ORCID Profile
0000-0001-7218-429X
Current Organisation
City University of Hong Kong
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Publisher: Wiley
Date: 11-05-2012
Publisher: MDPI AG
Date: 12-05-2022
DOI: 10.20944/PREPRINTS202205.0157.V1
Abstract: Feline panleukopenia (FPL), a highly contagious and frequently fatal disease of cats, is caused by Feline parvovirus (FPV) and Canine parvovirus (CPV). We characterized the ersity of these Carnivore protoparvovirus 1 variants in 18 faecal s les collected from domestic cats with FPL during an outbreak, using targeted parvoviral DNA metagenomics to a mean depth of & ,000 X coverage per site. All s les comprised FPV alone. Compared to the reference FPV genome, isolated in 1967, 44 mutations were detected. Ten of these were non-synonymous, including 9 in non-structural genes and one in VP1/VP2 (Val232Ile), which was the only one to exhibit inter-host ersity, being present in five sequences. There were five other polymorphic nucleotide positions, all with synonymous mutations. Intra-host ersity at all polymorphic positions was low with sub-consensus variant frequencies (SVF) of & % except for two positions (2108 and 3208) in two s les with SVF of 1.1 & ndash 1.3%. Intra-host nucleotide ersity was measured across the whole genome (0.7 - 1.5%) and for each gene, and was highest in the NS2 gene of four s les (1.2 & ndash 1.9%). Overall, intra-host viral genetic ersity was limited and most mutations observed were synonymous, indicative of a low background mutation rate and strong selective constraints.
Publisher: MDPI AG
Date: 12-11-2020
DOI: 10.3390/V12111301
Abstract: Astroviruses, isolated from numerous avian and mammalian species including humans, are commonly associated with enteritis and encephalitis. Two astroviruses have previously been identified in cats, and while definitive evidence is lacking, an association with enteritis is suggested. Using metagenomic next-generation sequencing of viral nucleic acids from faecal s les, we identified two novel feline astroviruses termed Feline astrovirus 3 and 4. These viruses were isolated from healthy shelter-housed kittens (Feline astrovirus 3 6448 bp) and from a kitten with diarrhoea that was co-infected with Feline parvovirus (Feline astrovirus 4, 6549 bp). Both novel astroviruses shared a genome arrangement of three open reading frames (ORFs) comparable to that of other astroviruses. Phylogenetic analysis of the concatenated ORFs, ORF1a, ORF1b and capsid protein revealed that both viruses were phylogenetically distinct from other feline astroviruses, although their precise evolutionary history could not be accurately determined due to a lack of resolution at key nodes. Large-scale molecular surveillance studies of healthy and diseased cats are needed to determine the pathogenicity of feline astroviruses as single virus infections or in co-infections with other enteric viruses.
Publisher: Research Square Platform LLC
Date: 23-11-2022
DOI: 10.21203/RS.3.RS-2301793/V1
Abstract: Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the ersity and abundance of viruses within bats at the level of in idual animals, and hence the frequency of virus co-infection and inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised the mammalian associated viruses present in 149 in idual bats s led from Yunnan province, China. This revealed a high frequency of virus co-infection and species spillover among the animals studied, with 12 viruses shared among different bat species, which in turn facilitates virus recombination and reassortment. Of note, we identified five viral species that are likely to be pathogenic to humans or livestock, including a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV-2 and SARS-CoV, with only five amino acid differences between its receptor-binding domain sequence and that of the earliest sequences of SARS-CoV-2. Functional analysis predicts that this recombinant coronavirus can utilize the human ACE2 receptor such that it is likely to be of high zoonotic risk. Our study highlights the common occurrence of inter-species transmission and co-infection of bat viruses, as well as their implications for virus emergence.
Publisher: Elsevier BV
Date: 08-2013
DOI: 10.1016/J.MEEGID.2013.03.015
Abstract: Recombination plays an important role in shaping the genetic ersity of a number of DNA and RNA viruses. Although some recent studies have reported bioinformatic evidence of mosaic sequences in a variety of influenza A viruses, it remains controversial as to whether these represent bona fide natural recombination events or laboratory artifacts. Importantly, mosaic genome structures can create significant topological incongruence during phylogenetic analyses, which can mislead additional phylogeny-based molecular evolutionary analyses such as molecular clock dating, the detection of selection pressures and phylogeographic inference. As a result, there is a strong need for systematic screenings for mosaic structures within the influenza virus genome database. We used a combination of sequence-based and phylogeny-based methods to identify 388 mosaic influenza genomic segments, of which 332 are previously unreported and are significantly supported by phylogenetic methods. It is impossible, however, to ascertain whether these represent natural recombinants. To facilitate the future identification of recombinants, reference sets of non-recombinant sequences were selected for use in an automatic screening protocol for detecting mosaic sequences. Tests using real and simulated mosaic sequences indicate that our screening protocol is both sensitive (average >90%) and accurate (average >77%) enough to identify a range of different mosaic patterns. The relatively high prevalence of mosaic influenza virus sequences implies that efficient systematic screens, such as that proposed here, should be performed routinely to detect natural recombinant strains, potential laboratory artifacts, and sequencing contaminants either prior to sequences being deposited in GenBank or before they are used for phylogenetic analyses.
Publisher: American Society for Microbiology
Date: 31-08-2021
DOI: 10.1128/MSYSTEMS.00510-21
Abstract: Despite the clinical importance of urinary diseases in cats, the presence of resident urine microbes has not been demonstrated in cats, and the role of these microbes as a community in urinary health remains unknown. Here, we have shown that cats with and without urinary tract disease harbor unique microbial communities in their urine.
Publisher: Springer Science and Business Media LLC
Date: 10-07-2023
DOI: 10.1038/S41467-023-39835-1
Abstract: Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the ersity and abundance of viruses within in idual bats, and hence the frequency of virus co-infection and spillover among them. We characterize the mammal-associated viruses in 149 in idual bats s led from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high frequency of virus co-infection (simultaneous infection of bat in iduals by multiple viral species) and spillover among the animals studied, which may in turn facilitate virus recombination and reassortment. Of note, we identify five viral species that are likely to be pathogenic to humans or livestock, based on phylogenetic relatedness to known pathogens or in vitro receptor binding assays. This includes a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV and SARS-CoV-2. In vitro assays indicate that this recombinant virus can utilize the human ACE2 receptor such that it is likely to be of increased emergence risk. Our study highlights the common occurrence of co-infection and spillover of bat viruses and their implications for virus emergence.
Publisher: Springer Science and Business Media LLC
Date: 07-12-2022
DOI: 10.1038/S41598-022-25808-9
Abstract: The inner ear controls hearing and balance, while the temporal molecular signatures and transcriptional regulatory dynamics underlying its development are still unclear. In this study, we investigated time-series transcriptome in the mouse inner ear from embryonic day 11.5 (E11.5) to postnatal day 7 (P7) using bulk RNA-Seq. A total of 10,822 differentially expressed genes were identified between pairwise stages. We identified nine significant temporal expression profiles using time-series expression analysis. The constantly down-regulated profiles throughout the development are related to DNA activity and neurosensory development, while the constantly upregulated profiles are related to collagen and extracellular matrix. Further co-expression network analysis revealed that several hub genes, such as Pnoc, Cd9, and Krt27, are related to the neurosensory development, cell adhesion, and keratinization. We uncovered three important transcription regulatory paths during mice inner ear development. Transcription factors related to Hippo/TGFβ signaling induced decreased expressions of genes related to the neurosensory and inner ear development, while a series of INF genes activated the expressions of genes in immunoregulation. In addition to deepening our understanding of the temporal and regulatory mechanisms of inner ear development, our transcriptomic data could fuel future multi-species comparative studies and elucidate the evolutionary trajectory of auditory development.
Publisher: Elsevier BV
Date: 03-2022
DOI: 10.1016/J.CELL.2022.02.014
Abstract: Game animals are wildlife species traded and consumed as food and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1,941 game animals, representing 18 species and five mammalian orders, s led across China. From this, we identified 102 mammalian-infecting viruses, with 65 described for the first time. Twenty-one viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high-risk viruses. We inferred the transmission of bat-associated coronavirus from bats to civets, as well as cross-species jumps of coronaviruses from bats to hedgehogs, from birds to porcupines, and from dogs to raccoon dogs. Of note, we identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.
Publisher: Springer Science and Business Media LLC
Date: 23-11-2016
DOI: 10.1038/NATURE20167
Abstract: Current knowledge of RNA virus bio ersity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the transcriptomes of over 220 invertebrate species s led across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently ergent to comprise new families. The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co- ergence. The invertebrate virome also reveals remarkable genomic flexibility that includes frequent recombination, lateral gene transfer among viruses and hosts, gene gain and loss, and complex genomic rearrangements. Together, these data present a view of the RNA virosphere that is more phylogenetically and genomically erse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution.
Publisher: Hindawi Limited
Date: 10-07-2022
DOI: 10.1111/TBED.14646
Abstract: Feline panleukopenia (FPL) is a severe, often fatal disease caused by feline panleukopenia virus (FPV). How infection with FPV might impact the composition of the entire eukaryotic enteric virome in cats has not been characterized. We used meta-transcriptomic and viral particle enrichment metagenomic approaches to characterize the enteric viromes of 23 cats naturally infected with FPV (FPV-cases) and 36 age-matched healthy shelter cats (healthy controls). Sequencing reads from mammalian infecting viral families largely belonged to the Coronaviridae, Parvoviridae and Astroviridae. The most abundant viruses among the healthy control cats were feline coronavirus, Mamastrovirus 2 and Carnivore bocaparvovirus 3 (feline bocavirus), with frequent coinfections of all three. Feline chaphamaparvovirus was only detected in healthy controls (6 out of 36, 16.7%). Among the FPV-cases, in addition to FPV, the most abundant viruses were Mamastrovirus 2, feline coronavirus and C. bocaparvovirus 4 (feline bocaparvovirus 2). The latter and feline bocaparvovirus 3 were detected significantly more frequently in FPV-cases than in healthy controls. Feline calicivirus was present in a higher proportion of FPV-cases (11 out of 23, 47.8%) compared to healthy controls (5 out of 36, 13.9%, p = 0.0067). Feline kobuvirus infections were also common among FPV-cases (9 out of 23, 39.1%) and were not detected in any healthy controls (p < .0001). While abundant in both groups, astroviruses were more frequently present in FPV-cases (19 out of 23, 82.6%) than in healthy controls (18 out of 36, p = .0142). The differences in eukaryotic virome composition revealed here indicate that further investigations are warranted to determine associations between enteric viral co-infections on clinical disease severity in cats with FPL.
Publisher: MDPI AG
Date: 28-06-2022
DOI: 10.3390/V14071412
Abstract: Feline panleukopenia (FPL), a highly contagious and frequently fatal disease of cats, is caused by Feline parvovirus (FPV) and Canine parvovirus (CPV). We characterised the ersity of these Carnivore protoparvovirus 1 variants in 18 faecal s les collected from domestic cats with FPL during an outbreak, using targeted parvoviral DNA metagenomics to a mean depth of ,000 × coverage per site. All s les comprised FPV alone. Compared with the reference FPV genome, isolated in 1967, 44 mutations were detected. Ten of these were nonsynonymous, including 9 in nonstructural genes and one in VP1/VP2 (Val232Ile), which was the only one to exhibit interhost ersity, being present in five sequences. There were five other polymorphic nucleotide positions, all with synonymous mutations. Intrahost ersity at all polymorphic positions was low, with subconsensus variant frequencies (SVF) of % except for two positions (2108 and 3208) in two s les with SVF of 1.1–1.3%. Intrahost nucleotide ersity was measured across the whole genome (0.7–1.5%) and for each gene and was highest in the NS2 gene of four s les (1.2–1.9%). Overall, intrahost viral genetic ersity was limited and most mutations observed were synonymous, indicative of a low background mutation rate and strong selective constraints.
Publisher: Elsevier BV
Date: 07-2022
Publisher: American Society for Microbiology
Date: 09-2010
DOI: 10.1128/JVI.02551-09
Abstract: Type 2 (or North American-like) porcine reproductive and respiratory syndrome virus (PRRSV) was first recorded in 1987 in the United States and now occurs in most commercial swine industries throughout the world. In this study, we investigated the epidemiological and evolutionary behaviors of type 2 PRRSV. Based on phylogenetic analyses of 8,624 ORF5 sequences, we described a comprehensive picture of the ersity of type 2 PRRSVs and systematically classified all available sequences into lineages and sublineages, including a number of previously undescribed lineages. With the rapid growth of sequence deposition into the databases, it would be technically difficult for veterinary researchers to genotype their sequences by reanalyzing all sequences in the databases. To this end, a set of reference sequences was established based on our classification system, which represents the principal ersity of all available sequences and can readily be used for further genotyping studies. In addition, we further investigated the demographic histories of these lineages and sublineages by using Bayesian coalescence analyses, providing evolutionary insights into several important epidemiological events of type 2 PRRSV. Moreover, by using a phylogeographic approach, we were able to estimate the transmission frequencies between the pig-producing states in the United States and identified several states as the major sources of viral spread, i.e., “transmission centers.” In summary, this study represents the most extensive phylogenetic analyses of type 2 PRRSV to date, providing a basis for future genotyping studies and dissecting the epidemiology of type 2 PRRSV from phylogenetic perspectives.
Publisher: Elsevier BV
Date: 08-2011
DOI: 10.1016/J.VETMIC.2011.04.014
Abstract: Complete genomes of four Newcastle disease virus (NDV) strains, isolated from ducks and wild birds in Guangdong province of China from 2003 to 2007, were sequenced and analyzed in this study. Pathogenicity tests in chicken embryos and chickens illustrate that D3 and R8 are lentogenic, and W4 and P4 are mesogenic strains. Phylogenetic analysis using all six genes provides a high resolution profile for genotype designation as genotype I for D3 and R8 strains and genotype VI for W4 and P4 strains. In addition, molecular dating based on different genes suggests that D3 and R8 erged from their common ancestor at around 1998 W4 and P4 erged from their common ancestor at around 1999. Subsequent selective pressure analysis displayed specific traits of genes evolution in all 4 strains since their ergence from the recent common ancestor. Furthermore, the geographic origins of 4 strains were deduced to be from Europe via two independent introduction events by phylogeographical analysis. This provides insights to the potential influence of waterfowl migration on NDV epidemiology.
No related grants have been discovered for Jun Li.