Compositional features analysis by machine learning in genome represents linear adaptation of monkeypox virus.

Introduction: The global headlines have been dominated by the sudden and widespread outbreak of monkeypox, a rare and endemic zoonotic disease caused by the monkeypox virus (MPXV). Genomic composition based machine learning (ML) methods have recently shown promise in identifying host adaptability and evolutionary patterns of virus. Our study aimed to analyze the genomic characteristics and evolutionary patterns of MPXV using ML methods. Methods: The open reading frame (ORF) regions of full-length MPXV genomes were filtered and 165 ORFs were selected as clusters with the highest homology. Unsupervised machine learning methods of t-distributed stochastic neighbor embedding (t-SNE), Principal Component Analysis (PCA), and hierarchical clustering were performed to observe the DCR characteristics of the selected ORF clusters. Results: The results showed that MPXV sequences post-2022 showed an obvious linear adaptive evolution, indicating that it has become more adapted to the human host after accumulating mutations. For further accurate analysis, the ORF regions with larger variations were filtered out based on the ranking of homology difference to narrow down the key ORF clusters, which drew the same conclusion of linear adaptability. Then key differential protein structures were predicted by AlphaFold 2, which meant that difference in main domains might be one of the internal reasons for linear adaptive evolution. Discussion: Understanding the process of linear adaptation is critical in the constant evolutionary struggle between viruses and their hosts, playing a significant role in crafting effective measures to tackle viral diseases. Therefore, the present study provides valuable insights into the evolutionary patterns of the MPXV in 2022 from the perspective of genomic composition characteristics analysis through ML methods.

Convolutional Neural Networks Based on Sequential Spike Predict the High Human Adaptation of SARS-CoV-2 Omicron Variants.

The COVID-19 pandemic has frequently produced more highly transmissible SARS-CoV-2 variants, such as Omicron, which has produced sublineages. It is a challenge to tell apart high-risk Omicron sublineages and other lineages of SARS-CoV-2 variants. We aimed to build a fine-grained deep learning (DL) model to assess SARS-CoV-2 transmissibility, updating our former coarse-grained model, with the training/validating data of early-stage SARS-CoV-2 variants and based on sequential Spike samples. Sequential amino acid (AA) frequency was decomposed into serially and slidingly windowed fragments in Spike. Unsupervised machine learning approaches were performed to observe the distribution in sequential AA frequency and then a supervised Convolutional Neural Network (CNN) was built with three adaptation labels to predict the human adaptation of Omicron variants in sublineages. Results indicated clear inter-lineage separation and intra-lineage clustering for SARS-CoV-2 variants in the decomposed sequential AAs. Accurate classification by the predictor was validated for the variants with different adaptations. Higher adaptation for the BA.2 sublineage and middle-level adaptation for the BA.1/BA.1.1 sublineages were predicted for Omicron variants. Summarily, the Omicron BA.2 sublineage is more adaptive than BA.1/BA.1.1 and has spread more rapidly, particularly in Europe. The fine-grained adaptation DL model works well for the timely assessment of the transmissibility of SARS-CoV-2 variants, facilitating the control of emerging SARS-CoV-2 variants.

Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses.

Influenza A viruses (IAV) modulate host antiviral responses to promote growth and pathogenicity. Here, we examined the multifunctional IAV nonstructural protein 1 (NS1) of influenza A virus to better understand factors that contribute to viral replication efficiency or pathogenicity. In 2009, a pandemic H1N1 IAV (A/California/07/2009 pH1N1) emerged in the human population from swine. Seasonal variants of this virus are still circulating in humans. Here, we compared the sequence of a seasonal variant of this H1N1 influenza virus (A/Urumqi/XJ49/2018(H1N1), first isolated in 2018) with the pandemic strain A/California/07/2009. The 2018 virus harbored amino acid mutations (I123V and N205S) in important functional sites; however, 108R and 189G were highly conserved between A/California/07/2009 and the 2018 variant. To better understand interactions between influenza viruses and the human innate immune system, we generated and rescued seasonal 2009 H1N1 IAV mutants expressing an NS1 protein harboring a dual mutation (R108K/G189D) at these conserved residues and then analyzed its biological characteristics. We found that the mutated NS1 protein exhibited systematic and selective inhibition of cytokine responses via a mechanism that may not involve binding to cleavage and polyadenylation specificity factor 30 (CPSF30). These results highlight the complexity underlying host-influenza NS1 protein interactions.

Machine Learning Methods for Predicting Human-Adaptive Influenza A Viruses Based on Viral Nucleotide Compositions.

Each influenza pandemic was caused at least partly by avian- and/or swine-origin influenza A viruses (IAVs). The timing of and the potential IAVs involved in the next pandemic are currently unpredictable. We aim to build machine learning (ML) models to predict human-adaptive IAV nucleotide composition. A total of 217,549 IAV full-length coding sequences of the PB2 (polymerase basic protein-2), PB1, PA (polymerase acidic protein), HA (hemagglutinin), NP (nucleoprotein), and NA (neuraminidase) segments were decomposed for their codon position-based mononucleotides (12 nts) and dinucleotides (48 dnts). A total of 68,742 human sequences and 68,739 avian sequences (1:1) were resampled to characterize the human adaptation-associated (d)nts with principal component analysis (PCA) and other ML models. Then, the human adaptation of IAV sequences was predicted based on the characterized (d)nts. Respectively, 9, 12, 11, 13, 10 and 9 human-adaptive (d)nts were optimized for the six segments. PCA and hierarchical clustering analysis revealed the linear separability of the optimized (d)nts between the human-adaptive and avian-adaptive sets. The results of the confusion matrix and the area under the receiver operating characteristic curve indicated a high performance of the ML models to predict human adaptation of IAVs. Our model performed well in predicting the human adaptation of the swine/avian IAVs before and after the 2009 H1N1 pandemic. In conclusion, we identified the human adaptation-associated genomic composition of IAV segments. ML models for IAV human adaptation prediction using large IAV genomic data sets can facilitate the identification of key viral factors that affect virus transmission/pathogenicity. Most importantly, it allows the prediction of pandemic influenza.

A Sensitive Nano Luciferase Immune Complex Assay System for Highly Sensitive and Specific Detection of Antibodies Against Tick-Borne Encephalitis Virus.

Tick-borne encephalitis virus (TBEV) can cause fever, headache, neurological disorders, and/or peripheral flaccid paralysis; therefore, it is a major threat to public health. A rapid, sensitive, and simple method for detecting anti-TBEV antibodies is needed urgently to determine infection and for vaccine evaluation. Here, a luciferase-based immunocomplex assay system (Luc-IC) was developed to detect TBEV antibodies. The system is based on a reporter Nano luciferase (NLuc) that is co-expressed as a fusion protein with viral envelope domain III (ED3) in COS7 cells. The cell supernatant was used directly to detect antigen without the need for a purification step. This simple procedure effectively improved the sensitivity of the assay. Sera from 50 patients with an acute tick-borne encephalitis infection were tested to determine the sensitivity of the NLuc-IC assay. Furthermore, 62 sera from individuals infected with Japanese encephalitis virus, West Nile virus, yellow fever virus, dengue virus, or Zika virus were also tested to determine specificity. The results demonstrated that the assay was 100% sensitive and 100% specific for TBEV antibodies. Thus, this very simple NLuc-IC assay is potentially useful for rapid and accurate diagnosis of TBEV infection in both humans and animals.

H5N1 influenza A virus with K193E and G225E double mutations in haemagglutinin is attenuated and immunogenic in mice.

Live-attenuated influenza vaccines (LAIVs) are now available for the prevention of influenza, with LAIV strains generally derived from serial passage in cultures or by reverse genetics (RG). The receptor-binding domain (RBD) in haemagglutinin (HA) of influenza virus is responsible for viral binding to the avian-type 2,3-α-linked or human-type 2,6-α-linked sialic acid receptor; however, the virulence determinants in the RBD of H5N1 virus remain largely unknown. In the present study, serial passage of H5N1 virus A/Vietnam/1194/2004 in Madin-Darby canine kidney cells resulted in the generation of adapted variants with large-plaque morphology, and genomic sequencing of selected variants revealed two specific amino acid substitutions (K193E and G225E) in the RBD. RG was used to generate H5N1 viruses containing either single or double substitutions in HA. The RG virus containing K193E and G225E mutations (rVN-K193E/G225E) demonstrated large-plaque morphology, enhanced replication and genetic stability after serial passage, without changing the receptor-binding preference. Importantly, in vivo virulence assessment demonstrated that rVN-K193E/G225E was significantly attenuated in mice. Microneutralization and haemagglutination inhibition assays demonstrated that immunization with rVN-K193E/G225E efficiently induced a robust antibody response against WT H5N1 virus in mice. Taken together, our experiments demonstrated that K193E and G225E mutations synergistically attenuated H5N1 virus without enhancing the receptor-binding avidity, and that the RG virus rVN-K193E/G225E represents a potential H5N1 LAIV strategy that deserves further development. These findings identify the RBD as a novel attenuation target for live vaccine development and highlight the complexity of RBD interactions.

The first complete genomic characterization of an Amur virus isolate from China.

Amur virus (AMRV) is a member of the genus Hantavirus in the family Bunyaviridae. In this study, we determined for the first time the complete genome sequence of the AMRV H8205 strain, which was isolated from a patient with hemorrhagic fever with renal syndrome (HFRS) in China. The complete nucleotide sequence of the S segment of AMRV H8205 is 1699 nt long, with a 5' noncoding region (5'NC) of 36 nt, followed by a coding sequence of 1290 nt and a 3'NC of 373 nt. The complete sequence of the M segment is 3615 nt long, with a 5'NC of 40 nt, followed by a coding sequence of 3408 nt and a 3'NC of 167 nt. The complete sequence of the L segment is 6536 nt long, with a 5'NC of 37 nt, followed by a coding sequence of 6453 nt and a 3'NC of 40 nt. The major open reading frame (ORF) of each of the three segments (S, nt 37-1326; M, nt 41-3445; L, nt 38-6490) has a coding capacity of 430 aa, 1135 aa, 2151 aa, respectively. Phylogenetic analysis of the nucleotide sequences using the NJ method indicated that H8205 virus, together with the Amur strains isolated from Far-Eastern Russia and Korea, forms a well-supported lineage. Our results will provide insights into the genetic diversity of hantaviruses (HNTV).

The confirmation of three repeated sequence elements in the 3' untranslated region of Chikungunya virus.

In this study, the complete genomic nucleotide sequence of Chikungunya virus (CHIKV) strain S27 African prototype was determined and three 21 nucleotides repeated sequence elements (RSEs) at positions 11398-11418, 11533-11553, and 11620-11640 in the 3' untranslated region (3'UTR) were confirmed. In addition, the 3'UTRs of all CHIKV strains deposited in GenBank were analyzed. The results displayed that the majority of the CHIKV strains consisted of the three 21 nucleotides RSEs in the 3'UTRs, and the third RSE was the most conservative. The conservation of the three RSEs of 21 nucleotides within the 3'UTR of CHIKV genome may play an important role on the virus replication cycle.

Expressed genes in regenerating rat liver after partial hepatectomy.

AIM: To reveal the liver regeneration (LR) and its control as well as the occurrence of liver disease and to study the gene expression profiles of 551 genes after partial hepatectomy (PH) in regenerating rat livers. METHODS: Five hundred and fifty-one expressed sequence tags screened by suppression subtractive hybridization were made into an in-house cDNA microarray, and the expressive genes and their expressive profiles in regenerating rat livers were analyzed by microarray and bioinformatics. RESULTS: Three hundred of the analyzed 551 genes were up- or downregulated more than twofolds at one or more time points during LR. Most of the genes were up- or downregulated 2-5 folds, but the highest reached 90 folds of the control. One hundred and thirty-nine of them showed upregulation, 135 displayed downregulation, and up or down expression of 26 genes revealed a dependence on regenerating livers. The genes expressed in 24-h regenerating livers were much more than those in the others. Cluster analysis and generalization analysis showed that there were at least six distinct temporal patterns of gene expression in the regenerating livers, that is, genes were expressed in the immediate early phase, early phase, intermediate phase, early-late phase, late phase, terminal phase. CONCLUSION: In LR, the number of down-regulated genes was almost similar to that of the upregulated genes; the successively altered genes were more than the rapidly transient genes. The temporal patterns of gene expression were similar 2 and 4 h, 12 and 16 h, 48 and 96 h, 72 and 144 h after PH. Microarray combined with suppressive subtractive hybridization can effectively identify the genes related to LR.

Identification of expressed genes in regenerating rat liver in 0-4-8-12 h short interval successive partial hepatectomy.

AIM: To identify the genes differentially expressed in the regenerating rat liver of 0-4-8-12 h short interval successive partial hepatectomy (SISPH) and to analyze their expression profiles. METHODS: Five hundred and fifty-one elements screened from subtractive cDNA libraries were made into a cDNA microarray (cDNA chip). Extensive gene expression analysis following 0-4-8-12 h SISPH was conducted by microarray. RESULTS: One hundred and eighty-three elements were selected, which were either up- or down-regulated more than 2-fold at one or more time points after SISPH. Cluster analysis and generalization analysis showed that there were five distinct temporal patterns of gene expression. Eighty-six genes were unreported, associated with liver regeneration (LR). CONCLUSION: Microarray analysis shows that the down regulated genes are much more than the up-regulated ones in SISPH; the numbers of genes expressed consistently are fewer than that expressed immediately; the genes expressed in high abundance are much fewer than that increased 2-5-fold. The comparison of SISPH with partial hepatectomy (PH) shows that the expression trends of most genes in SISPH and in PH are similar, but the expression of 43 genes is specifically altered in SISPH.

[Optimization of reaction conditions for RAPD analysis of freshwater planarians in China].

Using the Genomic DNA purification kit, the total DNA of the freshwater planarian was extracted and developed one single band through 0.8% agarose gel electrophoresis with OD260/OD280 between 1.5 and 2.2, which could satisfy the requirements of RAPD and PCR on DNA. With the extracted DNA template, we tested experimental conditions that might affect RAPD results including annealing temperature, concentrations of template DNA, primer, Mg2+ and dNTPs. Through comparision we found that it was necessary and important to optimize the experimental conditions for producing stable and repeatable RAPD results. The optimized reaction conditions of RAPD for freshwater planarian in 25 microl reaction volume were as follows: 20 ng template DNA, 37 degrees C annealing temperature, 0.2 micromol/L primer, 2.0 mmol/L Mg2+ and 200 micromol/L dNTPs.

Gene expression differences of regenerating rat liver in a short interval successive partial hepatectomy.

AIM: To identify the genes expressed differentially in the regenerating rat liver in a short interval successive partial hepatectomy (SISPH), and to analyze their expression profiles. METHODS: Five hundred and fifty-one elements selected from subtractive cDNA libraries were conformed to a cDNA microarray (cDNA chip). An extensive gene expression analysis following 0-36-72-96-144 h SISPH was performed by microarray. RESULTS: Two hundred and sixteen elements were identified either up- or down-regulated more than 2-fold at one or more time points of SISPH. By cluster analysis and generalization analysis, 8 kinds of ramose gene expression clusters were generated in the SISPH. Of the 216 elements, 111 were up-regulated and 105 down-regulated. Except 99 unreported genes, 117 reported genes were categorized into 22 groups based on their biological functions. Comparison of the gene expression in SISPH with that after partial hepatectomy (PH) disclosed that 56 genes were specially altered in SISPH, and 160 genes were simultaneously up-regulated or down-regulated in SISPH and after PH, but in various amount and at different time points. CONCLUSION: Genes expressed consistently are far less than that intermittently; the genes strikingly increased are much less than that increased only 2-5 fold; the expression trends of most genes in SISPH and in PH are similar, but the expression of 56 genes is specifically altered in SISPH. Microarray combined with suppressive subtractive hybridization can in a large scale effectively identify the genes related to liver regeneration.

[Cloning and analysis of rat heat shock factor binding protein 1 cDNA].

Heat shock factor binding protein 1(HSBP1) is a nuclear-localized, novel, conserved, low molecular weight (< 100 residues) transcriptional factor, which may repress the activity of the heat shock factor 1 (HSF1) by binding HSF1 active trimerization domain. HSBP1 gene have been cloned in human and mouse, but not reported in rat. In this paper, a pair of consensus degenerate primers were designed based on N-terminal and C-terminal conservative amino acid sequence. Using RT-PCR method, hsbp1 gene fragment was amplified and cloned from total RNA extracted from rat C6 glioma cells. Then the EST was probed to isolate the rat full-length hsbp1 cDNA by in situ hybridization from a rat C6 glioma cells cDNA library. The full-length hsbp1 was deposited in GenBank (accession No. AY522937). It was blasted in RGD (rat genome database) and was localized in 19q12 and composed of four extrons and three introns. The distance between the first extron and the fourth extron was 5829bp. Then its Uinigene was searched, results showed HSBP1 existed widely in all kinds of organs and tissues, the data suggested that it may play a important roles in physiological activity. In addition, the sequence similarity and phylogenetic relationship were compared with DNAman tool. The result showed the relationship is consistent between the similarity of amino acid sequence and phylogenetic evolution from morphological of those species which were nearly in evolution.

[Construction of Chang Liver cDNA library and immunoscreening of ADAMS related genes].

Total RNA was isolated from Chang Liver cell. The full-length cDNA was synthesized using LD PCR by RNA 5' end switching mechanism, oligo(dT) as primer. SfiI digestion sites were introduced at both 3' and 5' end of cDNA. The cDNA was ligated with gammaTriplEX2 vector and packaged. Twenty-two positive clones were obtained by immunoscreening to the library, they were sequenced and blast in NCBI, one of them was identified a novel gene. It was submitted to GenBank and obtained accession number AY078070. It may lay down a foundation for studying on functions of ADAMs related gene.

Isolation and analysis of a novel gene over-expressed during liver regeneration.

AIM: To isolate and analyze a novel gene over-expressed during liver regeneration. METHODS: Total RNA of regenerating liver was extracted from liver tissue after 0-4-36-36-36 hr short interval successive partial hepatectomy (SISPH). Reverse transcription-polymerase chain reaction was used to synthesize double strand cDNA, after the tissue was digested by proteinase K and Sfi A/B. The double-strand cDNA was ligated to lambdaTriplEx2. lambdaphage packaging reaction was performed and E. coli XL1-Blue was infected for titering and amplifying. One expressed sequence tag was probed by Dig and phage in situ hybridization was carried out to isolate positive clones. Positive recombinant lambdaTriplEx2 was converted to the corresponding pTriplEx2, and bioinformatics was used to analyze full-length cDNA. RESULTS: We isolated a novel full-length cDNA during liver regeneration following SISPH. CONCLUSION: We have succeeded in cloning a novel gene, based on bioinformatics. We postulate that this gene may function in complicated network in liver regeneration. On the one hand, it may exert initiation of liver regeneration via regulating nitric oxide synthesis. On the other hand, it may protect damaged residue lobus following SISPH.

Cloning and analysing the up-regulated expression of transthyretin-related gene (LR1) in rat liver regeneration following short interval successive partial hepatectomy.

AIM: Cloning and analysing the up-regulated expression of transthyretin-related gene following short interval successive partial hepatectomy (SISPH) to elucidate the mechanism of differentiation, division, dedifferentiation and redifferentiation in rat liver regeneration (LR). METHODS: Lobus external sinister and lobus centralis sinister, lobus centralis, lobus dexter, lobus candatus were removed one by one from rat liver at four different time points 4, 36, 36 and 36 hr (total time: 4 hr, 40 hr, 76 hr, 112 hr) respectively. Suppression subtractive hybridization (SSH) was carried out by using normal rat liver tissue as driver and the tissue following short interval successive partial hepatectomy (SISPH) as tester to construct a highly efficient forward-subtractive cDNA library. After screening, an interested EST fragment was selected by SSH and primers were designed according to the sequence of the EST to clone the full-length cDNA fragment using RACE (rapid amplification of cDNA end). Homologous detection was performed between the full-lenth cDNA and Genbank. RESULTS: Forward suppression subtractive hybridization (FSSH) library between 0 h and 112 h following SISPH was constructed and an up-regulated full-length cDNA (named LR1), which was related with the transthyretin gene, was cloned by rapid amplification of cDNA end. It was suggested that the gene is involved in the cellular dedifferentiation in LR following SISPH. CONCLUSION: Some genes were up-regulated in 112 h following SISPH in rat. LR(1) is one of these up-regulated expression genes which may play an important role in rat LR.

[Cloning differentially expressed genes by suppression subtractive hybridization in rat liver regeneration].

The cDNA from rat regenerating liver tissue was used as the tester and that from normal liver was used as the driver. A highly efficient subtractive cDNA library was constructed by suppression subtractive hybridization(SSH). After screening, 31 clones from 50 clones which were derived from the cDNA library were inserted by 60-400 bp cDNA fragments. 24 cDNA fragments corresponded to known genes and 7 cDNA fragments were unknown sequences (GenBank accession number: BG447490-447496).