Genetic characteristics and geographic distribution of rabies virus in China.

China is one of the largest countries with endemic rabies. In this study, we examined the full-length genome sequences of 87 rabies virus (RABV) strains identified in China from 1931 to 2019. Chinese RABV isolates were divided into two major clades, GI and GII. Clade GI consisted of viruses from the Asian clade, which was further divided into three subclades: Asian1, Asian2, and Asian3. Clade GII consisted of viruses from the Cosmopolitan, Arctic-related, and Indian clades. A phylogeographic network showed that the variation of rabies virus was more closely associated with geographic location than with the host species. Recombination appears to be one of the factors driving the emergence of new viral strains.

Evolutionary plasticity of zoonotic porcine Deltacoronavirus (PDCoV): genetic characteristics and geographic distribution.

The emergence and rapid spread of the acute respiratory syndrome coronavirus-2 have confirmed that animal coronaviruses represent a potential zoonotic source. Porcine deltacoronavirus is a worldwide evolving enteropathogen of swine, detected first in Hong Kong, China, before its global identification. Following the recent detection of PDCoV in humans, we attempted in this report to re-examine the status of PDCoV phylogenetic classification and evolutionary characteristics. A dataset of 166 complete PDCoV genomes was analyzed using the Maximum Likelihood method in IQ-TREE with the best-fitting model GTR + F + I + G4, revealing two major genogroups (GI and GII), with further seven and two sub-genogroups, (GI a-g) and (GII a-b), respectively. PDCoV strains collected in China exhibited the broadest genetic diversity, distributed in all subgenotypes. Thirty-one potential natural recombination events were identified, 19 of which occurred between China strains, and seven involved at least one China strain as a parental sequence. Importantly, we identified a human Haiti PDCoV strain as recombinant, alarming a possible future spillover that could become a critical threat to human health. The similarity and recombination analysis showed that PDCoV spike ORF is highly variable compared to ORFs encoding other structural proteins. Prediction of linear B cell epitopes of the spike glycoprotein and the 3D structural mapping of amino acid variations of two representative strains of GI and GII showed that the receptor-binding domain (RBD) of spike glycoprotein underwent a significant antigenic drift, suggesting its contribution in the genetic diversity and the wider spread of PDCoV.

Antibiogram of ESBL and MBL producing Pseudomonas aeruginosa among the population of Hazara division, KPK, Pakistan.

OBJECTIVE: To investigate the frequency rate and sensitivity pattern of extended-spectrum beta-lactamase and metallobeta- lactamase producing Pseudomonas aeruginosa isolated from major hospitals. METHODS: The cross-sectional study was conducted in the Microbiology section of the Pathology Department of Ayub Medical College, Abbottabad, Pakistan, from September 2017 to April 2018, and comprised clinical samples collected from different medical wards of major hospitals in the study area. For the selective growth of Pseudomonas aeruginosa, Cetrimide agar was used, and different antibiotics were evaluated for the sensitivity pattern following Kirby-Bauer diffusion method. Pseudomonas aeruginosa producing extended-spectrum beta lactamase and metallo-beta-lactamase were identified through double disk synergy test and imipenem ethylenediaminetetraacetic acid tests respectively. Patient's demographic and medical history was noted on a proforma. Data was analysed using SPSS 22.0. RESULTS: Of the 242 samples screened, 46 (19%) were positive for Pseudomonas aeruginosa. These samples were highly sensitive to levofloxacin, amikacin, imipenem, meropenem and ciprofloxacin (p<0.05). Of the positive cases, 11 (23.91%) were detected for extended-spectrum beta-lactamase production, while 3 (6.52%) samples were detected for metallo-beta-lactamase production. CONCLUSIONS: Pseudomonas aeruginosa samples were widely resistant to most antibiotics, but were sensitive for some antibiotics which may be recommended by physicians when treating Pseudomonas aeruginosa infection.

Reply to Abrantes et al. Recombination-Based Perspectives on Lagovirus Classification, Phylogenetic Patterns, and Evolutionary Dynamics. Comment on "Shah et al. Genetic Characteristics and Phylogeographic Dynamics of Lagoviruses, 1988-2021. Viruses 2023, 15, 815".

Recently, Abrantes et al [...].

Genetic diversity and phylogeographic dynamics of avihepadnavirus: a comprehensive full-length genomic view.

Avihepadnavirus is a genus of the Hepadnaviridae family. It primarily infects birds, including species of duck, geese, cranes, storks, and herons etc. To understand the genetic relatedness and evolutionary diversity among avihepadnavirus strains, a comprehensive analysis of the available 136 full-length viral genomes (n = 136) was conducted. The genomes were classified into two major genotypes, i.e., GI and GII. GI viruses were further classified into 8 sub-genotypes including DHBV-I (duck hepatitis B virus-I), DHBV-II (Snow goose Hepatitis B, SGHBV), DHBV-III, RGHBV (rossgoose hepatitis B virus), CHBV (crane hepatitis B virus), THBV (Tinamou hepatitis B virus), STHBV (stork hepatitis B virus), and HHBV (Heron hepatitis B virus). DHBV-I contains two sub-clades DHBV-Ia and DHBV-Ib. Parrot hepatitis B virus (PHBV) stains fall into GII which appeared as a separate phylogenetic branch/clade. All the subtypes of viruses in GI and GII seem to be genetically connected with viruses of DHBV-I by multiple mutational steps in phylogeographic analysis. Furthermore, 16 potential recombination events among different sub-genotypes in GI and one in GII were identified, but none of which is inter-genotypic between GI and GII. Overall, the results provide a whole picture of the genetic relatedness of avihepadnavirus strains, which may assist in the surveillance of virus spreading.

Evolutionary History and Genetic Variation of Zika Virus: Connection Between Thailand Zika Viruses and Global Outbreaks Strains.

Background: Zika virus (ZIKV) has significant potential to cause future outbreaks due to insufficient countermeasures. The evolution of ZIKV in Southeast Asian countries remains poorly understood. Materials and Methods: The phylogenetic, phylogeographic network, and recombination analyses of 366 ZIKV complete genome sequences identified between 1947 and 2021 were performed and the amino acid variation landscape was determined to reveal the evolutionary characteristics. Results: ZIKV falls into two major genogroups: GI and GII, segregated into further subgenogroups (GI-1 to GI-3) and (GII-1 to GII-3), respectively. Importantly, Thailand strains cluster with Southeast Asian outbreak strains (Singapore 2016, the Philippines 2012, Cambodia 2010) into GII-2 and form a lineage independent of French Polynesia and the Americas large outbreak strains. Thailand ZIKV strains shared their ancestral route to the strains from French Polynesia, which further connects to Brazil ZIKV through a short mutational branch. Both recombination and specific mutations may contribute to the emergence of new virus lineage in Thailand. Conclusion: This report provides insights into the evolutionary characteristics of ZIKV in Southeast Asia, which may be helpful for epidemiological investigation, vaccine development, and surveillance of the virus.

Insights into the genetic characteristics, clustering patterns, and phylogeographic dynamics of the JC polyomavirus, 1993 to 2023.

The human JC polyomavirus (JCV) is a widespread, neurotropic, opportunistic pathogen responsible for progressive multifocal leukoencephalopathy (PML) as well as other diseases in immunosuppressed individuals, including granule cell neuronopathy, JCV-associated nephropathy, encephalitis, and meningitis in rare cases. JCV classification is still unclear, where the ICTV (International Committee on Taxonomy of Viruses) has grouped all the strains into human polyomavirus 2, with no classification on clade and subclade levels. Therefore, JCV strains were previously classified using different genomic regions, e.g., full-length, VP1, and the V-T intergenic region etc., and the strains were grouped into several types related to various geographic locations and human ethnicities. However, neither of these classifications and nomenclature contemplates all the groups described so far. Herein, we evaluated all the available full-length coding genomes, VP1, and large T antigen nucleotide sequences of JCV reported during 1993-2023 and classified them into four major phylogenetic clades, i.e., GI-GIV, where GI is further grouped into two types GI.1 and GI.2 with five sub-clades each (GI.1/GI.2 a-e), GII into three (GII a-c), GIII as a separate clade, and GIV into seven sub-clades (GIV a-g). Similarly, the phylogeographic network analysis indicated four major clusters corresponding to GI-GIV clades, each with multiple subclusters and mutational sub-branches corresponding to the subclades. GI and GIV clusters are connected via GI.1-e reported from Europe and America, GII, GIII and GIV clusters are connected by GII-b and GII-c strains reported from Africa, while GIV cluster strains are connected to the Russia-Italy JCV haplotype. Furthermore, we identified JCV-variant-GS/B-Germany-1997 (GenBank ID: AF004350.1) as an inter-genotype recombinant having major and minor parents in the GI.1-e and GII-a clades, respectively. Additionally, the amino acid variability analysis revealed high entropy across all proteins. The large T antigen exhibited the highest variability, while the small t antigen showed the lowest variability. Our phylogenetic and phylogeographic analyses provide a new approach to genotyping and sub-genotyping and present a comprehensive classification system of JCV strains based on their genetic characteristics and geographic distribution, while the genetic recombination and amino acid variability can help identify pathogenicity and develop effective preventive and control measures against JCV infections.

Genetic Characteristics and Phylogeographic Dynamics of Echovirus.

Echoviruses belong to the genus Enterovirus in the Picornaviridae family, forming a large group of Enterovirus B (EV-B) within the Enteroviruses. Previously, Echoviruses were classified based on the coding sequence of VP1. In this study, we performed a reliable phylogenetic classification of 277 sequences isolated from 1992 to 2019 based on the full-length genomes of Echovirus. In this report, phylogenetic, phylogeographic, recombination, and amino acid variability landscape analyses were performed to reveal the evolutional characteristics of Echovirus worldwide. Echoviruses were clustered into nine major clades, e.g., G1-G9. Phylogeographic analysis showed that branches G2-G9 were linked to common strains, while the branch G1 was only linked to G5. In contrast, strains E12, E14, and E16 clustered separately from their G3 and G7 clades respectively, and became a separate branch. In addition, we identified a total of 93 recombination events, where most of the events occurred within the VP1-VP4 coding regions. Analysis of amino acid variation showed high variability in the a positions of VP2, VP1, and VP3. This study updates the phylogenetic and phylogeographic information of Echovirus and indicates that extensive recombination and significant amino acid variation in the capsid proteins drove the emergence of new strains.

Duck hepatitis a virus: Full-length genome-based phylogenetic and phylogeographic view during 1986-2020.

Duck hepatitis A virus (DHAV) is one of key pathogens for duck viral hepatitis, especially in Asian duck industry. Currently, two main genotypes (DHAV-1 and -3) exist. To explore insightfully the evolutionary character, we assessed the available 141 full-length genome sequences of DHAV isolated in 1986-2020 globally and divided DHAV-1 and DHAV-3 into further seven (DHAV-1 a-g) and five (DHAV-3 a-e) sub-clades, respectively. Phylogenetic and phylogeographic network analyses indicated great genetic diversity of DHAV identified in China, where the DHAV-1 cluster and DHAV-3 cluster were linked by virus strain HDHV1-BJ (GenBank ID: FJ157172.1) and Du_CH_LSD_090612 (GenBank ID: JF828995.1) via a long mutational branch and intermediate strains. Several strains previously identified as DHAV-1 according to the partial gene sequences were actually clustered within DHAV-3 in full-length genome-based analysis. Furthermore, we identified 32 recombination events across virus genome with the recombination hotspot at the 5' end and upstream of the capsid coding region. The highest variability of DHAV polyprotein was shown at the upstream region of the N terminus P-loop region, e.g., amino acids 672-716, followed by the aa 334-359 in the Capsid encoding region. The results presented here provides a robust insight into the genetic exchange patterns of DHAV genomes during the past decades, which may be used to map the evolutionary history and facilitate preventive measures of DHAVs.

Genetic Characteristics and Phylogeographic Dynamics of Lagoviruses, 1988-2021.

Rabbit haemorrhagic disease virus (RHDV), European brown hare syndrome virus (EBHSV), rabbit calicivirus (RCV), and hare calicivirus (HaCV) belong to the genus Lagovirus of the Caliciviridae family that causes severe diseases in rabbits and several hare (Lepus) species. Previously, Lagoviruses were classified into two genogroups, e.g., GI (RHDVs and RCVs) and GII (EBHSV and HaCV) based on partial genomes, e.g., VP60 coding sequences. Herein, we provide a robust phylogenetic classification of all the Lagovirus strains based on full-length genomes, grouping all the available 240 strains identified between 1988 and 2021 into four distinct clades, e.g., GI.1 (classical RHDV), GI.2 (RHDV2), HaCV/EBHSV, and RCV, where the GI.1 clade is further classified into four (GI.1a-d) and GI.2 into six sub-clades (GI.2a-f). Moreover, the phylogeographic analysis revealed that the EBHSV and HaCV strains share their ancestor with the GI.1, while the RCV shares with the GI.2. In addition, all 2020-2021 RHDV2 outbreak strains in the USA are connected to the strains from Canada and Germany, while RHDV strains isolated in Australia are connected with the USA-Germany haplotype RHDV strain. Furthermore, we identified six recombination events in the VP60, VP10, and RNA-dependent RNA polymerase (RdRp) coding regions using the full-length genomes. The amino acid variability analysis showed that the variability index exceeded the threshold of 1.00 in the ORF1-encoded polyprotein and ORF2-encoded VP10 protein, respectively, indicating significant amino acid drift with the emergence of new strains. The current study is an update of the phylogenetic and phylogeographic information of Lagoviruses that may be used to map the evolutionary history and provide hints for the genetic basis of their emergence and re-emergence.

The phylogenetic and phylogeographic landscape of the beak and feather disease virus, 1996-2022.

The beak and feather disease virus (BFDV), causative agent of Psittacine beak and feather disease (PBFD), is a highly fatal and widespread virus that infects both the wild and captive Psittaciformes around the world. The BFDV genome is a ssDNA of approximately 2 kb in size, making it among the smallest known pathogenic viruses. Though, the virus is placed in Circoviridae family of the Circovirus genus, there is no classification system on clade and sub-clade level according to the International Committee on Taxonomy of Viruses and the strains are grouped on the bases of geographic locations. Thus, we provide the latest and robust phylogenetic classification of BFDVs in this study based on full-length genomic sequences, grouping all the available 454 strains detected during 1996-2022 into two distinct clades, e.g., GI and GII. The GI clade is further divided into six sub-clades (GI a-f), while GII into two sub-clades (GII a and b). In addition, the phylogeographic network identified high variability among the BFDV strains, showing several branches, where all the branches are connected to four strains, e.g., BFDV-ZA-PGM-70A(GenBank ID: HM748921.1, 2008-South Africa), BFDV-ZA-PGM-81A(GenBank ID: JX221009.1, 2008-South Africa), BFDV14(GenBank ID: GU015021.1, 2010-Thailand) and BFDV-isolate-9IT11(GenBank ID: KF723390.1, 2014-Italy). Furthermore, we identified 27 recombination events in the rep (replication-associated protein) and cap (capsid protein) coding regions using the complete genomes of BFDVs. Similarly, the amino acids variability analysis indicated that both the rep and cap regions are highly variable with values exceeding the variability coefficient estimation limit of 1.00, speculating the possible amino acids drift with the emergence of new strains. The findings provided in this study may offer the latest phylogenetic, phylogeographic and evolutionary landscape of the BFDVs.

Genetic diversity, distribution, and evolution of chicken anemia virus: A comparative genomic and phylogenetic analysis.

Chicken infectious anemia (CIA) is an immunosuppressive poultry disease that causes aplastic anemia, immunosuppression, growth retardation and lymphoid tissue atrophy in young chickens and is responsible for huge economic losses to the poultry industry worldwide. The disease is caused by the chicken anemia virus (CAV), which belongs to the genus Gyrovirus, family Anelloviridae. Herein, we analyzed the full-length genomes of 243 available CAV strains isolated during 1991-2020 and classified them into two major clades, GI and GII, divided into three and four sub-clades, GI a-c, and GII a-d, respectively. Moreover, the phylogeographic analysis revealed that the CAVs spread from Japan to China, China to Egypt and subsequently to other countries, following multiple mutational steps. In addition, we identified eleven recombination events within the coding and non-coding regions of CAV genomes, where the strains isolated in China were the most active and involved in ten of these events. Furthermore, the amino acids variability analysis indicated that the variability coefficient exceeded the estimation limit of 1.00 in VP1, VP2, and VP3 proteins coding regions, demonstrating substantial amino acid drift with the rise of new strains. The current study offers robust insights into the phylogenetic, phylogeographic and genetic diversity characteristics of CAV genomes that may provide valuable data to map the evolutionary history and facilitate preventive measures of CAVs.

Multiple potential recombination events among Newcastle disease virus genomes in China between 1946 and 2020.

Introduction: Newcastle Disease Virus (NDV) is a highly adaptable virus with large genetic diversity that has been widely studied for its oncolytic activities and potential as a vector vaccine. This study investigated the molecular characteristics of 517 complete NDV strains collected from 26 provinces across China between 1946-2020. Methods: Herein, phylogenetic, phylogeographic network, recombination, and amino acid variability analyses were performed to reveal the evolutionary characteristics of NDV in China. Results and discussions: Phylogenetic analysis revealed the existence of two major groups: GI, which comprises a single genotype Ib, and GII group encompassing eight genotypes (I, II, III, VI. VII. VIII, IX and XII). The Ib genotype is found to dominate China (34%), particularly South and East China, followed by VII (24%) and VI (22%). NDV strains from the two identified groups exhibited great dissimilarities at the nucleotide level of phosphoprotein (P), matrix protein (M), fusion protein (F), and haemagglutinin-neuraminidase (HN) genes. Consistently, the phylogeographic network analysis revealed two main Network Clusters linked to a possible ancestral node from Hunan (strain MH289846.1). Importantly, we identified 34 potential recombination events that involved mostly strains from VII and Ib genotypes. A recombinant of genotype XII isolated in 2019 seems to emerge newly in Southern China. Further, the vaccine strains are found to be highly involved in potential recombination. Therefore, since the influence of recombination on NDV virulence cannot be predicted, this report's findings need to be considered for the security of NDV oncolytic application and the safety of NDV live attenuated vaccines.

THP-1 cell line model for tuberculosis: A platform for in vitro macrophage manipulation.

Macrophages are large mononuclear phagocytic cells that play a vital role in the immune response. They are present in all body tissues with extremely heterogeneous and plastic phenotypes that adapt to the organs and tissues in which they live and respond in the first-line against invading microorganisms. Tuberculosis (TB) is caused by the pathogenic bacteria Mycobacterium tuberculosis (Mtb), which is among the top 10 global infectious agents and the leading cause of mortality, ranking above human immunodeficiency virus (HIV), as a single infectious agent. Macrophages, upon Mtb infection, not only phagocytose the bacteria and present the antigens to T-cells, but also react rapidly by developing antimycobacterial immune response depending highly on the production of cytokines. However, Mtb is also capable of intracellular survival in instances of sub-optimal activation of macrophages. Hence, several systems have been established to evaluate the Mtb-macrophage interaction, where the THP-1 monocytes have been developed as an attractive model for in vitro polarized monocyte-derived macrophages. This model is extensively used for Mtb as well as other intracellular bacterial studies. Herein, we have summarized the updated implications of the THP-1 model for TB-related studies and discussed the pros and cons compared to other cell models of TB.

Bovine viral diarrhea virus in China: A comparative genomic and phylogenetic analysis with complete genome sequences.

Bovine viral diarrhea virus (BVDV), causing bovine viral diarrhea (BVD) in cattle, is one of the highly contagious and devastating diseases of cattle. Since 1980, BVDV has been identified all-over China in a variety of animal species including cattle, camels, yaks, sheep, water buffalo, goats, Sika deer and pigs. In this study, 31 BVDV complete genomes reported in China (from 2004 to 2020) with other 112 genomes reported around the world were comparatively analyzed. Phylogenetic analysis shows that BVDV genomes reported worldwide clustered in three major clades i.e., BVDV-1, BVDV-2, and BVDV-3. The BVDV-1 is genetically the most diverged genotype and phylogenetically classified into 7 sub-clades in our study based on full-length genomes. The China BVDV genomes fall into all three major clades, e.g., BVDV-1, BVDV-2 and BVDV-3. China BVDV-1 clustered into five sub-clades, e.g., 1, 2, 3, 6 and 7, where sub-clade 7 clustered as a separate sub-clade. Full-length genome recombination analysis reveals that the BVDV-1 reported in China appears to be mainly involved in recombination events. In addition, comparative analysis of E2 proteins between BVDV-1, BVDV-2, and BVDV-3 reveals that the amino acid variations could affect 12 potential linear B cell epitopes, demonstrating a dramatic antigen drift in the E2 protein. These results provide a thorough view of the information about the genetic and antigenic diversity of BVDVs circulating in China and therefore could benefit the development of suitable strategies for disease control.