A5033703745- Influenza Virus Research Studies
- SARS-CoV-2 and COVID-19 Research
- Animal Disease Management and Epidemiology
- Animal Virus Infections Studies
- Viral Infections and Vectors
- Genomics and Phylogenetic Studies
- Respiratory viral infections research
- Viral gastroenteritis research and epidemiology
- COVID-19 epidemiological studies
- Mosquito-borne diseases and control
- Plant Virus Research Studies
- Vector-borne infectious diseases
- Virology and Viral Diseases
- Viral Infections and Immunology Research
- COVID-19 Clinical Research Studies
- RNA and protein synthesis mechanisms
- SARS-CoV-2 detection and testing
- Gut microbiota and health
- Insect symbiosis and bacterial influences
- Zoonotic diseases and public health
- Identification and Quantification in Food
- Antibiotic Resistance in Bacteria
- Viral Infections and Outbreaks Research
- Clostridium difficile and Clostridium perfringens research
- Virus-based gene therapy research
University of Hong Kong
2016-2025
Laboratory of Data Discovery for Health
2021-2025
HKU-Pasteur Research Pole
2022-2025
Hong Kong Science and Technology Parks Corporation
2021-2025
Shantou University Medical College
2011-2024
Shantou University
2012-2024
City University of Hong Kong, Shenzhen Research Institute
2024
University of Edinburgh
2013-2024
Istituto Zooprofilattico Sperimentale delle Venezie
2024
China Agricultural University
2024
The initial cases of novel coronavirus (2019-nCoV)-infected pneumonia (NCIP) occurred in Wuhan, Hubei Province, China, December 2019 and January 2020. We analyzed data on the first 425 confirmed Wuhan to determine epidemiologic characteristics NCIP.We collected information demographic characteristics, exposure history, illness timelines laboratory-confirmed NCIP that had been reported by 22, described estimated key time-delay distributions. In early period exponential growth, we epidemic...
Summary We present an r package, ggtree , which provides programmable visualization and annotation of phylogenetic trees. can read more tree file formats than other softwares, including newick nexus NHX phylip jplace formats, support phylo, multiphylo, phylo4, phylo4d, obkdata phyloseq objects defined in packages. It also extract the tree/branch/node‐specific data from analysis outputs beast epa hyphy paml phylodog pplacer r8s raxml revbayes software, allows using these to annotate tree. The...
The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This has been tentatively seafood market Wuhan, China, where sale wild animals may be source zoonotic infection2. Although bats are probable reservoir hosts for SARS-CoV-2, identity any intermediate host that have facilitated transfer to humans unknown. Here we report identification SARS-CoV-2-related coronaviruses Malayan pangolins (Manis javanica) seized anti-smuggling...
Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the question undergo measurable amounts evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common several fields biology, most notably epidemiology rapidly evolving viruses. Here we introduce cross-platform software tool, TempEst (formerly known as Path-O-Gen), for...
Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The contigs (2.25 gigabases (Gb)) cover approximately 94% whole genome, remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats tandem repeats. Comparisons with dog human showed that genome has lower divergence rate. assessment genes potentially underlying some its unique traits indicated bamboo diet might be more dependent on gut microbiome...
Two new SARS-CoV-2 lineages with the N501Y mutation in receptor-binding domain of spike protein spread rapidly United Kingdom. We estimated that earlier 501Y lineage without amino acid deletion Δ69/Δ70, circulating mainly between early September and mid-November, was 10% (6–13%) more transmissible than 501N lineage, since late September, 75% (70–80%) lineage.
Ggtree is a comprehensive R package for visualizing and annotating phylogenetic trees with associated data. It can also map visualize external data on phylogenies two general methods. Method 1 allows to be mapped the tree structure used as visual characteristic in visualization. 2 plots side by using different geometric functions after reordering based structure. These methods integrate phylogeny further exploration comparison evolutionary biology context. available from...
Phylogenetic trees and data are often stored in incompatible inconsistent formats. The outputs of software tools that contain with analysis findings not compatible each other, making it hard to integrate the results different analyses a comparative study. treeio package is designed connect phylogenetic tree input output. It supports extracting as well commonly used analytical software. can link external phylogenies merge obtained from sources, enabling phylogeny-associated disciplines an...
Coronaviruses in the Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe acute illness and kills about a third of people infected. The virus is common dromedary camels, which can be source human infections. In survey for MERSCoV over 1300 Saudi Arabian Sabir et al. found that dromedaries share three species with humans. Diverse MERS lineages camels have caused infections, suggests transfer among host occurs quite easily. Haagmans made MERS-CoV vaccine use using poxvirus as...
Type 2 (or North American-like) porcine reproductive and respiratory syndrome virus (PRRSV) was first recorded in 1987 the United States now occurs most commercial swine industries throughout world. In this study, we investigated epidemiological evolutionary behaviors of type PRRSV. Based on phylogenetic analyses 8,624 ORF5 sequences, described a comprehensive picture diversity PRRSVs systematically classified all available sequences into lineages sublineages, including number previously...
Background The human gut microbiota has profound influence on host metabolism and immunity. This study characterized the fecal in patients with nonalcoholic steatohepatitis (NASH). relationship between changes hepatic steatosis was also studied. Methods Fecal of histology-proven NASH healthy controls analyzed by 16S ribosomal RNA pyrosequencing. were from a previously reported randomized trial probiotic treatment. Proton-magnetic resonance spectroscopy performed to monitor intrahepatic...
Abstract While phylogenetic trees and associated data have been getting easier to generate, it has difficult reuse, combine, synthesize the information they provided, because published are often only available as image files stored in incompatible formats. To increase reproducibility reusability of data, ggtree object was designed for storing tree well visualization directives. The itself is a graphic can be rendered static image. More importantly, input that used extracted from object,...
Abstract The ongoing outbreak of viral pneumonia in China and beyond is associated with a novel coronavirus, provisionally termed 2019-nCoV. This has been tentatively seafood market Wuhan, China, where the sale wild animals may be source zoonotic infection. Although bats are likely reservoir hosts for 2019-nCoV, identity any intermediate host facilitating transfer to humans unknown. Here, we report identification 2019-nCoV related coronaviruses pangolins ( Manis javanica ) seized...
The identification of the conserved and variable regions in multiple sequence alignment (MSA) is critical to accelerating process understanding function genes. MSA visualizations allow us transform features into understandable visual representations. As sequence-structure-function relationship gains increasing attention molecular biology studies, simple display nucleotide or protein not satisfied. A more scalable visualization required broaden scope investigation. Here we present ggmsa, an R...
Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys human and animal under "One-Health" framework. However, there are substantial challenges comparing synthesizing results multiple studies that employ different test methods approaches bioinformatic analysis. In this article, we consider commonly used quantification units (ARG copy per cell, ARG genome, density, 16S rRNA gene, RPKM, coverage, PPM, etc.) for...
Abstract The increasing prevalence and expanding distribution of tick-borne viruses globally have raised health concerns, but the full repertoire tick virome has not been assessed. We sequenced meta-transcriptomes 31 different species in Ixodidae Argasidae families from across mainland China, identified 724 RNA with distinctive compositions among genera. A total 1,801 assembled complete or nearly viral genomes revealed an extensive diversity genome architectures tick-associated viruses,...
Bats have been identified as the natural reservoir of severe acute respiratory syndrome (SARS)-like and SARS coronaviruses (SLCoV SCoV). However, previous studies suggested that none currently sampled bat SLCoVs is descendant direct ancestor SCoV, based on their relatively distant phylogenetic relationship. In this study, evidence recombinant origin genome a SLCoV demonstrated. We potential recombination breakpoint immediately after consensus intergenic sequence between open reading frame 1...
Human enterovirus 71 (EV-71) is one of the major etiologic causes hand, foot, and mouth disease (HFMD) among young children worldwide, with fatal instances neurological complications becoming increasingly common. Global VP1 capsid sequences (n = 628) sampled over 4 decades were collected subjected to comprehensive evolutionary analysis using a suite phylogenetic population genetic methods. We estimated that common ancestor human EV-71 likely emerged around 1941 (95% confidence interval [CI],...
Objectives: We sought to comprehensively analyze the origin, transmission patterns and sub-epidemic clusters of HIV-1 CRF01_AE strains in China. Methods: Available samples indentified national molecular epidemiologic surveys were used generate near full-length genome (NFLG) sequences. The new globally available NFLG sequences subjected phylogenetic Bayesian clock analyses, combined with data elucidate history Results: generated 75 from various risk populations covering all major epidemic...