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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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Zhang LN, Tan JT, Ng HY, Liao YS, Zhang RQ, Chan KH, Hung IFN, Lam TTY, Cheung KS. Association between Gut Microbiota Composition and Long-Term Vaccine Immunogenicity following Three Doses of CoronaVac. Vaccines (Basel) 2024; 12:365. [PMID: 38675747 PMCID: PMC11055114 DOI: 10.3390/vaccines12040365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Neutralizing antibody level wanes with time after COVID-19 vaccination. We aimed to study the relationship between baseline gut microbiota and immunogenicity after three doses of CoronaVac. METHODS This was a prospective cohort study recruiting three-dose CoronaVac recipients from two centers in Hong Kong. Blood samples were collected at baseline and one year post-first dose for virus microneutralization (vMN) assays to determine neutralization titers. The primary outcome was high immune response (defined as with vMN titer ≥ 40). Shotgun DNA metagenomic sequencing of baseline fecal samples identified potential bacterial species and metabolic pathways using Linear Discriminant Analysis Effect Size (LEfSe) analysis. Univariate and multivariable logistic regression models were used to identify high response predictors. RESULTS In total, 36 subjects were recruited (median age: 52.7 years [IQR: 47.9-56.4]; male: 14 [38.9%]), and 18 had low immune response at one year post-first dose vaccination. Eubacterium rectale (log10LDA score = 4.15, p = 0.001; relative abundance of 1.4% vs. 0, p = 0.002), Collinsella aerofaciens (log10LDA score = 3.31, p = 0.037; 0.39% vs. 0.18%, p = 0.038), and Streptococcus salivarius (log10LDA score = 2.79, p = 0.021; 0.05% vs. 0.02%, p = 0.022) were enriched in low responders. The aOR of high immune response with E. rectale, C. aerofaciens, and S. salivarius was 0.03 (95% CI: 9.56 × 10-4-0.32), 0.03 (95% CI: 4.47 × 10-4-0.59), and 10.19 (95% CI: 0.81-323.88), respectively. S. salivarius had a positive correlation with pathways enriched in high responders like incomplete reductive TCA cycle (log10LDA score = 2.23). C. aerofaciens similarly correlated with amino acid biosynthesis-related pathways. These pathways all showed anti-inflammation functions. CONCLUSION E. rectale,C. aerofaciens, and S. salivarius correlated with poorer long-term immunogenicity following three doses of CoronaVac.
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Affiliation(s)
- Li-Na Zhang
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Jing-Tong Tan
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Ho-Yu Ng
- School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Yun-Shi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong
- Centre for Immunology & Infection Limited, 17W Hong Kong Science & Technology Parks, Hong Kong
| | - Rui-Qi Zhang
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Kwok-Hung Chan
- Centre for Immunology & Infection Limited, 17W Hong Kong Science & Technology Parks, Hong Kong
| | - Ivan Fan-Ngai Hung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong
| | - Ka-Shing Cheung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
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Ye Y, Shum MH, Tsui JL, Yu G, Smith DK, Zhu H, Wu JT, Guan Y, Lam TTY. Robust expansion of phylogeny for fast-growing genome sequence data. PLoS Comput Biol 2024; 20:e1011871. [PMID: 38330139 PMCID: PMC10898724 DOI: 10.1371/journal.pcbi.1011871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/27/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
Massive sequencing of SARS-CoV-2 genomes has urged novel methods that employ existing phylogenies to add new samples efficiently instead of de novo inference. 'TIPars' was developed for such challenge integrating parsimony analysis with pre-computed ancestral sequences. It took about 21 seconds to insert 100 SARS-CoV-2 genomes into a 100k-taxa reference tree using 1.4 gigabytes. Benchmarking on four datasets, TIPars achieved the highest accuracy for phylogenies of moderately similar sequences. For highly similar and divergent scenarios, fully parsimony-based and likelihood-based phylogenetic placement methods performed the best respectively while TIPars was the second best. TIPars accomplished efficient and accurate expansion of phylogenies of both similar and divergent sequences, which would have broad biological applications beyond SARS-CoV-2. TIPars is accessible from https://tipars.hku.hk/ and source codes are available at https://github.com/id-bioinfo/TIPars.
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Affiliation(s)
- Yongtao Ye
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Marcus H Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Joseph L Tsui
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - David K Smith
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
- Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou, Guangdong, P. R. China
- EKIH (Gewuzhikang) Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, P. R. China
| | - Joseph T Wu
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
- Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou, Guangdong, P. R. China
- EKIH (Gewuzhikang) Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, P. R. China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
- Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou, Guangdong, P. R. China
- EKIH (Gewuzhikang) Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, P. R. China
- Centre for Immunology & Infection Limited, 17W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
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Chen P, Jin Z, Peng L, Zheng Z, Cheung YM, Guan J, Chen L, Huang Y, Fan X, Zhang Z, Shi D, Xie J, Chen R, Xiao B, Yip CH, Smith DK, Hong W, Liu Y, Li L, Wang J, Holmes EC, Lam TTY, Zhu H, Guan Y. Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health. J Virol 2023; 97:e0043423. [PMID: 37289052 PMCID: PMC10308888 DOI: 10.1128/jvi.00434-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/08/2023] [Indexed: 06/09/2023] Open
Abstract
Although influenza A viruses of several subtypes have occasionally infected humans, to date only those of the H1, H2, and H3 subtypes have led to pandemics and become established in humans. The detection of two human infections by avian H3N8 viruses in April and May of 2022 raised pandemic concerns. Recent studies have shown the H3N8 viruses were introduced into humans from poultry, although their genesis, prevalence, and transmissibility in mammals have not been fully elucidated. Findings generated from our systematic influenza surveillance showed that this H3N8 influenza virus was first detected in chickens in July 2021 and then disseminated and became established in chickens over wider regions of China. Phylogenetic analyses revealed that the H3 HA and N8 NA were derived from avian viruses prevalent in domestic ducks in the Guangxi-Guangdong region, while all internal genes were from enzootic poultry H9N2 viruses. The novel H3N8 viruses form independent lineages in the glycoprotein gene trees, but their internal genes are mixed with those of H9N2 viruses, indicating continuous gene exchange among these viruses. Experimental infection of ferrets with three chicken H3N8 viruses showed transmission through direct contact and inefficient transmission by airborne exposure. Examination of contemporary human sera detected only very limited antibody cross-reaction to these viruses. The continuing evolution of these viruses in poultry could pose an ongoing pandemic threat. IMPORTANCE A novel H3N8 virus with demonstrated zoonotic potential has emerged and disseminated in chickens in China. It was generated by reassortment between avian H3 and N8 virus(es) and long-term enzootic H9N2 viruses present in southern China. This H3N8 virus has maintained independent H3 and N8 gene lineages but continues to exchange internal genes with other H9N2 viruses to form novel variants. Our experimental studies showed that these H3N8 viruses were transmissible in ferrets, and serological data suggest that the human population lacks effective immunological protection against it. With its wide geographical distribution and continuing evolution in chickens, other spillovers to humans can be expected and might lead to more efficient transmission in humans.
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Affiliation(s)
- Peiwen Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Ziying Jin
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Liuxia Peng
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Zuoyi Zheng
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Yiu-Man Cheung
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Jing Guan
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Liming Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Yiteng Huang
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaohui Fan
- Department of Microbiology, Guangxi Medical University, Nanning, Guangxi, China
| | - Zengfeng Zhang
- Department of Microbiology, Guangxi Medical University, Nanning, Guangxi, China
| | - Dongmei Shi
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Jin Xie
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Rirong Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Boheng Xiao
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Chun Hung Yip
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - David K. Smith
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Wenshan Hong
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Yongmei Liu
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lifeng Li
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Jia Wang
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Edward C. Holmes
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tommy Tsan-Yuk Lam
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Huachen Zhu
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Yi Guan
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
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Yin X, Li L, Chen X, Liu YY, Lam TTY, Topp E, Zhang T. Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses. Water Res 2023; 235:119875. [PMID: 36996751 DOI: 10.1016/j.watres.2023.119875] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
The widely distributed antibiotic resistance genes (ARGs) were unevenly proliferated in various habitats. Great endeavors are needed to resolve the resistome features that can differentiate or connect different habitats. This study retrieved a broad spectrum of resistome profiles from 1723 metagenomes categorized into 13 habitats, encompassing industrial, urban, agricultural, and natural environments, and spanning most continents and oceans. The resistome features (ARG types, subtypes, indicator ARGs, and emerging mobilizable ARGs: mcr and tet(X)) in these habitats were benchmarked via a standardized workflow. We found that wastewater and wastewater treatment works were characterized to be reservoirs of more diverse genotypes of ARGs than any other habitats including human and livestock fecal samples, while fecal samples were with higher ARG abundance. Bacterial taxonomy composition was significantly correlated with resistome composition across most habitats. Moreover, the source-sink connectivities were disentangled by developing the resistome-based microbial attribution prediction model. Environmental surveys with standardized bioinformatic workflow proposed in this study will help comprehensively understand the transfer of ARGs in the environment, thus prioritizing the critical environments with high risks for intervention to tackle the problem of ARGs.
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Affiliation(s)
- Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Xi Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China; Centre for Immunology & Infection, The Hong Kong Science Park, Hong Kong SAR, China; Laboratory of Data Discovery for Health, The Hong Kong Science Park, Hong Kong SAR, China
| | - Edward Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, ON, Canada; Department of Biology, University of Western Ontario, London, ON, Canada
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR, China.
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Wu WG, Shum MHH, Wong ITF, Lu KK, Lee LK, Leung JSL, Lao HY, Lee AWT, Hau PT, Chan CTM, Wong HFT, Fung SKY, Wong SCY, Ng ICF, Ng TTL, Chow N, Ho AYM, Hung MF, Chow FWN, Wong MML, To WK, Lam TTY, Luk KS, Siu GKH. Probable Airborne Transmission of Burkholderia pseudomallei Causing an Urban Outbreak of Melioidosis during Typhoon Season in Hong Kong, China. Emerg Microbes Infect 2023; 12:2204155. [PMID: 37070526 PMCID: PMC10155638 DOI: 10.1080/22221751.2023.2204155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Between January 2015 and October 2022, 38 patients with culture-confirmed melioidosis were identified in the Kowloon West (KW) Region, Hong Kong. Notably, thirty of them were clustered in the Sham Shui Po (SSP) district, which covers an estimated area of 2.5 km2. Between August and October 2022, 18 patients were identified in this district after heavy rainfall and typhoons. The sudden upsurge in cases prompted an environmental investigation, which involved collecting 20 air samples and 72 soil samples from residential areas near the patients. A viable isolate of Burkholderia pseudomallei was obtained from an air sample collected at a building site five days after a typhoon. B. pseudomallei DNA was also detected in 21 soil samples collected from the building site and adjacent gardening areas using full-length 16S rRNA gene sequencing, suggesting that B. psuedomallei is widely distributed in the soil environment surrounding the district. Core genome-multilocus sequence typing showed that the air sample isolate was phylogenetically clustered with the outbreak isolates in KW Region. Multispectral satellite imagery revealed a continuous reduction in vegetation region in SSP district by 162,255 m2 from 2016 to 2022, supporting the hypothesis of inhalation of aerosols from the contaminated soil as the transmission route of melioidosis during extreme weather events. This is because the bacteria in unvegetated soil are more easily spread by winds. In consistent with inhalational melioidosis, 24 (63.2%) patients had pneumonia. Clinicians should be aware of melioidosis during typhoon season and initiate appropriate investigation and treatment for patients with compatible symptoms.
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Affiliation(s)
- Wing-Gi Wu
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ivan Tak-Fai Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Kelvin Keru Lu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Annie Wing-Tung Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Pak-Ting Hau
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Harmen Fung-Tin Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sharon Ka-Yee Fung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sally Choi-Ying Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Iain Chi-Fung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Ning Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Alex Yat-Man Ho
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Mei Fan Hung
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Maureen Mo-Lin Wong
- Department of Medicine and Geriatrics/Intensive Care Unit, Caritas Medical Centre, Hong Kong Special Administrative Region, China
| | - Wing-Kin To
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kristine Shik Luk
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
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Su J, Lui WW, Lee Y, Zheng Z, Siu GKH, Ng TTL, Zhang T, Lam TTY, Lao HY, Yam WC, Tam KKG, Leung KSS, Lam TW, Leung AWS, Luo R. Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling. Sci Rep 2023; 13:5237. [PMID: 37002338 PMCID: PMC10066345 DOI: 10.1038/s41598-023-32378-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Sensitive detection of Mycobacterium tuberculosis (TB) in small percentages in metagenomic samples is essential for microbial classification and drug resistance prediction. However, traditional methods, such as bacterial culture and microscopy, are time-consuming and sometimes have limited TB detection sensitivity. Oxford nanopore technologies (ONT) MinION sequencing allows rapid and simple sample preparation for sequencing. Its recently developed adaptive sequencing selects reads from targets while allowing real-time base-calling to achieve sequence enrichment or depletion during sequencing. Another common enrichment method is PCR amplification of the target TB genes. In this study, we compared both methods using ONT MinION sequencing for TB detection and variant calling in metagenomic samples using both simulation runs and those with synthetic and patient samples. We found that both methods effectively enrich TB reads from a high percentage of human (95%) and other microbial DNA. Adaptive sequencing with readfish and UNCALLDE achieved a 3.9-fold and 2.2-fold enrichment compared to the control run. We provide a simple automatic analysis framework to support the detection of TB for clinical use, openly available at https://github.com/HKU-BAL/ONT-TB-NF . Depending on the patient's medical condition and sample type, we recommend users evaluate and optimize their workflow for different clinical specimens to improve the detection limit.
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Affiliation(s)
- Junhao Su
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Wui Wang Lui
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - YanLam Lee
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Zhenxian Zheng
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Tong Zhang
- Department of Computer Science and Engineering, Department of Mathematics, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Pak Shek Kok, Hong Kong SAR, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, Lee Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kingsley King-Gee Tam
- Department of Microbiology, Lee Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kenneth Siu-Sing Leung
- Department of Microbiology, Lee Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Tak-Wah Lam
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Amy Wing-Sze Leung
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China.
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China.
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8
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Du LF, Zhang MZ, Yuan TT, Ni XB, Wei W, Cui XM, Wang N, Xiong T, Zhang J, Pan YS, Zhu DY, Li LJ, Xia LY, Wang TH, Wei R, Liu HB, Sun Y, Zhao L, Lam TTY, Cao WC, Jia N. New insights into the impact of microbiome on horizontal and vertical transmission of a tick-borne pathogen. Microbiome 2023; 11:50. [PMID: 36915209 PMCID: PMC10012463 DOI: 10.1186/s40168-023-01485-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The impact of host skin microbiome on horizontal transmission of tick-borne pathogens , and of pathogen associated transstadial and transovarial changes in tick microbiome are largely unknown, but are important to control increasingly emerging tick-borne diseases worldwide. METHODS Focusing on a rickettsiosis pathogen, Rickettsia raoultii, we used R. raoultii-positive and R. raoultii-negative Dermacentor spp. tick colonies to study the involvement of skin microbiota in cutaneous infection with rickettsiae in laboratory mice, and the function of the tick microbiome on maintenance of rickettsiae through all tick developmental stages (eggs, larvae, nymphs, adults) over two generations. RESULTS We observed changes in the skin bacteria community, such as Chlamydia, not only associated with rickettsial colonization but also with tick feeding on skin. The diversity of skin microbiome differed between paired tick-bitten and un-bitten sites. For vertical transmission, significant differences in the tick microbiota between pathogenic rickettsia-positive and -negative tick chorts was observed across all developmental stages at least over two generations, which appeared to be a common pattern not only for R. raoultii but also for another pathogenic species, Candidatus Rickettsia tarasevichiae. More importantly, bacterial differences were complemented by functional shifts primed for genetic information processing during blood feeding. Specifically, the differences in tick microbiome gene repertoire between pathogenic Rickettsia-positive and -negative progenies were enriched in pathways associated with metabolism and hormone signals during vertical transmission. CONCLUSIONS We demonstrate that host skin microbiome might be a new factor determining the transmission of rickettsial pathogens through ticks. While pathogenic rickettsiae infect vertebrate hosts during blood-feeding by the tick, they may also manipulate the maturation of the tick through changing the functional potential of its microbiota over the tick's life stages. The findings here might spur the development of new-generation control methods for ticks and tick-borne pathogens. Video Abstract.
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Affiliation(s)
- Li-Feng Du
- Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan, 250012, Shandong, People's Republic of China
| | - Ming-Zhu Zhang
- Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan, 250012, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Ting-Ting Yuan
- School of Medicine, Nankai University, Tianjin, 300071, People's Republic of China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People's Republic of China
| | - Wei Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Ning Wang
- Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan, 250012, Shandong, People's Republic of China
| | - Tao Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Jie Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yu-Sheng Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Dai-Yun Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Liang-Jing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Luo-Yuan Xia
- Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan, 250012, Shandong, People's Republic of China
| | - Tian-Hong Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Ran Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
- The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, People's Republic of China
| | - Hong-Bo Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, People's Republic of China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan, 250012, Shandong, People's Republic of China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, People's Republic of China.
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, People's Republic of China.
- Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou, Guangdong, 515063, People's Republic of China.
- EKIH (Gewuzhikang) Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, People's Republic of China.
- Centre for Immunology & Infection Limited, 17W Hong Kong Science & Technology Parks, Hong Kong SAR, People's Republic of China.
| | - Wu-Chun Cao
- Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan, 250012, Shandong, People's Republic of China.
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
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Zhang J, Zheng YC, Chu YL, Cui XM, Wei R, Bian C, Liu HB, Yao NN, Jiang RR, Huo QB, Yuan TT, Li J, Zhao L, Li LF, Wang Q, Wei W, Zhu JG, Chen MC, Gao Y, Wang F, Ye JL, Song JL, Jiang JF, Lam TTY, Ni XB, Jia N. Skin infectome of patients with a tick bite history. Front Cell Infect Microbiol 2023; 13:1113992. [PMID: 36923591 PMCID: PMC10008932 DOI: 10.3389/fcimb.2023.1113992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/09/2023] [Indexed: 03/03/2023] Open
Abstract
Introduction Ticks are the most important obligate blood-feeding vectors of human pathogens. With the advance of high-throughput sequencing, more and more bacterial community and virome in tick has been reported, which seems to pose a great threat to people. Methods A total of 14 skin specimens collected from tick-bite patients with mild to severe symptoms were analyzed through meta-transcriptomic sequencings. Results Four bacteria genera were both detected in the skins and ticks, including Pseudomonas, Acinetobacter, Corynebacterium and Propionibacterium, and three tick-associated viruses, Jingmen tick virus (JMTV), Bole tick virus 4 (BLTV4) and Deer tick mononegavirales-like virus (DTMV) were identified in the skin samples. Except of known pathogens such as pathogenic rickettsia, Coxiella burnetii and JMTV, we suggest Roseomonas cervicalis and BLTV4 as potential new agents amplified in the skins and then disseminated into the blood. As early as 1 day after a tick-bite, these pathogens can transmit to skins and at most four ones can co-infect in skins. Discussion Advances in sequencing technologies have revealed that the diversity of tick microbiome and virome goes far beyond our previous understanding. This report not only identifies three new potential pathogens in humans but also shows that the skin barrier is vital in preventing horizontal transmissions of tick-associated bacteria or virus communities to the host. It is the first research on patients' skin infectome after a tick bite and demonstrates that more attention should be paid to the cutaneous response to prevent tick-borne illness.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuan-Chun Zheng
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Yan-Li Chu
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ran Wei
- The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Cai Bian
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Hong-Bo Liu
- Department of Infectious Diseases Control and Prevention, Chinese People's Liberation Army of China (PLA) Center for Disease Control and Prevention, Beijing, China
| | - Nan-Nan Yao
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Rui-Ruo Jiang
- Institute of Nuclear, Biological, and Chemical weapons (NBC) Defence, PLA Army, Beijing, China
| | - Qiu-Bo Huo
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | | | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Lian-Feng Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Qian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jin-Guo Zhu
- Department of Health Quarantine, ManZhouLi Customs District, Manzhouli, China
| | - Mei-Chao Chen
- Department of Health Quarantine, ManZhouLi Customs District, Manzhouli, China
| | - Yan Gao
- Department of Health Quarantine, ManZhouLi Customs District, Manzhouli, China
| | - Fei Wang
- Department of Health Quarantine, ManZhouLi Customs District, Manzhouli, China
| | - Jin-Ling Ye
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Ju-Liang Song
- Department of Cardiology, Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- *Correspondence: Na Jia, ; Xue-Bing Ni, ; Tommy Tsan-Yuk Lam,
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- *Correspondence: Na Jia, ; Xue-Bing Ni, ; Tommy Tsan-Yuk Lam,
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- *Correspondence: Na Jia, ; Xue-Bing Ni, ; Tommy Tsan-Yuk Lam,
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10
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Yeo FKS, Cheok YH, Wan Ismail WN, Kueh-Tai FF, Lam TTY, Chong YL. Genotype and organ effect on the occupancy of phyllosphere prokaryotes in different rice landraces. Arch Microbiol 2022; 204:600. [PMID: 36056990 DOI: 10.1007/s00203-022-03209-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/26/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022]
Abstract
Bacteria community provides essential ecological services to rice plants. The bacterial diversity of rice varies across host plant genotype and organs. This study employed 16S rDNA amplicon sequencing to characterise the bacterial community associated with three rice landraces using leaf blade and stem samples. The prokaryotic community found in these rice landraces comprised of two kingdoms, 12 phyla, 25 classes, 40 orders, 80 families, and 118 genera. Proteobacteria (53.9%) was the most abundant phylum. The most abundant genus was an undefined genus under Cyanobacteria (33.0%). Homogeneity of prokaryotic community was observed across the three rice landraces, which may suggest a high similarity in biological and genetical properties of the rice landraces. The difference in prokaryotic composition between leaf blade and stem was depicted based on principal coordinate analysis. This study observed that the prokaryotic inhabitants in rice plants is predominantly determined by rice plant organs.
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Affiliation(s)
- Freddy Kuok San Yeo
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Yin Hui Cheok
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Wan Nurainie Wan Ismail
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Felicia Fui Kueh-Tai
- Agriculture Research Centre, Semongok, 12th Mile, Kuching-Serian Road, P.O. Box 977, 93720, Kuching, Sarawak, Malaysia
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Yee Ling Chong
- Department of Science and Environmental Studies, Faculty of Liberal Arts and Social Sciences, The Education University of Hong Kong, 10 Lo Ping Road, Ting Kok, Hong Kong SAR, China
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11
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Wu T, Xiao CL, Lam TTY, Yu G. Editorial: Biomedical Data Visualization: Methods and Applications. Front Genet 2022; 13:890775. [PMID: 35571011 PMCID: PMC9092592 DOI: 10.3389/fgene.2022.890775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Tianzhi Wu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Chuan-Le Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong, Hong Kong SAR, China
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Guangchuang Yu,
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12
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Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nat Methods 2022; 19:374-380. [PMID: 35396471 PMCID: PMC9467803 DOI: 10.1038/s41592-022-01444-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated development of testing methods, and allowed timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific, and organizational challenges. Here, we discuss the application of genomic and computational methods for the efficient data driven COVID-19 response, advantages of democratization of viral sequencing around the world, and challenges associated with viral genome data collection and processing.
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Affiliation(s)
- Sergey Knyazev
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karishma Chhugani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Varuni Sarwal
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
| | - Ram Ayyala
- Department of Translational Biomedical Informatics, University of Southern California, Los Angeles, CA, USA
| | - Harman Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, India
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dhrithi Deshpande
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Pelin Icer Baykal
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Zoia Comarova
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Angela Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Yuri Porozov
- World-Class Research Center "Digital biodesign and personalized healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
| | - Tetyana I Vasylyeva
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, P.R. China
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Malak S Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Victoria M Pak
- Emory University, School of Nursing, Atlanta, GA, CA, USA
- Emory University, Rollins School of Public Health, Department of Epidemiology, Atlanta, GA, CA, USA
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Pavel Skums
- Department of Computer Science, College of Art and Science, Georgia State University, Atlanta, GA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrey Komissarov
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, CA, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Fyodor Kondrashov
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P.R. China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, P.R. China
- Centre for Immunology & Infection Limited, Hong Kong SAR, P.R. China
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alex Zelikovsky
- Department of Computer Science, College of Art and Science, Georgia State University, Atlanta, GA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
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13
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Jing X, Xu M, Song D, Yue T, Wang Y, Zhang P, Zhong Y, Zhang M, Lam TTY, Faria NR, De Clercq E, Li G. Association between inflammatory cytokines and anti-SARS-CoV-2 antibodies in hospitalized patients with COVID-19. Immun Ageing 2022; 19:12. [PMID: 35248063 PMCID: PMC8897556 DOI: 10.1186/s12979-022-00271-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/11/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND COVID-19 patients may experience "cytokine storm" when human immune system produces excessive cytokines/chemokines. However, it remains unclear whether early responses of inflammatory cytokines would lead to high or low titers of anti-SARS-CoV-2 antibodies. METHODS This retrospective study enrolled a cohort of 272 hospitalized patients with laboratory-confirmed SARS-CoV-2. Laboratory assessments of serum cytokines (IL-2R, IL-6, IL-8, IL-10, TNF-α), anti-SARS-CoV-2 IgG/IgM antibodies, and peripheral blood biomarkers were conducted during hospitalization. RESULTS At hospital admission, 36.4% patients were severely ill, 51.5% patients were ≥ 65 years, and 60.3% patients had comorbidities. Higher levels of IL-2R and IL-6 were observed in older patients (≥65 years). Significant differences of IL-2R (week 2 to week ≥5 from symptom onset), IL-6 (week 1 to week ≥5), IL-8 (week 2 to week ≥5), and IL-10 (week 1 to week 3) were observed between moderately-ill and severely ill patients. Anti-SARS-CoV-2 IgG titers were significantly higher in severely ill patients than in moderately ill patients, but such difference was not observed for IgM. High titers of early-stage IL-6, IL-8, and TNF-α (≤2 weeks after symptom onset) were positively correlated with high titers of late-stage IgG (≥5 weeks after symptom onset). Deaths were mostly observed in severely ill older patients (45.9%). Survival analyses revealed risk factors of patient age, baseline COVID-19 severity, and baseline IL-6 that affected survival time, especially in severely ill older patients. CONCLUSION Early responses of elevated cytokines such as IL-6 reflect the active immune responses, leading to high titers of IgG antibodies against COVID-19.
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Affiliation(s)
- Xixi Jing
- grid.216417.70000 0001 0379 7164Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, 410078 China
| | - Min Xu
- grid.452708.c0000 0004 1803 0208Department of Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Deye Song
- grid.452708.c0000 0004 1803 0208Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
| | - Tingting Yue
- grid.216417.70000 0001 0379 7164Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, 410078 China
| | - Yali Wang
- grid.216417.70000 0001 0379 7164Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, 410078 China
| | - Pan Zhang
- grid.216417.70000 0001 0379 7164Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, 410078 China
| | - Yanjun Zhong
- grid.452708.c0000 0004 1803 0208Department of Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Min Zhang
- grid.216417.70000 0001 0379 7164Institute of Hepatology and Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
| | - Tommy Tsan-Yuk Lam
- grid.194645.b0000000121742757State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, SAR China
| | - Nuno Rodrigues Faria
- grid.7445.20000 0001 2113 8111Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK ,grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK
| | - Erik De Clercq
- grid.415751.3Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, 410078, China.
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14
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Li LJ, Ning NZ, Zheng YC, Chu YL, Cui XM, Zhang MZ, Guo WB, Wei R, Liu HB, Sun Y, Ye JL, Jiang BG, Yuan TT, Li J, Bian C, Bell-Sakyi L, Wang H, Jiang JF, Song JL, Cao WC, Tsan-Yuk Lam T, Ni XB, Jia N. Virome and Blood Meal-Associated Host Responses in Ixodes persulcatus Naturally Fed on Patients. Front Microbiol 2022; 12:728996. [PMID: 35250897 PMCID: PMC8891964 DOI: 10.3389/fmicb.2021.728996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
The long-lasting co-evolution of ticks with pathogens results in mutual adaptation. Blood-feeding is one of the critical physiological behaviors that have been associated with the tick microbiome; however, most knowledge was gained through the study of laboratory-reared ticks. Here we detached Ixodes persulcatus ticks at different stages of blood-feeding from human patients and performed high-throughput transcriptomic analysis on them to identify their virome and genes differentially expressed between flat and fully fed ticks. We also traced bloodmeal sources of those ticks and identified bats and three other potential mammalian hosts, highlighting the public health significance. We found Jingmen tick virus and 13 putative new viruses belonging to 11 viral families, three of which even exhibited high genetic divergence from viruses previously reported in the same tick species from the same geographic region. Furthermore, differential expression analysis suggested a downregulation of antioxidant genes in the fully fed I. persulcatus ticks, which might be related to bloodmeal-related redox homeostasis. Our work highlights the significance of active surveillance of tick viromes and suggests a role of reactive oxygen species (ROS) in modulating changes in the microbiome during blood-feeding.
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Affiliation(s)
- Liang-Jing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Nian-Zhi Ning
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | - Yan-Li Chu
- Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ming-Zhu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wen-Bin Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ran Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Hong-Bo Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jin-Ling Ye
- Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, China
| | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Cai Bian
- Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Lesley Bell-Sakyi
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Hui Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ju-Liang Song
- Mudanjiang Forestry Central Hospital, Mudanjiang, China
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Joint Institute of Virology (SU/HKU), Shantou University, Shantou, China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- *Correspondence: Xue-Bing Ni,
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Na Jia,
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15
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Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Comarova Z, Lu A, Porozov Y, Wu A, Abedalthagafi MS, Nagaraj SH, Smith AL, Skums P, Ladner J, Tsan-Yuk Lam T, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of viral genomics for the COVID-19 pandemic response. ARXIV 2021. [PMCID: PMC8109901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies, the rapid global spread of SARS-CoV-2, and its persistent threat to public health. However, distinguishing the most epidemiologically relevant information encoded in these vast amounts of data requires substantial effort across the research and public health communities. Studies of SARS-CoV-2 genomes have been critical in tracking the spread of variants and understanding its epidemic dynamics, and may prove crucial for controlling future epidemics and alleviating significant public health burdens. Together, genomic data and bioinformatics methods enable broad-scale investigations of the spread of SARS-CoV-2 at the local, national, and global scales and allow researchers the ability to efficiently track the emergence of novel variants, reconstruct epidemic dynamics, and provide important insights into drug and vaccine development and disease control. Here, we discuss the tremendous opportunities that genomics offers to unlock the effective use of SARS-CoV-2 genomic data for efficient public health surveillance and guiding timely responses to COVID-19.
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Affiliation(s)
- Sergey Knyazev
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Room 618, Atlanta, GA 30303, USA,Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, 30333 GA, USA,Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Karishma Chhugani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Varuni Sarwal
- Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Ram Ayyala
- Department of Neuroscience, College of Life Sciences, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Harman Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dhrithi Deshpande
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Zoia Comarova
- Paradigm Environmental, 3911 Old Lee Highway, Fairfax, VA 22030
| | - Angela Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089-9121, USA
| | - Yuri Porozov
- World-Class Research Center “Digital biodesign and personalized healthcare”, I.M. Sechenov First Moscow State Medical University, Moscow, Russia,Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China,Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Shivashankar H. Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia,Translational Research Institute, Brisbane, Australia
| | - Adam L. Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089
| | - Pavel Skums
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
| | - Jason Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alex Zelikovsky
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA,The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA,Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Keith A. Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
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16
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Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Comarova Z, Lu A, Porozov Y, Wu A, Abedalthagafi MS, Nagaraj SH, Smith AL, Skums P, Ladner J, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of viral genomics for the COVID-19 pandemic response. ArXiv 2021:arXiv:2104.14005v3. [PMID: 33948451 PMCID: PMC8095210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 06/04/2021] [Indexed: 12/25/2022]
Abstract
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies, the rapid global spread of SARS-CoV-2, and its persistent threat to public health. However, distinguishing the most epidemiologically relevant information encoded in these vast amounts of data requires substantial effort across the research and public health communities. Studies of SARS-CoV-2 genomes have been critical in tracking the spread of variants and understanding its epidemic dynamics, and may prove crucial for controlling future epidemics and alleviating significant public health burdens. Together, genomic data and bioinformatics methods enable broad-scale investigations of the spread of SARS-CoV-2 at the local, national, and global scales and allow researchers the ability to efficiently track the emergence of novel variants, reconstruct epidemic dynamics, and provide important insights into drug and vaccine development and disease control. Here, we discuss the tremendous opportunities that genomics offers to unlock the effective use of SARS-CoV-2 genomic data for efficient public health surveillance and guiding timely responses to COVID-19.
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Affiliation(s)
- Sergey Knyazev
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Room 618, Atlanta, GA 30303, USA
| | - Karishma Chhugani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Varuni Sarwal
- Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Ram Ayyala
- Department of Neuroscience, College of Life Sciences, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Harman Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dhrithi Deshpande
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Zoia Comarova
- Paradigm Environmental, 3911 Old Lee Highway, Fairfax, VA 22030
| | - Angela Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089-9121, USA
| | - Yuri Porozov
- World-Class Research Center "Digital biodesign and personalized healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Malak S Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
- Translational Research Institute, Brisbane, Australia
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089
| | - Pavel Skums
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
| | - Jason Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alex Zelikovsky
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
- The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
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17
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Huang XH, Yu G, Zheng C, Zhou PP, Anderson C, Zhao J, Lam TTY, Li Y, Chen L, Lin P, Zhang M, Yan J, He X. Genomic characterization of a new CRF01_AE/CRF07_BC case from a MSM patient in Guangdong, China. J Med Virol 2021; 93:6383-6387. [PMID: 33448453 DOI: 10.1002/jmv.26799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/18/2020] [Accepted: 01/12/2021] [Indexed: 11/06/2022]
Abstract
The CRF01_AE and CRF07_BC clades dominate the human immunodeficiency virus (HIV) epidemics in China. Both clades have been identified in the men who have sex with men (MSM) population in Guangdong province, raising a serious concern of possible complex recombination events ahead. Here, we report the first case of CRF01_AE/CRF07_BC recombinant sampled from a MSM patient in southern China. The genomic structure of this case is a mosaic with some regions resembling the CRF01_AE and CRF07_BC clades. Our phylogenetic analyses show that the two parental lineages of this recombinant virus were mainly found in the MSM population. This case has a different genomic composition compared with other recombinants descended from the same parental clades CRF01_AE and CRF07_BC. Our finding suggests that the MSM populations have become a hotspot for expanding viral diversity through the viral recombination mechanism. Therefore, further epidemiologic surveillance and monitoring should be conducted within the MSM populations to help advance our knowledge of viral transmission mechanisms. Additionally, these measures will serve to enhance the control and prevention of HIV/acquired immunodeficiency syndrome in China.
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Affiliation(s)
- Xu-He Huang
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Guolong Yu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ping-Ping Zhou
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Claire Anderson
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, USA
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, HKSAR, Hong Kong, China
| | - Yan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Peng Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, USA
| | - Jin Yan
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Xiang He
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
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18
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Boni MF, Lemey P, Jiang X, Lam TTY, Perry BW, Castoe TA, Rambaut A, Robertson DL. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 2020; 5:1408-1417. [PMID: 32724171 DOI: 10.1101/2020.03.30.015008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/10/2020] [Indexed: 05/22/2023]
Abstract
There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses-the viral subgenus containing SARS-CoV and SARS-CoV-2-undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879-1999), 1969 (95% HPD: 1930-2000) and 1982 (95% HPD: 1948-2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.
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Affiliation(s)
- Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Leuven, Belgium.
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Blair W Perry
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Todd A Castoe
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
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19
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Wang LG, Lam TTY, Xu S, Dai Z, Zhou L, Feng T, Guo P, Dunn CW, Jones BR, Bradley T, Zhu H, Guan Y, Jiang Y, Yu G. Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data. Mol Biol Evol 2020; 37:599-603. [PMID: 31633786 DOI: 10.1093/molbev/msz240] [Citation(s) in RCA: 225] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.
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Affiliation(s)
- Li-Gen Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Disease and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Shuangbin Xu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Zehan Dai
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Lang Zhou
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Tingze Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Pingfan Guo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Bradley R Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Tyler Bradley
- Civil, Architectural, and Environmental Engineering, Drexel University, Philadelphia, PA
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Disease and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.,Joint Institute of Virology (Shantou University - The University of Hong Kong), Shantou University, Shantou, Guangdong, China.,State Key Laboratory of Emerging Infectious Disease (HKU Shenzhen Base), Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Disease and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.,Joint Institute of Virology (Shantou University - The University of Hong Kong), Shantou University, Shantou, Guangdong, China.,State Key Laboratory of Emerging Infectious Disease (HKU Shenzhen Base), Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
| | - Yong Jiang
- Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
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20
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Jia N, Wang J, Shi W, Du L, Sun Y, Zhan W, Jiang JF, Wang Q, Zhang B, Ji P, Bell-Sakyi L, Cui XM, Yuan TT, Jiang BG, Yang WF, Lam TTY, Chang QC, Ding SJ, Wang XJ, Zhu JG, Ruan XD, Zhao L, Wei JT, Ye RZ, Que TC, Du CH, Zhou YH, Cheng JX, Dai PF, Guo WB, Han XH, Huang EJ, Li LF, Wei W, Gao YC, Liu JZ, Shao HZ, Wang X, Wang CC, Yang TC, Huo QB, Li W, Chen HY, Chen SE, Zhou LG, Ni XB, Tian JH, Sheng Y, Liu T, Pan YS, Xia LY, Li J, Zhao F, Cao WC. Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities. Cell 2020; 182:1328-1340.e13. [PMID: 32814014 DOI: 10.1016/j.cell.2020.07.023] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/01/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Among arthropod vectors, ticks transmit the most diverse human and animal pathogens, leading to an increasing number of new challenges worldwide. Here we sequenced and assembled high-quality genomes of six ixodid tick species and further resequenced 678 tick specimens to understand three key aspects of ticks: genetic diversity, population structure, and pathogen distribution. We explored the genetic basis common to ticks, including heme and hemoglobin digestion, iron metabolism, and reactive oxygen species, and unveiled for the first time that genetic structure and pathogen composition in different tick species are mainly shaped by ecological and geographic factors. We further identified species-specific determinants associated with different host ranges, life cycles, and distributions. The findings of this study are an invaluable resource for research and control of ticks and tick-borne diseases.
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Affiliation(s)
- Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, P.R. China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, P.R. China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Wenqiang Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Lifeng Du
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Wei Zhan
- Annoroad Gene Technology (Beijing) Company Limited, Beijing 100176, P.R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, P.R. China
| | - Qian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China
| | - Bing Zhang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Peifeng Ji
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Lesley Bell-Sakyi
- Department of Infection Biology and Microbiomes, Institute of Infection, Ecological and Veterinary Sciences, University of Liverpool, Liverpool L3 5RF, UK
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, P.R. China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Wei-Fei Yang
- Annoroad Gene Technology (Beijing) Company Limited, Beijing 100176, P.R. China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Qiao-Cheng Chang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, P.R. China
| | - Shu-Jun Ding
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Jinan 250014, Shandong, P.R. China
| | - Xian-Jun Wang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Jinan 250014, Shandong, P.R. China
| | - Jin-Guo Zhu
- ManZhouLi Customs District, Manzhouli 021400, Inner Mongolia, P.R. China
| | - Xiang-Dong Ruan
- Academy of Forest Inventory and Planning, State Forestry and Grassland Administration, Beijing 100714, P.R. China
| | - Lin Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China
| | - Jia-Te Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China
| | - Run-Ze Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China
| | - Teng Cheng Que
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-aid and Monitoring Epidemic Diseases Research Center, Nanjing 530028, Guangxi, P.R. China
| | - Chun-Hong Du
- Yunnan Institute for Endemic Diseases Control and Prevention, Dali 671000, Yunnan, P.R. China
| | - Yu-Hao Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Jing Xia Cheng
- Shanxi Provence Center for Disease Control and Prevention, Xian 030012, Shanxi, P.R. China
| | - Pei-Fang Dai
- Shanxi Provence Center for Disease Control and Prevention, Xian 030012, Shanxi, P.R. China
| | - Wen-Bin Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Xiao-Hu Han
- Shenyang Agriculture University, Shenyang 110866, Liaoning, P.R. China
| | - En-Jiong Huang
- Fuzhou International Travel Healthcare Center, Fuzhou 350001, Fujian, P.R. China
| | - Lian-Feng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Wei Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Yu-Chi Gao
- Annoroad Gene Technology (Beijing) Company Limited, Beijing 100176, P.R. China
| | - Jing-Ze Liu
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, Hebei, P.R. China
| | - Hong-Ze Shao
- Animal Husbandry and Veterinary Science Research Institute of Jilin Province, Changchun 130062, Jilin, P.R. China
| | - Xin Wang
- Qingjiangpu District Center for Disease Control and Prevention, Huai'an 223001, Jiangsu, P.R. China
| | - Chong-Cai Wang
- Hainan International Travel Healthcare Center, Haikou 570311, Hainan, P.R. China
| | - Tian-Ci Yang
- State Key Lab of Mosquito-borne Diseases, Hangzhou International Tourism Healthcare Center, Hangzhou Customs of China, Hangzhou 310012, Zhejiang, P.R. China
| | - Qiu-Bo Huo
- Mudanjiang Forestry Central Hospital, Mudanjiang 157000, Heilongjiang, P.R. China
| | - Wei Li
- Xinjiang Center for Disease Control and Prevention, Urumqi 830002, Xinjiang, P.R. China
| | - Hai-Ying Chen
- Collaboration Unit for Field Epidemiology of the State Key Laboratory for Infectious Disease Prevention and Control, Nanchang Center for Disease Control and Prevention. Nanchang 330038, Jiangxi, P.R. China
| | - Shen-En Chen
- Collaboration Unit for Field Epidemiology of the State Key Laboratory for Infectious Disease Prevention and Control, Nanchang Center for Disease Control and Prevention. Nanchang 330038, Jiangxi, P.R. China
| | - Ling-Guo Zhou
- Shaanxi Natural Reserve and Wildlife Administration Station, Xi'an 710082, Shaanxi, P.R. China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Jun-Hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan 430015, Hubei, P.R. China
| | - Yue Sheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Company Limited, Beijing 100176, P.R. China
| | - Yu-Sheng Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Luo-Yuan Xia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, P.R. China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China; Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, P.R. China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, Yunan, P.R. China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, Zhejiang, P.R. China; University of the Chinese Academy of Sciences, Beijing 100049, P.R. China.
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China; Institute of EcoHealth, School of Public Health, Shandong University, 44 Wenhuaxi Street, Jinan 250012, Shandong, P.R. China; Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing 100071, P.R. China.
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21
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Chung HH, Kamar CKA, Lim LWK, Roja JS, Liao Y, Lam TTY, Chong YL. Sequencing and characterization of complete mitogenome DNA of Rasbora tornieri (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance. J Genet 2020. [DOI: 10.1007/s12041-020-01221-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Zhou Y, Van Tan L, Luo K, Liao Q, Wang L, Qiu Q, Zou G, Liu P, Anh NT, Hong NTT, He M, Wei X, Yu S, Lam TTY, Cui J, van Doorn HR, Yu H. Genetic Variation of Multiple Serotypes of Enteroviruses Associated with Hand, Foot and Mouth Disease in Southern China. Virol Sin 2020; 36:61-74. [PMID: 32725479 PMCID: PMC7385209 DOI: 10.1007/s12250-020-00266-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/06/2020] [Indexed: 12/04/2022] Open
Abstract
Enteroviruses (EVs) species A are a major public health issue in the Asia–Pacific region and cause frequent epidemics of hand, foot and mouth disease (HFMD) in China. Mild infections are common in children; however, HFMD can also cause severe illness that affects the central nervous system. To molecularly characterize EVs, a prospective HFMD virological surveillance program was performed in China between 2013 and 2016. Throat swabs, rectal swabs and stool samples were collected from suspected HFMD patients at participating hospitals. EVs were detected using generic real-time and nested reverse transcription-polymerase chain reactions (RT-PCRs). Then, the complete VP1 regions of enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16) and CVA6 were sequenced to analyze amino acid changes and construct a viral molecular phylogeny. Of the 2836 enrolled HFMD patients, 2,517 (89%) were EV positive. The most frequently detected EVs were CVA16 (32.5%, 819), CVA6 (31.2%, 785), and EV-A71 (20.4%, 514). The subgenogroups CVA16_B1b, CVA6_D3a and EV-A71_C4a were predominant in China and recombination was not observed in the VP1 region. Sequence analysis revealed amino acid variations at the 30, 29 and 44 positions in the VP1 region of EV-A71, CVA16 and CVA6 (compared to the respective prototype strains BrCr, G10 and Gdula), respectively. Furthermore, in 21 of 24 (87.5%) identified EV-A71 samples, a known amino acid substitution (D31N) that may enhance neurovirulence was detected. Our study provides insights about the genetic characteristics of common HFMD-associated EVs. However, the emergence and virulence of the described mutations require further investigation.
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Affiliation(s)
- Yonghong Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, 700000, Vietnam
| | - Kaiwei Luo
- Hunan Provincial Center for Disease Control and Prevention, Changsha, 410005, China
| | - Qiaohong Liao
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China.,Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, 102206, China
| | - Lili Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Qi Qiu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Gang Zou
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ping Liu
- Anhua County Center for Disease Control and Prevention, Anhua, 413000, China
| | - Nguyen To Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, 700000, Vietnam
| | | | - Min He
- Anhua County Center for Disease Control and Prevention, Anhua, 413000, China
| | - Xiaoman Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shuanbao Yu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, 102206, China
| | - Tommy Tsan-Yuk Lam
- Centre of Influenza Research & State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, 999077, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200032, China
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, 700000, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China.
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23
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Boni MF, Lemey P, Jiang X, Lam TTY, Perry BW, Castoe TA, Rambaut A, Robertson DL. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 2020; 5:1408-1417. [DOI: 10.1038/s41564-020-0771-4] [Citation(s) in RCA: 568] [Impact Index Per Article: 142.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]
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24
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Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 2020; 583:282-285. [PMID: 32218527 DOI: 10.1101/2020.02.13.945485] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/17/2020] [Indexed: 05/24/2023]
Abstract
The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are probable reservoir hosts for SARS-CoV-2, the identity of any intermediate host that may have facilitated transfer to humans is unknown. Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ya-Wei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Hua-Chen Zhu
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yi-Gang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Yong-Xia Shi
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yun-Shi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Wen-Juan Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Wei Wei
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Kui Zheng
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Guang-Qian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Xin Qiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - William Yiu-Man Cheung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Lian-Feng Li
- School of Information and Management, Guangxi Medical University, Nanning, P. R. China
| | - Fang-Fang Sun
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Si Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ji-Cheng Huang
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Gabriel M Leung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Yan-Ling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China.
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, P. R. China.
| | - Yi Guan
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China.
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.
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25
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Abstract
There is considerable public and scientific interest in the origin, spread, and evolution of SARS-CoV-2. Lu et al. recently conducted genomic sequencing and analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local transmission chains.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
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26
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Chung HH, Lim LWK, Liao Y, Lam TTY, Chong YL. Sequencing and Characterisation of Complete Mitochondrial DNA Genome for Trigonopoma pauciperforatum (Cypriniformes: Cyprinidae: Danioninae) with Phylogenetic Consideration. Trop Life Sci Res 2020; 31:107-121. [PMID: 32963714 PMCID: PMC7485528 DOI: 10.21315/tlsr2020.31.1.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Trigonopoma pauciperforatum or the redstripe rasbora is a cyprinid commonly found in marshes and swampy areas with slight acidic tannin-stained water in the tropics. In this study, the complete mitogenome sequence of T. pauciperforatum was first amplified in two parts using two pairs of overlapping primers and then sequenced. The size of the mitogenome is 16,707 bp, encompassing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organisation was detected between this species and other family members. The heavy strand accommodates 28 genes while the light strand houses the remaining nine genes. Most protein-coding genes utilise ATG as start codon except for COI gene which uses GTG instead. The terminal associated sequence (TAS), central conserved sequence block (CSB-F, CSB-D and CSB-E) as well as variable sequence block (CSB-1, CSB-2 and CSB-3) are conserved in the control region. The maximum likelihood phylogenetic tree revealed the divergence of T. pauciperforatum from the basal region of the major clade, where its evolutionary relationships with Boraras maculatus, Rasbora cephalotaenia and R. daniconius are poorly resolved as suggested by the low bootstrap values. This work contributes towards the genetic resource enrichment for peat swamp conservation and comprehensive in-depth comparisons across other phylogenetic researches done on the Rasbora-related genus.
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Affiliation(s)
- Hung Hui Chung
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Leonard Whye Kit Lim
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Yunshi Liao
- School of Public Health, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong
| | - Tommy Tsan-Yuk Lam
- School of Public Health, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong
| | - Yee Ling Chong
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
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Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 2020. [DOI: 10.1038/s41586-020-2169-0 10.1101/2020.02.13.945485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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28
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Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 2020; 583:282-285. [PMID: 32218527 DOI: 10.1038/s41586-020-2169-0] [Citation(s) in RCA: 1121] [Impact Index Per Article: 280.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/17/2020] [Indexed: 11/09/2022]
Abstract
The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are probable reservoir hosts for SARS-CoV-2, the identity of any intermediate host that may have facilitated transfer to humans is unknown. Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.,State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ya-Wei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Hua-Chen Zhu
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.,State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yi-Gang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Yong-Xia Shi
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yun-Shi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Wen-Juan Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Wei Wei
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Kui Zheng
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Guang-Qian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Xin Qiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - William Yiu-Man Cheung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Lian-Feng Li
- School of Information and Management, Guangxi Medical University, Nanning, P. R. China
| | - Fang-Fang Sun
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Si Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ji-Cheng Huang
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Gabriel M Leung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Yan-Ling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China. .,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, P. R. China.
| | - Yi Guan
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China. .,State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China.
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.
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Chung HH, Anak Kamar CK, Kit Lim LW, Roja JS, Liao Y, Tsan-Yuk Lam T, Chong YL. Sequencing and characterization of complete mitogenome DNA of Rasbora tornieri (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance. J Genet 2020; 99:67. [PMID: 32893838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The yellowtail rasbora (Rasbora tornieri) is a miniature ray-finned fish categorized under the genus Rasbora in the family of Cyprinidae. In this study, a complete mitogenome sequence of R. tornieri was sequenced using four primers targeting two halves of the mitogenome with overlapping flanking regions. The size of mitogenome was 16,573 bp, housing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organization was detected between this species and other members of Rasbora genus. The heavy strand encompassed 28 genes while the light strand accommodated the other nine genes. Most protein-coding genes execute ATG as start codon, excluding COI and ND3 genes, which utilized GTG instead. The central conserved sequence blocks (CSB-E, CSB-F and CSB-D), variable sequence blocks (CSB-1, CSB-3 and CSB-2) as well as the terminal associated sequence (TAS) were conserved within the control region. The maximum likelihood phylogenetic family tree revealed the divergence of R. tornieri from the basal region of the Rasbora clade, where its evolutionary relationships with other Rasbora members are poorly resolved as indicated by the low bootstrap values. This work acts as window for further population genetics and molecular evolution studies of Rasbora genus in future.
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Affiliation(s)
- Hung Hui Chung
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Sarawak, Malaysia
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Lim LWK, Roja JS, Kamar CKA, Chung HH, Liao Y, Lam TTY, Chong YL. Sequencing and characterization of complete mitogenome DNA for Rasbora myersi (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance. Gene Reports 2019. [DOI: 10.1016/j.genrep.2019.100499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
Ggtree is a comprehensive R package for visualizing and annotating phylogenetic trees with associated data. It can also map and visualize associated external data on phylogenies with two general methods. Method 1 allows external data to be mapped on the tree structure and used as visual characteristic in tree and data visualization. Method 2 plots the data with the tree side by side using different geometric functions after reordering the data based on the tree structure. These two methods integrate data with phylogeny for further exploration and comparison in the evolutionary biology context. Ggtree is available from http://www.bioconductor.org/packages/ggtree.
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Affiliation(s)
- Guangchuang Yu
- Institute of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.,Joint Institute of Virology (Shantou University-The University of Hong Kong), Shantou University, Shantou, Guangdong, China.,State Key Laboratory of Emerging Infectious Diseases (HKU Shenzhen Base), Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.,Joint Institute of Virology (Shantou University-The University of Hong Kong), Shantou University, Shantou, Guangdong, China.,State Key Laboratory of Emerging Infectious Diseases (HKU Shenzhen Base), Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
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Abstract
Detecting the temporally and spatially varying correlations is important to understand the biological and disease systems. Here we proposed a geographically weighted temporally correlated logistic regression (GWTCLR) model to identify such dynamic correlation of predictors on binomial outcome data, by incorporating spatial and temporal information for joint inference. The local likelihood method is adopted to estimate the spatial relationship, while the smoothing method is employed to estimate the temporal variation. We present the construction and implementation of GWTCLR and the study of the asymptotic properties of the proposed estimator. Simulation studies were conducted to evaluate the robustness of the proposed model. GWTCLR was applied on real epidemiologic data to study the climatic determinants of human seasonal influenza epidemics. Our method obtained results largely consistent with previous studies but also revealed certain spatial and temporal varying patterns that were unobservable by previous models and methods.
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Affiliation(s)
- Yang Liu
- Center of Influenza Research, State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China.,School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Kwok-Fai Lam
- Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Joseph T Wu
- School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- Center of Influenza Research, State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China. .,School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong, China.
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Wang G, Zheng W, Zhu S, Wu Z, Lam TTY, Tong Y, Qi R. A cluster of Zika virus infection among travellers returning to China from Samoa: a case tracing study. J Travel Med 2018; 25:4989866. [PMID: 29718403 DOI: 10.1093/jtm/tay022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/07/2018] [Indexed: 11/13/2022]
Abstract
BACKGROUND A febrile man, who returned to China after a 9-day travel in Fiji and Samoa, was detected to be infected with Zika virus (ZIKV) at the port by Shenzhen Entry-Exit Inspection and Quarantine Bureau on 14 February 2016. METHODS The patient and his 32 travelling companions were traced for ZIKV infection. A standardised questionnaire was used to obtain the information on demographics, clinical manifestations and exposure history. Their samples were tested for ZIKV by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). The positive samples were subjected to viral culture and genome sequencing. FINDINGS Four of the 33 travellers were confirmed to be infected by ZIKV through qRT-PCR and viral culture, with an overall infection rate of 12%. Interestingly, one case (Patient 3) where high viremia levels were tested 4 days prior to symptoms. In addition, a 7-year-old girl was identified to have ZIKV infection on 17 February, but never had any manifestation. ZIKV was isolated from the four imported cases. Phylogenetic analysis based on whole genome sequences revealed that these isolates were similar to each other and close to the strain causing the French Polynesia outbreak in 2013. INTERPRETATION The travellers should be informed of the high risk for ZIKV infection during their stay in areas with active transmission and measures to prevent mosquito bites.
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Affiliation(s)
- Gang Wang
- Zhejiang Entry-exit Inspection and Quarantine Bureau, Hangzhou, China
| | - Wei Zheng
- Zhejiang Entry-exit Inspection and Quarantine Bureau, Hangzhou, China
| | - Sheng Zhu
- Yiwu Entry-Exit Inspection and Quarantine Bureau, Yiwu, China
| | - Zhonghua Wu
- Zhejiang Entry-exit Inspection and Quarantine Bureau, Hangzhou, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Yuanhua Tong
- Yiwu Entry-Exit Inspection and Quarantine Bureau, Yiwu, China
| | - Runzi Qi
- Zhejiang Entry-exit Inspection and Quarantine Bureau, Hangzhou, China
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Liu Y, Lam TTY, Zhu H, Guan Y. A24 Application of large-scale sequencing and data analysis to research on emerging infectious diseases. Virus Evol 2017; 3:vew036.023. [PMID: 28845278 PMCID: PMC5565992 DOI: 10.1093/ve/vew036.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Yongmei Liu
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
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Cheung YM, Lam TTY, Zhu H, Guan Y. A42 Evolution and spatial dissemination of the highly pathogenic Asian H5 avian influenza viruses. Virus Evol 2017; 3:vew036.041. [PMID: 28845256 PMCID: PMC5565942 DOI: 10.1093/ve/vew036.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Y M Cheung
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research School of Public Health Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - T T Y Lam
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research School of Public Health Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - H Zhu
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research School of Public Health Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Y Guan
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research School of Public Health Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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Affiliation(s)
- Lifeng Li
- Shantou University Medical College, Shantou, China
| | - Wenshan Hong
- Shantou University Medical College, Shantou, China
| | - Lian Duan
- Shenzhen Third People's Hospital, Shenzhen, China
| | - Jia Wang
- Shantou University Medical College, Shantou, China
| | - Tommy Tsan-Yuk Lam
- Centre of Influenza Research & State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Huachen Zhu
- Shantou University Medical College, Shantou, China
| | - Yi Guan
- Shantou University Medical College, Shantou, China
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37
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Huang PY, Lee CCD, Yip CH, Cheung CL, Yu G, Lam TTY, Smith DK, Zhu H, Guan Y. Genetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015. Infect Genet Evol 2016; 38:96-100. [PMID: 26690663 DOI: 10.1016/j.meegid.2015.12.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/08/2015] [Accepted: 12/09/2015] [Indexed: 02/05/2023]
Abstract
Phylogenetic analysis of the highly pathogenic avian influenza (HPAI) H5 viruses causing recent outbreaks in Taiwan showed that they belonged to the Asian HPAI H5 lineage, clade 2.3.4.4 viruses, and were apparently introduced by migratory birds. These viruses reassorted with Eurasian influenza gene pool viruses and formed five genotypic variants. As Taiwan has a similar influenza ecosystem to southern China, the HPAI H5 lineage could become established and enzootic in the island.
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Affiliation(s)
- Pei-Yu Huang
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong, China; Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region
| | | | - Chun-Hung Yip
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region; State Key Laboratory of Emerging Infectious Diseases (Shenzhen Base), Shenzhen Third People's Hospital, Shenzhen, China
| | - Chung-Lam Cheung
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Guangchuang Yu
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Tommy Tsan-Yuk Lam
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region
| | - David K Smith
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Huachen Zhu
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong, China; Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region; State Key Laboratory of Emerging Infectious Diseases (Shenzhen Base), Shenzhen Third People's Hospital, Shenzhen, China.
| | - Yi Guan
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong, China; Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region; State Key Laboratory of Emerging Infectious Diseases (Shenzhen Base), Shenzhen Third People's Hospital, Shenzhen, China.
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Abstract
The occurrence of human infections with avian H7N9 viruses since 2013 demonstrates the continuing pandemic threat posed by the current influenza ecosystem in China. Influenza surveillance and phylogenetic analyses showed that these viruses were generated by multiple interspecies transmissions and reassortments among the viruses resident in domestic ducks and the H9N2 viruses enzootic in chickens. A large population of domestic ducks hosting diverse influenza viruses provided the precondition for these events to occur, while acquiring internal genes from enzootic H9N2 influenza viruses in chickens promoted the spread of these viruses. Human infections effectively act as sentinels, reflecting the intensity of the activity of these viruses in poultry.
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Affiliation(s)
- Huachen Zhu
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China; State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China; Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China.
| | - Tommy Tsan-Yuk Lam
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - David Keith Smith
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Yi Guan
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China; State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China; Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
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39
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Wang J, Wu M, Hong W, Fan X, Chen R, Zheng Z, Zeng Y, Huang R, Zhang Y, Lam TTY, Smith DK, Zhu H, Guan Y. Infectivity and Transmissibility of Avian H9N2 Influenza Viruses in Pigs. J Virol 2016; 90:3506-14. [PMID: 26764002 PMCID: PMC4794674 DOI: 10.1128/jvi.02605-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 01/10/2016] [Indexed: 02/05/2023] Open
Abstract
UNLABELLED The H9N2 influenza viruses that are enzootic in terrestrial poultry in China pose a persistent pandemic threat to humans. To investigate whether the continuous circulation and adaptation of these viruses in terrestrial poultry increased their infectivity to pigs, we conducted a serological survey in pig herds with H9N2 viruses selected from the aquatic avian gene pool (Y439 lineage) and the enzootic terrestrial poultry viruses (G1 and Y280 lineages). We also compared the infectivity and transmissibility of these viruses in pigs. It was found that more than 15% of the pigs sampled from 2010 to 2012 in southern China were seropositive to either G1 or Y280 lineage viruses, but none of the sera were positive to the H9 viruses from the Y439 lineage. Viruses of the G1 and Y280 lineages were able to infect experimental pigs, with detectable nasal shedding of the viruses and seroconversion, whereas viruses of the Y439 lineage did not cause a productive infection in pigs. Thus, adaptation and prevalence in terrestrial poultry could lead to interspecies transmission of H9N2 viruses from birds to pigs. Although H9N2 viruses do not appear to be continuously transmissible among pigs, repeated introductions of H9 viruses to pigs naturally increase the risk of generating mammalian-adapted or reassorted variants that are potentially infectious to humans. This study highlights the importance of monitoring the activity of H9N2 viruses in terrestrial poultry and pigs. IMPORTANCE H9N2 subtype of influenza viruses has repeatedly been introduced into mammalian hosts, including humans and pigs, so awareness of their activity and evolution is important for influenza pandemic preparedness. However, since H9N2 viruses usually cause mild or even asymptomatic infections in mammalian hosts, they may be overlooked in influenza surveillance. Here, we found that the H9N2 viruses established in terrestrial poultry had higher infectivity in pigs than those from aquatic birds, which suggests that adaptation of the H9N2 viruses in terrestrial poultry might have increased the infectivity of the virus to mammals. Therefore, monitoring the prevalence and evolution of H9 viruses prevalent in terrestrial birds and conducting risk assessment of their threat to mammals are critical for evaluating the pandemic potential of this virus.
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Affiliation(s)
- Jia Wang
- Joint Influenza Research Center, Shantou University Medical College, Shantou, China State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Maocai Wu
- Joint Influenza Research Center, Shantou University Medical College, Shantou, China
| | - Wenshan Hong
- Joint Influenza Research Center, Shantou University Medical College, Shantou, China
| | - Xiaohui Fan
- Department of Microbiology, Guangxi Medical University, Nanning, China
| | - Rirong Chen
- Joint Influenza Research Center, Shantou University Medical College, Shantou, China
| | - Zuoyi Zheng
- Joint Influenza Research Center, Shantou University Medical College, Shantou, China
| | - Yu Zeng
- Joint Influenza Research Center, Shantou University Medical College, Shantou, China
| | - Ren Huang
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Yu Zhang
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - David K Smith
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Huachen Zhu
- Joint Influenza Research Center, Shantou University Medical College, Shantou, China State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Yi Guan
- Joint Influenza Research Center, Shantou University Medical College, Shantou, China State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China Department of Microbiology, Guangxi Medical University, Nanning, China
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40
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Watson SJ, Langat P, Reid SM, Lam TTY, Cotten M, Kelly M, Van Reeth K, Qiu Y, Simon G, Bonin E, Foni E, Chiapponi C, Larsen L, Hjulsager C, Markowska-Daniel I, Urbaniak K, Dürrwald R, Schlegel M, Huovilainen A, Davidson I, Dán Á, Loeffen W, Edwards S, Bublot M, Vila T, Maldonado J, Valls L, Brown IH, Pybus OG, Kellam P. Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013. J Virol 2015; 89:9920-31. [PMID: 26202246 PMCID: PMC4577897 DOI: 10.1128/jvi.00840-15] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/14/2015] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED The emergence in humans of the A(H1N1)pdm09 influenza virus, a complex reassortant virus of swine origin, highlighted the importance of worldwide influenza virus surveillance in swine. To date, large-scale surveillance studies have been reported for southern China and North America, but such data have not yet been described for Europe. We report the first large-scale genomic characterization of 290 swine influenza viruses collected from 14 European countries between 2009 and 2013. A total of 23 distinct genotypes were identified, with the 7 most common comprising 82% of the incidence. Contrasting epidemiological dynamics were observed for two of these genotypes, H1huN2 and H3N2, with the former showing multiple long-lived geographically isolated lineages, while the latter had short-lived geographically diffuse lineages. At least 32 human-swine transmission events have resulted in A(H1N1)pdm09 becoming established at a mean frequency of 8% across European countries. Notably, swine in the United Kingdom have largely had a replacement of the endemic Eurasian avian virus-like ("avian-like") genotypes with A(H1N1)pdm09-derived genotypes. The high number of reassortant genotypes observed in European swine, combined with the identification of a genotype similar to the A(H3N2)v genotype in North America, underlines the importance of continued swine surveillance in Europe for the purposes of maintaining public health. This report further reveals that the emergences and drivers of virus evolution in swine differ at the global level. IMPORTANCE The influenza A(H1N1)pdm09 virus contains a reassortant genome with segments derived from separate virus lineages that evolved in different regions of the world. In particular, its neuraminidase and matrix segments were derived from the Eurasian avian virus-like ("avian-like") lineage that emerged in European swine in the 1970s. However, while large-scale genomic characterization of swine has been reported for southern China and North America, no equivalent study has yet been reported for Europe. Surveillance of swine herds across Europe between 2009 and 2013 revealed that the A(H1N1)pdm09 virus is established in European swine, increasing the number of circulating lineages in the region and increasing the possibility of the emergence of a genotype with human pandemic potential. It also has implications for veterinary health, making prevention through vaccination more challenging. The identification of a genotype similar to the A(H3N2)v genotype, causing zoonoses at North American agricultural fairs, underlines the importance of continued genomic characterization in European swine.
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Affiliation(s)
- Simon J Watson
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Pinky Langat
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Scott M Reid
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | | | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Michael Kelly
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | | | - Yu Qiu
- Laboratory of Virology, Ghent University, Merelbeke, Belgium
| | - Gaëlle Simon
- Anses, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France
| | - Emilie Bonin
- Anses, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France
| | - Emanuela Foni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Chiara Chiapponi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Lars Larsen
- Department of Veterinary Diagnostics and Research, Technical University of Denmark, Copenhagen, Denmark
| | - Charlotte Hjulsager
- Department of Veterinary Diagnostics and Research, Technical University of Denmark, Copenhagen, Denmark
| | | | - Kinga Urbaniak
- Department of Swine Diseases, Panstwowy Instytut Weterynaryjny, Pulawy, Poland
| | | | | | | | - Irit Davidson
- Division of Avian Diseases, Kimron Veterinary Institute, Bet Dagan, Israel
| | - Ádám Dán
- National Food Chain Safety Office, Budapest, Hungary
| | - Willie Loeffen
- Central Veterinary Institute, Wageningen UR, Lelystad, The Netherlands
| | | | - Michel Bublot
- Virology Department, Discovery Research, Merial, Lyon, France
| | - Thais Vila
- Virology Department, Discovery Research, Merial, Lyon, France
| | - Jaime Maldonado
- Veterinary Diagnostic Services DIAGNOS, Laboratorios HIPRA SA, Gerona, Spain
| | - Laura Valls
- Veterinary Diagnostic Services DIAGNOS, Laboratorios HIPRA SA, Gerona, Spain
| | - Ian H Brown
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom Division of Infection & Immunity, University College London, London, United Kingdom
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Oong XY, Ng KT, Lam TTY, Pang YK, Chan KG, Hanafi NS, Kamarulzaman A, Tee KK. Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014. PLoS One 2015; 10:e0136254. [PMID: 26313754 PMCID: PMC4552379 DOI: 10.1371/journal.pone.0136254] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/01/2015] [Indexed: 12/16/2022] Open
Abstract
Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012-2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1%) patients infected with at least one respiratory virus, 287 (14.3%) and 183 (9.1%) samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors-total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10). Phylogenetic reconstruction of haemagglutinin (HA) gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%), Yamagata Clade 2 (48, 28.6%) and Victoria Clade 1 (55, 32.7%). With neuraminidase (NA) phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1) and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA) reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012-2013), and a clade shift from Yamagata Clade 2 to Clade 3 (2013-2014). Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013), with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion and sore throat. This study describes the evolution of influenza B viruses in Malaysia and highlights the importance of continuous surveillance for better vaccination policy in this region.
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Affiliation(s)
- Xiang Yong Oong
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tommy Tsan-Yuk Lam
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Nik Sherina Hanafi
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Lam TTY, Zhou B, Wang J, Chai Y, Shen Y, Chen X, Ma C, Hong W, Chen Y, Zhang Y, Duan L, Chen P, Jiang J, Zhang Y, Li L, Poon LLM, Webby RJ, Smith DK, Leung GM, Peiris JSM, Holmes EC, Guan Y, Zhu H. Dissemination, divergence and establishment of H7N9 influenza viruses in China. Nature 2015; 522:102-5. [PMID: 25762140 DOI: 10.1038/nature14348] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/24/2015] [Indexed: 02/05/2023]
Abstract
Since 2013 the occurrence of human infections by a novel avian H7N9 influenza virus in China has demonstrated the continuing threat posed by zoonotic pathogens. Although the first outbreak wave that was centred on eastern China was seemingly averted, human infections recurred in October 2013 (refs 3-7). It is unclear how the H7N9 virus re-emerged and how it will develop further; potentially it may become a long-term threat to public health. Here we show that H7N9 viruses have spread from eastern to southern China and become persistent in chickens, which has led to the establishment of multiple regionally distinct lineages with different reassortant genotypes. Repeated introductions of viruses from Zhejiang to other provinces and the presence of H7N9 viruses at live poultry markets have fuelled the recurrence of human infections. This rapid expansion of the geographical distribution and genetic diversity of the H7N9 viruses poses a direct challenge to current disease control systems. Our results also suggest that H7N9 viruses have become enzootic in China and may spread beyond the region, following the pattern previously observed with H5N1 and H9N2 influenza viruses.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- 1] State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China [2] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [3] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Boping Zhou
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Jia Wang
- 1] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [2] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Yujuan Chai
- 1] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [2] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Yongyi Shen
- 1] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [2] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Xinchun Chen
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Chi Ma
- 1] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [2] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Wenshan Hong
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China
| | - Yin Chen
- Key Laboratory of Emergency Detection for Public Health of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China
| | - Yanjun Zhang
- Key Laboratory of Emergency Detection for Public Health of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China
| | - Lian Duan
- 1] State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China [2] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [3] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Peiwen Chen
- 1] State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China [2] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China
| | - Junfei Jiang
- 1] State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China [2] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Yu Zhang
- 1] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [2] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Lifeng Li
- 1] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [2] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Leo Lit Man Poon
- 1] State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China [2] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Richard J Webby
- Division of Virology, Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - David K Smith
- 1] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [2] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Gabriel M Leung
- Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Joseph S M Peiris
- 1] State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China [2] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Yi Guan
- 1] State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China [2] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [3] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
| | - Huachen Zhu
- 1] State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China [2] Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou 515041, China [3] Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong, China
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Ma C, Lam TTY, Chai Y, Wang J, Fan X, Hong W, Zhang Y, Li L, Liu Y, Smith DK, Webby RJ, Peiris JSM, Zhu H, Guan Y. Emergence and evolution of H10 subtype influenza viruses in poultry in China. J Virol 2015; 89:3534-41. [PMID: 25589662 PMCID: PMC4403437 DOI: 10.1128/jvi.03167-14] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/31/2014] [Indexed: 02/05/2023] Open
Abstract
UNLABELLED The cases of human infections with H10N8 viruses identified in late 2013 and early 2014 in Jiangxi, China, have raised concerns over the origin, prevalence, and development of these viruses in this region. Our long-term influenza surveillance of poultry and migratory birds in southern China in the past 12 years showed that H10 influenza viruses have been introduced from migratory to domestic ducks over several winter seasons at sentinel duck farms at Poyang Lake, where domestic ducks share their water body with overwintering migratory birds. H10 viruses were never detected in terrestrial poultry in our survey areas until August 2013, when they were identified at live-poultry markets in Jiangxi. Since then, we have isolated 124 H10N8 or H10N6 viruses from chickens at local markets, revealing an ongoing outbreak. Phylogenetic analysis of H10 and related viruses showed that the chicken H10N8 viruses were generated through multiple reassortments between H10 and N8 viruses from domestic ducks and the enzootic chicken H9N2 viruses. These chicken reassortant viruses were highly similar to the human isolate, indicating that market chickens were the source of human infection. Recently, the H10 viruses further reassorted, apparently with H5N6 viruses, and generated an H10N6 variant. The emergence and prevalence of H10 viruses in chickens and the occurrence of human infections provide direct evidence of the threat from the current influenza ecosystem in China. IMPORTANCE After the outbreak of avian-origin H7N9 influenza viruses in China, fatal human infections with a novel H10N8 virus were reported. Utilizing data from 12 years of influenza surveillance in southern China, we showed that H10 viruses were regularly introduced by migratory ducks to domestic ducks on Poyang Lake, a major aggregative site of migratory birds in Asia. The H10 viruses were maintained and amplified in domestic ducks and then transmitted to chickens and reassorted with enzootic H9N2 viruses, leading to an outbreak and human infections at live-poultry markets. The emergence of the H10N8 virus, following a pathway similar to that of the recent H7N9 virus, highlights the role of domestic ducks and the current influenza ecosystem in China that facilitates influenza viruses moving from their reservoir hosts through the live-poultry system to cause severe consequences for public health.
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Affiliation(s)
- Chi Ma
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China
| | - Tommy Tsan-Yuk Lam
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Yujuan Chai
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Jia Wang
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaohui Fan
- Department of Microbiology, Guangxi Medical University, Nanning, China
| | - Wenshan Hong
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Yu Zhang
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Lifeng Li
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Yongmei Liu
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - David K Smith
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Richard J Webby
- Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Joseph S M Peiris
- Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China
| | - Huachen Zhu
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China
| | - Yi Guan
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China
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Liang H, Lam TTY, Fan X, Chen X, Zeng Y, Zhou J, Duan L, Tse M, Chan CH, Li L, Leung TY, Yip CH, Cheung CL, Zhou B, Smith DK, Poon LLM, Peiris M, Guan Y, Zhu H. Expansion of genotypic diversity and establishment of 2009 H1N1 pandemic-origin internal genes in pigs in China. J Virol 2014; 88:10864-74. [PMID: 25008935 PMCID: PMC4178866 DOI: 10.1128/jvi.01327-14] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/02/2014] [Indexed: 02/05/2023] Open
Abstract
UNLABELLED Two-way transmission of influenza viruses between humans and swine has been frequently observed, and the occurrence of the 2009 H1N1 pandemic influenza virus (pdm/09) demonstrated that swine-origin viruses could facilitate the genesis of a pandemic strain. Although multiple introductions to and reassortment in swine of the pdm/09 virus have been repeatedly reported in both Eurasia and the Americas, its long-term impact on the development of swine influenza viruses (SIVs) has not been systematically explored. Our comprehensive evolutionary studies of the complete genomes of 387 SIVs obtained from 2009 to 2012 by influenza virus surveillance in China revealed 17 reassortant genotypes with pdm/09-origin genes. Even though the entire 2009 pandemic virus and its surface genes cannot persist, its internal genes have become established and are now the predominant lineages in pigs in the region. The main persistent pdm/09-origin reassortant forms had at least five pdm/09-origin internal genes, and their surface genes were primarily of European avian-like (EA) or human H3N2-like SIV origin. These findings represent a marked change in the evolutionary patterns and ecosystem of SIVs in China. It is possible that the pdm/09-origin internal genes are in the process of replacing EA or triple-reassortant-like internal genes. These alterations in the SIV gene pool need to be continually monitored to assess changes in the potential for SIV transmission to humans. IMPORTANCE Shortly after the emergence of the 2009 pandemic H1N1 (pdm/09) influenza virus, it was transmitted from humans to pigs and this continues to occur around the world. Many reassortants between pdm/09-origin viruses and enzootic swine influenza viruses (SIVs) have been detected. However, the long-term impact of pdm/09-origin viruses on the SIV gene pool, which could lead to the generation of influenza viruses with the potential to infect humans, has not been systematically examined. From extensive surveillance of SIVs over a 38-month period in southern China, it was found that although neither complete pdm/09 viruses nor their surface genes could persist in pigs, their internal genes did persist. Over the survey period, these internal genes became predominant, potentially replacing those of the enzootic SIV lineages. The altered diversity of the SIV gene pool needs to be closely monitored for changes in the potential for SIV transmission to humans.
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Affiliation(s)
- Huyi Liang
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Xiaohui Fan
- Department of Microbiology, Guangxi Medical University, Nanning, China
| | - Xinchun Chen
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China
| | - Yu Zeng
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Ji Zhou
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Lian Duan
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Maying Tse
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China
| | - Chung-Hei Chan
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China
| | - Lifeng Li
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Tak-Ying Leung
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China
| | - Chun-Hung Yip
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China
| | - Chung-Lam Cheung
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China
| | - Boping Zhou
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China
| | - David K Smith
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Leo Lit-Man Poon
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China
| | - Malik Peiris
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
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Le MQ, Lam HM, Cuong VD, Lam TTY, Halpin RA, Wentworth DE, Hien NT, Thanh LT, Phuong HVM, Horby P, Boni MF. Migration and persistence of human influenza A viruses, Vietnam, 2001-2008. Emerg Infect Dis 2014; 19:1756-65. [PMID: 24188643 PMCID: PMC3837676 DOI: 10.3201/eid1911.130349] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Understanding global influenza migration and persistence is crucial for vaccine strain selection. Using 240 new human influenza A virus whole genomes collected in Vietnam during 2001-2008, we looked for persistence patterns and migratory connections between Vietnam and other countries. We found that viruses in Vietnam migrate to and from China, Hong Kong, Taiwan, Cambodia, Japan, South Korea, and the United States. We attempted to reduce geographic bias by generating phylogenies subsampled at the year and country levels. However, migration events in these phylogenies were still driven by the presence or absence of sequence data, indicating that an epidemiologic study design that controls for prevalence is required for robust migration analysis. With whole-genome data, most migration events are not detectable from the phylogeny of the hemagglutinin segment alone, although general migratory relationships between Vietnam and other countries are visible in the hemagglutinin phylogeny. It is possible that virus lineages in Vietnam persisted for >1 year.
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Tan Y, Lam TTY, Wu C, Lee SS, Viboud C, Zhang R, Weinberger DM. Increasing similarity in the dynamics of influenza in two adjacent subtropical Chinese cities following the relaxation of border restrictions. J Gen Virol 2013; 95:531-538. [PMID: 24310518 DOI: 10.1099/vir.0.059998-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The drivers of influenza seasonality remain heavily debated, especially in tropical/subtropical regions where influenza activity can peak in winter, during the rainy season, or remain constant throughout the year. We compared the epidemiological and evolutionary patterns of seasonal influenza epidemics in Hong Kong and Shenzhen, two adjacent cities in subtropical southern China. This comparison represents a unique natural experiment, as connectivity between these two cities has increased over the past decade. We found that, whilst summer influenza epidemics in Shenzhen used to peak 1-3 months later than those in Hong Kong, the difference decreased after 2005 (P<0.0001). Phylogenetic analysis revealed that influenza isolates from Shenzhen have become genetically closer to those circulating in Hong Kong over time (P = 0.045). Furthermore, although Shenzhen isolates used to be more distant from the global putative source of influenza viruses than isolates from Hong Kong (P<0.001), this difference has narrowed (P = 0.02). Overall, our study reveals that influenza activities show remarkably distinct epidemiological and evolutionary patterns in adjacent subtropical cities and suggests that human mobility patterns can play a major role in influenza dynamics in the subtropics.
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Affiliation(s)
- Yi Tan
- Stanley Ho Centre for Emerging Infectious Diseases, School of Public Health and Primary Care, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China.,Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Chunli Wu
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, Guangdong, China
| | - Shui-Shan Lee
- Stanley Ho Centre for Emerging Infectious Diseases, School of Public Health and Primary Care, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Renli Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, Guangdong, China
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA.,Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
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Lee HK, Tang JWT, Kong DHL, Loh TP, Chiang DKL, Lam TTY, Koay ESC. Comparison of mutation patterns in full-genome A/H3N2 influenza sequences obtained directly from clinical samples and the same samples after a single MDCK passage. PLoS One 2013; 8:e79252. [PMID: 24223916 PMCID: PMC3815150 DOI: 10.1371/journal.pone.0079252] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/19/2013] [Indexed: 11/19/2022] Open
Abstract
Human influenza viruses can be isolated efficiently from clinical samples using Madin-Darby canine kidney (MDCK) cells. However, this process is known to induce mutations in the virus as it adapts to this non-human cell-line. We performed a systematic study to record the pattern of MDCK-induced mutations observed across the whole influenza A/H3N2 genome. Seventy-seven clinical samples collected from 2009-2011 were included in the study. Two full influenza genomes were obtained for each sample: one from virus obtained directly from the clinical sample and one from the matching isolate cultured in MDCK cells. Comparison of the full-genome sequences obtained from each of these sources showed that 42% of the 77 isolates had acquired at least one MDCK-induced mutation. The presence or absence of these mutations was independent of viral load or sample origin (in-patients versus out-patients). Notably, all the five hemagglutinin missense mutations were observed at the hemaggutinin 1 domain only, particularly within or proximal to the receptor binding sites and antigenic site of the virus. Furthermore, 23% of the 77 isolates had undergone a MDCK-induced missense mutation, D151G/N, in the neuraminidase segment. This mutation has been found to be associated with reduced drug sensitivity towards the neuraminidase inhibitors and increased viral receptor binding efficiency to host cells. In contrast, none of the neuraminidase sequences obtained directly from the clinical samples contained the D151G/N mutation, suggesting that this mutation may be an indicator of MDCK culture-induced changes. These D151 mutations can confound the interpretation of the hemagglutination inhibition assay and neuraminidase inhibitor resistance results when these are based on MDCK isolates. Such isolates are currently in routine use in the WHO influenza vaccine and drug-resistance surveillance programs. Potential data interpretation miscalls can therefore be avoided by careful exclusion of such D151 mutants after further sequence analysis.
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Affiliation(s)
- Hong Kai Lee
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Julian Wei-Tze Tang
- Alberta Provincial Laboratory for Public Health, University of Alberta Hospital, Edmonton, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Canada
- * E-mail: (JW-TT); (ES-CK)
| | - Debra Han-Lin Kong
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Donald Kok-Leong Chiang
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | | | - Evelyn Siew-Chuan Koay
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
- * E-mail: (JW-TT); (ES-CK)
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Lam TTY, Wang J, Shen Y, Zhou B, Duan L, Cheung CL, Ma C, Lycett SJ, Leung CYH, Chen X, Li L, Hong W, Chai Y, Zhou L, Liang H, Ou Z, Liu Y, Farooqui A, Kelvin DJ, Poon LLM, Smith DK, Pybus OG, Leung GM, Shu Y, Webster RG, Webby RJ, Peiris JSM, Rambaut A, Zhu H, Guan Y. The genesis and source of the H7N9 influenza viruses causing human infections in China. Nature 2013; 502:241-4. [PMID: 23965623 PMCID: PMC3801098 DOI: 10.1038/nature12515] [Citation(s) in RCA: 360] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/01/2013] [Indexed: 02/05/2023]
Abstract
A novel H7N9 influenza A virus first detected in March 2013 has since caused more than 130 human infections in China, resulting in 40 deaths. Preliminary analyses suggest that the virus is a reassortant of H7, N9 and H9N2 avian influenza viruses, and carries some amino acids associated with mammalian receptor binding, raising concerns of a new pandemic. However, neither the source populations of the H7N9 outbreak lineage nor the conditions for its genesis are fully known. Using a combination of active surveillance, screening of virus archives, and evolutionary analyses, here we show that H7 viruses probably transferred from domestic duck to chicken populations in China on at least two independent occasions. We show that the H7 viruses subsequently reassorted with enzootic H9N2 viruses to generate the H7N9 outbreak lineage, and a related previously unrecognized H7N7 lineage. The H7N9 outbreak lineage has spread over a large geographic region and is prevalent in chickens at live poultry markets, which are thought to be the immediate source of human infections. Whether the H7N9 outbreak lineage has, or will, become enzootic in China and neighbouring regions requires further investigation. The discovery here of a related H7N7 influenza virus in chickens that has the ability to infect mammals experimentally, suggests that H7 viruses may pose threats beyond the current outbreak. The continuing prevalence of H7 viruses in poultry could lead to the generation of highly pathogenic variants and further sporadic human infections, with a continued risk of the virus acquiring human-to-human transmissibility.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China
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Chong YL, Lam TTY, Kim O, Lu H, Dunn P, Poss M. Successful establishment and global dispersal of genotype VI avian paramyxovirus serotype 1 after cross species transmission. Infect Genet Evol 2013; 17:260-8. [PMID: 23628639 PMCID: PMC7106292 DOI: 10.1016/j.meegid.2013.04.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/08/2013] [Accepted: 04/22/2013] [Indexed: 02/02/2023]
Abstract
The evolutionary history of avian paramyxovirus serotype 1 (PMV1), which includes the agents of Newcastle disease (ND), is characterized by a series of strain emergence events since viruses in this family were first recognized in the 1920s. Despite the importance of ND to the poultry industry, little is known about PMV1 strain emergence events and the subsequent dispersal and evolution of new strains. The genotype VI-PMV1 was first identified in the 1980s and has been named pigeon paramyxovirus-1 (PPMV1) because of unusual host specificity with Columbiformes (Collins et al., 1996); it has been responsible for panzootics in both chickens and pigeons during that time. Here, we used evolutionary analyses to characterize the emergence of this contemporary PMV1 lineage. We demonstrate that GVI-PMV1 arose through cross-species transmission events from Galliformes (i.e. chicken) to Columbiformes, and quickly established in pigeon populations. Our studies revealed a close association between the time of viral emergence and panzootic events of this virus. The virus appeared first in Southeastern Europe and quickly spread across the European continent, which became the epicenter for global virus dissemination. With new viral gene sequences, we show that GVI-PMV1 viruses currently circulating in North America resulted from multiple invasion events from Europe, one associated with an exotic European Columbiformes species, and that extant lineages have diversified locally. This study extends our understanding of successful viral emergence subsequent to cross-species transmission and dispersal patterns of newly emerged avian viruses, which may improve surveillance awareness and disease control of this and other important avian pathogens.
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Affiliation(s)
- Yee Ling Chong
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Wong VWS, Tse CH, Lam TTY, Wong GLH, Chim AML, Chu WCW, Yeung DKW, Law PTW, Kwan HS, Yu J, Sung JJY, Chan HLY. Molecular characterization of the fecal microbiota in patients with nonalcoholic steatohepatitis--a longitudinal study. PLoS One 2013; 8:e62885. [PMID: 23638162 PMCID: PMC3636208 DOI: 10.1371/journal.pone.0062885] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/27/2013] [Indexed: 12/18/2022] Open
Abstract
Background The human gut microbiota has profound influence on host metabolism and immunity. This study characterized the fecal microbiota in patients with nonalcoholic steatohepatitis (NASH). The relationship between microbiota changes and changes in hepatic steatosis was also studied. Methods Fecal microbiota of histology-proven NASH patients and healthy controls was analyzed by 16S ribosomal RNA pyrosequencing. NASH patients were from a previously reported randomized trial on probiotic treatment. Proton-magnetic resonance spectroscopy was performed to monitor changes in intrahepatic triglyceride content (IHTG). Results A total of 420,344 16S sequences with acceptable quality were obtained from 16 NASH patients and 22 controls. NASH patients had lower fecal abundance of Faecalibacterium and Anaerosporobacter but higher abundance of Parabacteroides and Allisonella. Partial least-square discriminant analysis yielded a model of 10 genera that discriminated NASH patients from controls. At month 6, 6 of 7 patients in the probiotic group and 4 of 9 patients in the usual care group had improvement in IHTG (P = 0.15). Improvement in IHTG was associated with a reduction in the abundance of Firmicutes (R2 = 0.4820, P = 0.0028) and increase in Bacteroidetes (R2 = 0.4366, P = 0.0053). This was accompanied by corresponding changes at the class, order and genus levels. In contrast, bacterial biodiversity did not differ between NASH patients and controls, and did not change with probiotic treatment. Conclusions NASH patients have fecal dysbiosis, and changes in microbiota correlate with improvement in hepatic steatosis. Further studies are required to investigate the mechanism underlying the interaction between gut microbes and the liver.
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Affiliation(s)
- Vincent Wai-Sun Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong.
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