Escherichia coli (E. coli) exhibited the same binding pattern as that of VLPs assembled in Sf9 cells. Immunization of mice with purified VLPs derived from pCold III-N38 demonstrated higher IgG antibody titers and blocking antibody titers when compared with full-length capsid protein assembled VLPs from recombinant baculovirus expression system. In conclusion, NoV VLPs produced in E. coli using pCold expression vector might be used for the development of NoV vaccine.

In this study, we successfully produced VLPs derived from full-length or chimeric VP1 of a documented GII.6 strain. Trypsin digestion of purified VLPs led to total cleavage of VP1, while the integrity of assembled VLPs was not affected. In vitro VLP-histo-blood group antigen (HBGA) binding and binding blockade assays indicated that trypsin digestion enhanced the binding of GII.6 VLPs to salivary HBGAs and that this binding could only be blocked by serum produced against a homologous strain. The data regarding the assembly, morphology and binding patterns of GII.6 NoV VLPs presented here might be useful for further study of GII.6 NoVs.

In this study, we found that addition of fecal extract significantly promoted the binding of GII.3 NoV VLPs to salivary HBGAs. SDS-PAGE analysis indicated that major capsid proteins (VP1) were cleaved into two major bands with molecular weights of 26 and 31kD, respectively. Pretreatment of fecal extract by boiling or addition of protease inhibitor cocktail or type specific protease inhibitor (leupeptin and aprotinin) during incubation all decreased VP1 cleavage and its binding to salivary HBGAs. Trypsin digestion led to cleavage of VP1 and promoted its binding to HBGAs, suggesting that the active enzyme(s) might be trypsin or trypsin-like enzymes. Trypsin and fecal extract pretreatment all led to loss of morphological intact VLPs, indicating enhanced signal was possible due to increased binding of fragmented subunits. N-terminal sequencing was performed to characterize the cleavage sites with indecisive results. In vitro VLP-salivary HBGAs binding blockade assay using VLPs derived from VP1 of different GII.3 strains and rabbit anti-genotype specific hyperimmune serum indicated that GII.3 NoVs might have conservative HBGA binding sites. In summary, our results provide evidence about the widespread presence of active enzyme in fecal samples that can cleave GII.3 NoV VLPs and demonstrate that GII.3 NoVs have conservative HBGA binding sites which might have implications in the design of multivalent NoV vaccines.

The objective of this study was to express and characterize the major capsid protein (VP1) of a GII.6 Norovirus (NoV)strain isolated in China. The newly identified GII.6 NoV strain was isolated from a five-year old boy presenting acute gastroenteritis. The genome of the GII.6 strain was 7550 nucleotides in length, excluding the poly-adenylation tail. Multiple sequence alignment and phylogenetic analysis based on deduced VP1 amino acid sequences from different genotypes indicated close relationship between GII.3 and GII.6 NoVs, as demonstrated by the presence of a short sequence insertion in the P2 domain and clustering in the same subgroup. Expression of GII.6 VP1 led to assembly of virus like particles (VLPs). In vitro VLP-salivary histo-blood group antigens (HBGAs) binding assay demonstrated wide-spectrum binding activities of assembled VLPs to blood type A, B, AB and O salivary HBGAs with highest binding capacity to type A salivary HBGAs and lowest to type AB and O salivary HBGAs. In vitro VLP-salivary HBGAs binding blockade assay indicated absence of cross-blocking effects for hyperimmune sera produced against different genotypes. In conclusion, our results suggest a rational VLPs-based multivalent NoV vaccine should contain capsid proteins of a GII.6 strain.

Human immunodeficiency virus type 1 (HIV-1) infection remains a severe public health problem worldwide. In this study, we investigated the distribution of HIV-1 subtypes and the prevalence of drug resistance mutations (DRMs) among patients with HIV-1 infection in Henan Province, China. HIV-1 strains in blood samples taken from inpatients and outpatients visiting the Sixth People's Hospital of Zhengzhou from August 2017 to July 2019 with a viral load (VL) greater than 1000 copies/ml were subjected to subtype and DRMs analysis. Out of a total of 769 samples, subtype and DRM data were obtained from 657 (85.43%) samples. Phylogenetic analysis based on partial pol gene sequences indicated that the most commonly found genotype was subtype B (45.51%, 299/657), followed by CRF01_AE (28.61%, 188/657), CRF07_BC (15.68%, 103/657), CRF08_BC (0.76%, 5/657), C (0.61%, 4/657), A (0.30%, 2/657), and others (8.52%, 56/657). Circulating recombinant forms (CRFs) were most commonly found in patients who were naive to antiretroviral treatment (ART) (68.67%, 160/233). The percentage of patients with one or more major drug-resistance mutations was 50.99% (335/657), and it was 6.44% (15/233) in ART-naive patients that were primarily infected with subtype B (17.74%). Resistance mutations were most common at codons 65, 103, 106, 184, and 190 of the reverse transcriptase gene and codon 46 of the protease gene. Our study provides detailed information about the distribution of HIV-1 subtypes and the incidence of drug resistance mutations of different subtypes in ART-experienced and naive patients. This can guide policymakers in making decisions about treatment strategies against HIV-1.

Zero-shot learning (ZSL) is originally designed to address the small sample size problem often encountered in computer vision by recognizing unseen object classes without any training samples. Existing ZSL models (particularly deep ones) often assume that hundreds of labelled samples are collected from each seen class. In real-world applications, this assumption tends to become invalid. Therefore, a new ZSL setting is concerned in this paper: each seen class only has few labelled samples, while each unseen class still has no samples. This is more challenging yet more useful/practical than the conventional ZSL setting. To overcome the extreme label scarcity, we choose to obtain more training samples from image search engine for data augmentation: the name of each seen class is used as the query of Google, and the top returned images can be viewed as the noisy labelled samples for this seen class. With the augmented but noisy labelled training data, a novel inductive ZSL model is proposed by formulating label noise reduction (LNR) and semantic projection learning (SPL) within a unified framework: (1) LNR aims to refine the noisy labelled samples for projection learning; (2) SPL aims to learn the projection function with the refined training data. Extensive experiments show that our ZSL model outperforms the state-of-the-art alternatives.

Trypsin digestion promotes disassembly of GII.3 NoV virus-like particles (VLPs) and binding of VLPs to salivary histo-blood group antigens (HBGAs), but it is not clear which specific regions or residues mediate viral attachment to HBGAs. An earlier study indicated that arginine residues in the predicted surface-exposed loop region are susceptible to trypsin digestion. Here, we introduced single or multiple substitutions of four arginine residues located in the predicted surface-exposed loop region of the GII.3 NoV capsid protein (VP1) and observed their effects on susceptibility to trypsin digestion and binding to HBGAs. All of the mutations in VP1, including single substitutions (R287G, R292G, R296G or R307G) and quadruple substitutions (R287G, R292G, R296G and R307G), permitted successful VLP assembly. After tryptic digestion, all VP1 proteins bearing single point mutations were cleaved, resulting in complete digestion or single fragments with various molecular sizes (27-35 kDa), while the VP1 protein bearing four substitutions was cleaved into two fragments (27-55 kDa). Binding assays using synthetic and salivary HBGAs showed that none of the VP1 mutants (singly or quadruply substituted) exhibited detectable binding to HBGA before or after trypsin cleavage. These results indicated that arginine residues within the predicted surface loop region of GII.3 NoV VP1 were involved directly or indirectly in binding salivary HBGAs and could potentially mediate the HBGA-GII.3 NoV interactions through which host cells become infected.

Noroviruses (NoVs) are the leading cause of non-bacterial acute gastroenteritis worldwide. Due to a lack of cell culture system and animal model, our understanding of NoVs has been lagging behind. In this study, NoV major capsid proteins (VP1) from three different genotypes (GI.2, GII.3 and GII.4) were expressed by using recombinant baculovirus expression system and which led to successful assembly of virus-like particles (VLPs). The receptor binding patterns of three kinds of VLPs were characterized by using synthetic and salivary HBGA-VLP binding assay. Cross-reactivity and cross-blocking activity of rabbit hyperimmune sera against these VLPs were determined by ELISA/Western blot analysis and saliva-VLP binding blockade assay, respectively. Expression of the major capsid proteins from three genotypes all led to smaller VLPs in dominance when sf9 cells were cultured in suspension, which was in consistence with our previous report. These smaller VLPs were used for in vitro synthetic and salivary HBGA-VLP binding and binding blockade assays. VLPs from GII.3 strain exhibited no binding to all synthetic HBGAs and saliva samples tested while VLPs from GI.2 and GII.4 strain showed similar binding pattern and bound to all salivary HBGAs tested. Rabbit anti-GII.3 VLPs hyperimmune serum didn't block the binding of GI.2 and GII.4 VLPs to salivary HBGAs while rabbit anti-GI.2 VLP hyperimmune serum blocked the binding of GII.4 VLPs to salivary HBGAs but not vice versa. Our results provide further evidence indirectly in support of presence of other factors involved in receptor binding other than HBGAs for NoVs, and demonstrate poor cross-blocking activities of antibodies against VLPs within or across genogroups.

GII.3 and GII.6 noroviruses (NoVs) are similar in several aspects, including the presence of a short sequence insertion in the P2 domain of the major capsid protein (VP1) and trypsin susceptibility of VP1-containing virus-like particles (VLPs). In this study, we generated two constructs with the S or P domains of VP1 from GII.3 and GII.6 NoV strains exchanged (GII.3S/GII.6P and GII.6S/GII.3P), and the resultant chimeric capsid proteins were expressed from recombinant baculoviruses. The assembly of VLPs was confirmed by electron microscopy, and the susceptibility of assembled VLPs to trypsin digestion was analyzed by SDS-PAGE. Salivary histo-blood group antigen (HBGA) binding and binding blockade assays were performed to determine the binding characteristics of chimeric VP1-containing VLPs with and without trypsin digestion. Our results indicated that both expressed GII.3S/GII.6P and GII.6S/GII.3P chimeric proteins successfully assembled into VLPs. Trypsin digestion of VLPs assembled from both chimeric proteins led to the generation of two fragments with molecular sizes similar to those of wild-type VP1-containing VLPs. An in vitro salivary HBGA binding assay demonstrated that VLPs assembled from both chimeric proteins exhibited enhanced binding after trypsin cleavage. An HBGA binding blockade assay indicated that the binding of GII.3S/GII.6P and GII.6S/GII.3P VLPs against salivary HBGAs could only be blocked by GII.3 and GII.6 NoV VLP-specific hyperimmune sera, respectively. For GII.6 and GII.3S/GII.6P VLPs, a difference in binding enhancement after trypsin cleavage was observed. Our results demonstrate that the S domains of GII.3 and GII.6 NoV VP1 are interchangeable and that the S domain affects the binding of the P domain to HBGAs.

Zero-shot learning (ZSL) can be regarded as transfer learning from seen classes to unseen ones so that the later can be recognized without any training samples. Its main difficulty lies in that there often exists a large domain gap between the seen and unseen class domains. Inspired by the fact that an unseen class is not strictly ‘zero-shot’ (thus easier to recognize) if it falls into a superclass that consists of one or more seen classes, we propose a new ZSL model, termed ZSL with superclasses (ZSLS), that leverages the superclasses as the bridge between seen and unseen classes to narrow the domain gap. By generating the superclasses with k-means clustering over all seen and unseen class prototypes, we formulate ZSLS as a min-min optimization problem. An efficient iterative algorithm is also developed for model optimization. Extensive experiments show that our model achieves the state-of-the-art results.

We present a novel generative adversarial network (GAN) model, called InsightGAN, for drug abuse detection. Our model is inspired by two closely related works on machine learning for healthcare applications: (1) drug abuse detection has been solved by machine learning with plentiful data from social media (where face pictures can be easily obtained); (2) facial characteristics have been explored in mental disorder diagnosis (drug addiction is also a mental disorder). In this paper, we adopt deep learning to extract discriminative facial features for drug abuse detection. However, in this application, the face pictures with ground-truth labels are far from sufficient for training a deep learning model. To alleviate the scarcity of labelled data, we thus propose a semi-supervised facial feature learning model based on GAN. Moreover, we also develop a robust algorithm for training our InsightGAN. Experimental results show the promising performance of our InsightGAN.

In this study, we isolated, amplified and sequenced GII.3 norovirus (NoV) strains from children admitted to a department of pediatric gastroenterology presenting with acute gastroenteritis from September 2015 to March 2016. A total of 35 stool samples were collected and eight were GII.3 NoV positive, based on sequencing. The complete genome sequences were determined for two strains while partial genome sequences, encompassing approximately 3.2 kb of the 3´end, were generated for the six other strains. Genotyping analysis of all strains indicated that they belonged to GII P12/GII.3. Phylogenetic analysis indicated that these isolated strains could be divided into two clusters. Strains in cluster IV were the most frequently isolated and exhibited less intra-cluster variation in nucleotide sequences. Our study demonstrated that the GII.P12/GII.3 recombinant strain was the dominant GII.3 NoVs in Zhengzhou city.

Expression of full-length major capsid protein of Noroviruses (NoVs) in sf9 cells using recombinant baculovirus expression system leads to the formation of virus-like particles (VLPs) with two sizes. In our pursuit of VLPs with uniform sizes, we find that N terminal truncated capsid protein formed primary VLPs with an average size of 21 nm. This kind of VLPs showed similar binding patterns to those produced with full-length major capsid protein. HBGA-VLPs binding assay and saliva-VLPs blocking analysis, as well as stability test demonstrate that the smaller 21 nm VLPs might be an excellent candidate for NoVs vaccine.

Noroviruses (NoVs) are increasingly recognized as the leading cause of acute non-bacterial gastroenteritis worldwide. To screen for NoV-specific monoclonal antibodies (mAbs) with wide spectrum binding activities that could be used for the development of NoV-related detection reagents, we immunized mice with a combination of virus like particles (VLPs) derived from eight different genotypes (two from genogroup I and six from genogroup II), of which two (GI.7 and GII.2) were newly produced VLPs. Indirect enzyme-linked immunosorbent assay (ELISA) confirmed that two mAbs (8D8 and 10B11) bound to all eight major capsid proteins (VP1) with varied binding abilities. Epitope mapping using short peptides covering the N-terminal half of GII.3 VP1 indicated that the binding site of mAb 8D8 was located between amino acid 31 and 60. Multiple amino acid sequence alignment of VP1 suggested that this site harbors conservative sequences across all genogroups. Indirect and sandwich ELISA indicated that mAb 8D8 was unable bind intact VLPs. In summary, we successfully produced GI.7 and GII.2 VLPs using recombinant baculovirus expression system and a cross-reactive mAb by immunizing mice with eight different VLPs that might be useful in the studying and detecting NoVs.

Genogroup II, genotype 3 noroviruses (GII.3 NoVs) are secondary to GII.4 NoVs in causing acute non-bacterial gastroenteritis worldwide. In our previous study, we found that virus-like particles (VLPs) derived from a GII.3 NoV strain exhibited no binding activity to any salivary and synthetic histo-blood group antigens (HBGAs) tested. In this study, the nucleotide sequence encoding the major capsid protein of another documented GII.3 NoV strain was codon-optimized and synthesized, and the major capsid protein was expressed using recombinant baculovirus virus expression system. The assembly of VLPs was verified by electron microscopy, and the binding profiles of the assembled VLPs to salivary HBGAs were determined, and in vitro VLP-salivary HBGAs binding blockade assay was used to test the cross-blocking effects of hyperimmune sera produced against different genotypes (GI.2, GII.3, and GII.4). The expression of the major capsid proteins led to the successful assembly of VLPs, and in vitro VLP-salivary HBGAs binding assay indicated that the assembled VLPs bound to salivary HBGAs from blood type A, B, AB, and O individuals, with the highest binding capacity to type A salivary HBGAs. In vitro VLP-salivary HBGAs binding blockade assay demonstrated the absence of blocking activities for hyperimmune sera produced against GI.2and GII.4 VLPs and the presence of blocking activity for that against GII.3 VLPs. Our results suggest the absence of cross-blocking activities among different genotypes and the presence of blocking activities between GII.3 NoVs from different clusters, which might have implications for the design of multivalent NoV vaccines.

Noroviruses (NoVs) are a leading cause of non-bacterial acute gastroenteritis worldwide. The prevalence of Genogroup II, genotype 3 (GII.3) NoVs is secondary to the epidemic GII.4 strains which show broad spectrum binding activities against multiple types of histo-blood group antigens (HBGAs). In our previous study it was found that GII.3 NoV VLPs exhibited no binding activity to all synthetic and salivary HBGAs tested. To determine the compatibility of P2 domains between different genotypes and its effect over the binding specificity to HBGAs, we swapped the P2 domain of a GII.4 strain (Sydney 2012-like variant) with that of a GII.3 strain (GII.4-VP1/GII.3-P2). In vitro VLP-HBGA binding and binding blockade assays were used to characterize the binding patterns of GII.4-VP1/GII.3-P2 chimeric capsid protein. Expression of GII.4-VP1/GII.3-P2 chimeric capsid protein using recombinant bacuolovirus expression system led to assembly of virus like particles (VLPs). In vitro VLP-HBGA binding assay using synthetic and salivary HBGAs indicated binding activities to blood type A (trimer), Le(x) and blood type A, B and O salivary HBGAs. In vitro VLP-HBGA binding blockade assay indicated that the binding could be blocked by rabbit hyperimmune serum against GII.3 VLPs, but not hyperimmune sera against GI.2 and GII.4 VLPs. These results indicate that the observed binding activities may be caused by conformational changes of inserted P2 domain and possibly reflect the actual binding profile of GII.3 VLPs. The currently observed absence of binding of GII.3 NoV VLPs to salivary or synthetic HBGAs might be due to absence of other unknown factors.

Objective: Noroviruses (NoVs) are the leading cause of non-bacterial gastroenteritis worldwide and genogroup II, genotype 4 variants have been responsible for the majority of outbreaks reported. In winter 2014-15, the transient burst outbreaks caused by a new GII.17 variant that differed from previous strains was observed in several countries. In this study, major capsid proteins derived from GII.17 and GII.7 NoVs were expressed in sf9 cells and used to produce hyperimmune sera in rabbits for characterization of GII.17 and GII7 NoV Virus like particles (VLPs). Methods: Baculovirus-insect cell expression system was used to assemble NoV VLPs. Salivary HBGA-viruslike particle (VLP) binding and binding blockade assays were performed. Results: High expression levels were observed for both capsid proteins and expression led to successful assembly of VLPs. CsCl density gradient centrifugation indicated presence of two bands for both VLPs and SDS-PAGE analysis of these two bands showed contradictory ratio of the full-length and truncated capsid proteins. Both VLPs bound to salivary HBGAs derived from blood type A, B, AB and O individuals. In vitro HBGA-VLP binding blockade assay using hyperimmune sera against multiple genotypes, including current pandemic Sydney 2012 GII.4, GI.2, GII.7 and GII.17 VLPs demonstrated absence of blocking antibodies against the binding of GII.17 and GII.7 VLPs to salivary HBGAs. Conclusion: The expression of GII.17 and GII.7 capsid proteins and VLP assembling allowed the antigenic comparison of different recombinant NoVs.

The newly emerged Norovirus (NoV) Sydney 2012 strain has been sweeping all over the world, causing acute non-bacterial gastroenteritis in adults and children. Due to a lack of cell culture system, virus like particles (VLPs) has been assembled and used as vaccine candidates in preclinical and clinical studies. Expression of the major capsid protein of NoVs using recombinant baculovirus expression system in Sf9 cells leads to formation of VLPs that are morphologically and antigenically similar to true virions. In this study, VLPs were successfully produced using the VP1 of Sydney-2012-like strain and its immunogenicity was evaluated by different routes and its capability in inducing mucosal immune responses in the presence and absence of adjuvants in BALB/c mice. Administration of NoV VLPs in the presence of Al(OH)3 or monophosphoryl lipid A (MPL-A) led to high titers of VLP-specific IgG antibodies. Administration of VLPs orally in the presence of cholera toxin subunit B (CTB) didn't enhance mucosal immune response as less fecal IgA positive mice were observed when compared with those given VLPs only. Our study represents the first immunogenicity study of VLPs derived from current pandemic Sydney 2012 strain and which might have implications in the development of NoVs vaccine in china.

A newly emerged pandemic Sydney GII.4-like norovirus (NoV) (Jingzhou GII.4) was isolated in Jingzhou, China in April, 2013, demonstrating the rapid spread of the variant to China. The complete nucleotide sequence was compared with the prototype Sydney 2012 variant and its VP1 gene with that of Huzhou strain (isolated in January 2013 in Huzhou, China). The result demonstrates that the new variant has evolved rapidly, including mutations in the hypervariable P2 domain of the major capsid protein VP1. Our study also shows that the new Jingzhou GII.4 variant co-circulated with GII.3 and GI.2 at the same time, supporting further monitoring of the evolution of the new NoV variant in China.