Virus Genes最新文献

Classical swine fever virus (CSFV) is a pathogen that affects pigs and wild boars. This contagious RNA virus is a high threat to swine industries throughout the world because it has high mortality and morbidity rates, leading to economic losses. Although some studies have analyzed whole-genome sequences, but often focus on isolates from only a few countries, while others started with whole-genome analysis before narrowing down to specific gene region like E2. In addition, several studies have predominantly focused on isolated geographic regions. Our study leverages a global dataset of 220 CSFV whole-genome sequences retrieved from the NCBI repository along with two CSFV complete genome sequence from our laboratory (Accession Number: MH734359.1 and OR4282229.1) and carefully curated to 66 sequences. The refined dataset was subjected to Bayesian analysis along with selection pressure analysis. The outcome of this experiment, the mean substitution rate was estimated at 2.06 × 10^-3 substitutions/site/year with the Highest Posterior Density (HPD) (95% HPD 6.8012 × 10^-4 to 3.3044 × 10^-3), and the estimated average time to the most recent common ancestor (tMRCA) for the analyzed dataset was the year 1877 (95% HPD 1833.8181-1932.3176). Among the curated dataset, 2 CSFV complete genome sequences (Accession Number: MH734359.1 and OR428229.1) from our laboratory showed a Chinese origin. In addition, pervasive and episodic selection pressure revealed that both had ongoing diversifying natural positive selection, which could lead to increased genetic diversity and possibly emergence of the new lineage. This potential information could be used for future evaluation of strategies to control emerging new genotypes of CSFV with high mortality and morbidity.

Acute bee paralysis virus (ABPV) is a notable pathogen frequently detected in managed honeybee (Apis mellifera) colonies. Although infections are often covert, they can lead to severe outcomes in the presence of Varroa destructor infestations. This study aims to evaluate the prevalence of ABPV and its correlation with a range of biotic and abiotic stressors in managed beehives located in the Central Anatolia and Mediterranean Regions of Türkiye during the spring-summer and autumn seasons of 2021. ABPV was identified in 38.6% of the samples (27/70) using real-time RT-PCR. The high prevalence observed was linked to Varroa destructor infestations, elevated temperatures and dry climatic conditions, migratory beekeeping practices, and disruptions in colony management during the COVID-19 pandemic. Phylogenetic relationships among ABPV strains were elucidated through partial sequencing of the capsid and RNA-dependent RNA polymerase protein coding genes, employing maximum likelihood tree construction with the Tamura 3-parameter model. Turkish ABPV strains clustered into a distinct subclade, sharing 98.4-99% nucleotide identity with European strains, indicative of a monophyletic origin and geographic segregation at the regional or continental level. These findings highlight the necessity for robust surveillance and research programs to monitor ABPV prevalence and mitigate its detrimental effects on colony health and productivity. Additionally, the phylogenetic insights provided by this study enhance our understanding of the geographic distribution and evolutionary dynamics of ABPV strains, offering critical information for future molecular epidemiological research and apicultural management strategies.

Arboviruses persist as a significant threat to global public and human health. The advent of macrogenomics technology has substantially expanded our understanding of mosquito-borne viruses by facilitating the direct identification and characterization of viruses from diverse environmental samples. In 2022, we conducted mosquito surveillance in the Shandong region of China and discovered a novel virus, tentatively named Gushan virus based on the site of discovery. In this study, a total of 3170 mosquitoes were collected and divided into 62 pools based on species and collection locations. Quantitative reverse transcription PCR (qRT-PCR) and nested PCR were employed to detect Gushan virus nucleic acids in all samples. The results revealed that 16 pools were positive, with a minimum infection rate (MIR) of 0.5% (16/3,170). Concurrently, we successfully obtained one complete genome sequence and six partial sequences. Nucleotide homology analysis demonstrated a high degree of sequence identity, indicating that Gushan virus may maintain a stable genetic profile in the region. Phylogenetic analyses revealed that Gushan virus is most closely related to Drosophila immigrans Nora virus of the family Noroviridae. Taxonomically, Gushan virus belongs to the order Picornavirales, family Noroviridae, and genus Orthonoravirus. This study contributes new insights into the diversity of mosquito-associated viruses.

Avian influenza virus (AIV) remains a significant global threat, with periodic reemergence in Iraq. This study marks the first molecular characterization of the highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in seagulls. The H5N1 AIV was identified during outbreaks in 2024 at Dukan Lake in Sulaimani province. Phylogenetic analysis of the HA gene revealed that the Dukan Lake strain belongs to subclade 2.3.4.4b, clustering closely with Kazakhstan HPAI strains (A/mute swan/Mangystau/1-S24R-2/2024(H5N1) and (A/Cygnus cygnus/Karakol lake/01/2024(H5N1)), with DNA identities of 99.38% and 98.82%, respectively. Genetic analysis showed a polybasic amino acid cleavage site motif (PLREKRRKRGLF) in the HA gene. Additionally, receptor-binding domain (RBD) analysis indicated a preference for the avian α-2, 3 Sialic acid (SA) receptor over the mammalian α-2, 6 SA receptor. The NA gene analysis revealed amino acid residues D199, I223, S247, and H275, which are susceptible to antiviral drugs. The molecular analysis of the H5N1 Dukan Lake seagull strain provides insights into how the virus spreads among different species and countries, which is crucial for global health security and the development of effective control measures.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused an unprecedented pandemic in human history. To date, more than 6.5 million lives have been lost to COVID-19 (coronavirus disease 2019). Following widespread efforts for COVID-19 vaccination in Brazil, there has been a drastic reduction in COVID-19 deaths, which was particularly evident in the city of Botucatu, SP, Brazil, after a campaign to a mass vaccination. Our objective was to assess the temporal and epidemiological spread of variants of concern (VOC) of SARS-CoV-2 in the four weeks preceding the massive vaccination campaign in the municipality. After randomizing 400 samples, Next-Generation Sequencing was used to produce sequences and determine the variants. Among high-quality sequences, 98.4% belonged to the VOC Gamma, with P.1 and P.1.14 being the most prevalent lineages. P.1 was more frequent in both men and women, and in younger individuals and adults (0-59 years) compared to P.1.14. There was no correlation between the variants and the presence of comorbidities or between them and moderate to severe clinical cases of COVID-19 or death. However, P.1 was more frequent than P.1.14 in people with mild forms of the disease and in those who exhibited symptoms. In the phylogenetic analyses, a small cluster of 9 P.1.14 samples containing mutations in ORF1a: M584V and A3620V was observed, which had not been found in any Gamma sequences to date. The importance of genomic surveillance of SARS-CoV-2 is evident in assisting public health decision-making and the management of COVID-19 and other diseases.

A novel plant virus was identified in fig trees exhibiting ring spot symptoms through high-throughput sequencing (HTS). The complete genome sequence was successfully determined using PCR and RT-PCR techniques. The virus features a circular DNA genome of 7233 nucleotides (nt) in length, encompassing four open reading frames (ORFs). ORF1 and ORF2 encode hypothetical proteins, while ORF3 encodes a putative polyprotein with conserved domains, including a zinc finger, aspartic protease, reverse transcriptase (RT), and RNase H. ORF4 encodes a putative protein of unknown function. Comparative nucleotide sequence analysis of the RT + RNase H region reveals 84.46% and 78.82% identity with grapevine badnavirus 1 (GBV-1, MF781082.1) and fig badnavirus 1 (FBV-1, MK348055.1), respectively. Notably, this virus's genomic organization diverges from GBV-1 but is similar to FBV-1. Phylogenetic analysis demonstrates that the three isolates of this virus form a distinct clade within the badnaviruses. Based on genomic structure and phylogenetic relationships, this novel virus represents a new member of the genus Badnavirus and is proposed to be named "Fig badnavirus 2" (FBV-2).

Influenza A viruses continue to pose a serious threat to public health and economic stability. To investigate the role of C1RL-AS1 in influenza A virus (IAV) pneumonia. Using RT-qPCR analysis, we determined C1RL-AS1 expression levels in children with IAV-infected pneumonia and A549 cells. C1RL-AS1 expression levels in children were subjected to ROC analysis. C1RL-AS1 was knocked down to investigate its role in IAV-infected A549 cells, including effects on viral nucleoprotein (NP) production, cell survival, and apoptosis. Downstream miRNAs of C1RL-AS1 were predicted and validated. MiR-16-5p target genes were predicted and validated. C1RL-AS1 was up-regulated in IAV-infected children and A549 cells. C1RL-AS1 expression levels distinguished children with IAV pneumonia from healthy children. Knockdown of C1RL-AS1 attenuated viral NP production, promoted A549 cell survival, and inhibited apoptosis. MiR-16-5p was a downstream C1RL-AS1 miRNA. miR-16-5p counteracted the anti-IAV infection effect brought about by C1RL-AS1 knockdown. LAMP3 was a miR-16-5p target gene associated with pneumonia. LAMP3 restored the cellular effects brought about by C1RL-AS1/miR-16-5p co-knockdown. C1RL-AS1 is a possible diagnostic factor for IAV pneumonia in children. C1RL-AS1 may participate in IAV pneumonia by sponging miR-16-5p and then moderating LAMP3.

A novel double-stranded RNA virus, designated as "Magnaporthe oryzae polymycovirus 1" (MoPmV1), was identified in Magnaporthe oryzae strain TM02. MoPmV1 has four dsRNA fragments, ranging from 1324 to 2401 bp in length. DsRNA1, 2, and 3 of MoPmV1 each possess a single large open reading frame (ORF), whereas dsRNA4 contains two ORFs. BLASTp analysis indicated that ORF1a, encoded by dsRNA1, shows 59.2% amino acid sequence identity with the RNA-dependent RNA polymerase (RdRp) of Beauveria bassiana polymycovirus 2; ORF2a, encoded by dsRNA2, shows 42.3% identity with the putative serine protease of Phaeoacremonium minimum tetramycovirus 1; ORF3a, encoded by dsRNA3, shows 40.6% identity with the methyltransferase of Aspergillus fumigatus tetramycovirus 1; ORF4a, encoded by dsRNA4, shows 41.7% identity with the proline-alanine-serine-rich (PASr) protein of Botryosphaeria dothidea virus 1, while ORF4b, encoded by dsRNA4, shows no significant similarity to any known proteins. Phylogenetic analysis of the RdRp domain indicated that MoPmV1 was grouped in a cluster with members of the genus Polymycovirus in the family Polymycoviridae. Based on these characteristics, MoPmV1 is a new member of the genus Polymycovirus in the family Polymycoviridae. This is the first report of a mycovirus of the family Polymycoviridae identified in rice blast fungus M. oryzae.

Researchers have identified Avastrovirus as a significant genus of bird viruses, linked to various avian diseases such as enteritis, growth retardation, nephritis and hepatitis. These infections can cause substantial economic losses in agrocultureand have a widespread impact on global food production. Although there have been numerous studies on these viruses, most of them-mainly focuses on poultry. Research on astroviruses in wild bird populations has revealed a wide genetic diversity of these viruses, yet our understanding of their biological and ecological characteristics remains limited. In this study, we for the first time detected avastrovirus in wild migratory birds of the families Anatidae and Columbidae from Sakhalin Island, North Pacific Ocean. Phylogenetic analysis revealed the presence of Avastrovirus 2 in wild doves and Avastrovirus 3 in wild ducks. These findings provide valuable insights into the circulation of astroviruses in wild bird populations of Sakhalin Island, which lies along the East Asian-Australasian Flyway.

Previous studies showed that deletion of the viral thymidine kinase (TK) gene in several alphaherpesviruses including EHV-1 reduced their virulence. Previously, we found that deletion of ORF37, which is located head-to-head with TK, decreased EHV-1 virulence in mice but did not affect the expression of TK mRNA. Therefore, deletion of ORF38 might also affect virulence by partially deleting the ORF37 promoter. To investigate the role of the TK gene-encoding region in the pathogenesis of EHV-1 as well as the expression of ORF37, we generated a TK deletion mutant by using a bacterial artificial chromosome carrying the neuropathogenic strain Ab4p. Deletion of TK increased the transcription of ORF37, did not cause any neurological disorders in CBA/N1 mice, and its growth in cultured neural cells was impaired. These results suggest deletion of ORF38 does not affect the ORF37 promoter and confirm that TK plays an important role in the neuropathogenicity of EHV-1.