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1
Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data
Wen-Bin Yu, Guang-Da Tang, Li Zhang, Richard T. Corlett
2020, 41(3): 247-257. doi: 10.24272/j.issn.2095-8137.2020.022

The outbreak of COVID-19 started in mid-December 2019 in Wuhan, China. Up to 29 February 2020, SARS-CoV-2 (HCoV-19 / 2019-nCoV) had infected more than 85 000 people in the world. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFluTM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak. We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau (τ) using the formula t=τ/2u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes. Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.

2
Why do we study animal toxins?
Yun ZHANG
2015, 36(4): 183-222. doi: 10.13918/j.issn.2095-8137.2015.4.183
+ 摘要 (3746) PDF (3538KB) (2286)
Venom (toxins) is an important trait evolved along the evolutionary tree of animals. Our knowledges on venoms, such as their origins and loss, the biological relevance and the coevolutionary patterns with other organisms are greatly helpful in understanding many fundamental biological questions, i.e., the environmental adaptation and survival competition, the evolution shaped development and balance of venoms, and the sophisticated correlations among venom, immunity, body power, intelligence, their genetic basis, inherent association, as well as the cost-benefit and trade-offs of biological economy. Lethal animal envenomation can be found worldwide. However, from foe to friend, toxin studies have led lots of important discoveries and exciting avenues in deciphering and fighting human diseases, including the works awarded the Nobel Prize and lots of key clinic therapeutics. According to our survey, so far, only less than 0.1% of the toxins of the venomous animals in China have been explored. We emphasize on the similarities shared by venom and immune systems, as well as the studies of toxin knowledge-based physiological toxin-like proteins/peptides (TLPs). We propose the natural pairing hypothesis. Evolution links toxins with humans. Our mission is to find out the right natural pairings and interactions of our body elements with toxins, and with endogenous toxin-like molecules. Although, in nature, toxins may endanger human lives, but from a philosophical point of view, knowing them well is an effective way to better understand ourselves. So, this is why we study toxins.
3
The role of wildlife (wild birds) in the global transmission of antimicrobial resistance genes
Jing Wang, Zhen-Bao Ma, Zhen-Ling Zeng, Xue-Wen Yang, Ying Huang, Jian-Hua Liu
2017, 38(2): 55-80. doi: 10.24272/j.issn.2095-8137.2017.003
+ 摘要 (1639) PDF (2143KB) (1866)
Antimicrobial resistance is an urgent global health challenge in human and veterinary medicine. Wild animals are not directly exposed to clinically relevant antibiotics; however, antibacterial resistance in wild animals has been increasingly reported worldwide in parallel to the situation in human and veterinary medicine. This underlies the complexity of bacterial resistance in wild animals and the possible interspecies transmission between humans, domestic animals, the environment, and wildlife. This review summarizes the current data on expanded-spectrum β-lactamase (ESBL), AmpC β-lactamase, carbapenemase, and colistin resistance genes in Enterobacteriaceae isolates of wildlife origin. The aim of this review is to better understand the important role of wild animals as reservoirs and vectors in the global dissemination of crucial clinical antibacterial resistance. In this regard, continued surveillance is urgently needed worldwide.
4
Kidney disease models: tools to identify mechanisms and potential therapeutic targets
Yin-Wu Bao, Yuan Yuan, Jiang-Hua Chen, Wei-Qiang Lin
2018, 39(2): 72-86. doi: 10.24272/j.issn.2095-8137.2017.055
+ 摘要 (1747) PDF (391KB) (1339)
Acute kidney injury (AKI) and chronic kidney disease (CKD) are worldwide public health problems affecting millions of people and have rapidly increased in prevalence in recent years. Due to the multiple causes of renal failure, many animal models have been developed to advance our understanding of human nephropathy. Among these experimental models, rodents have been extensively used to enable mechanistic understanding of kidney disease induction and progression, as well as to identify potential targets for therapy. In this review, we discuss AKI models induced by surgical operation and drugs or toxins, as well as a variety of CKD models (mainly genetically modified mouse models). Results from recent and ongoing clinical trials and conceptual advances derived from animal models are also explored.
5
Creating animal models, why not use the Chinese tree shrew (Tupaia belangeri chinensis)?
Yong-Gang Yao
2017, 38(3): 118-126. doi: 10.24272/j.issn.2095-8137.2017.032
+ 摘要 (2026) PDF (540KB) (1405)
The Chinese tree shrew (Tupaia belangeri chinensis), a squirrel-like and rat-sized mammal, has a wide distribution in Southeast Asia, South and Southwest China and has many unique characteristics that make it suitable for use as an experimental animal. There have been many studies using the tree shrew (Tupaia belangeri) aimed at increasing our understanding of fundamental biological mechanisms and for the modeling of human diseases and therapeutic responses. The recent release of a publicly available annotated genome sequence of the Chinese tree shrew and its genome database (www.treeshrewdb.org) has offered a solid base from which it is possible to elucidate the basic biological properties and create animal models using this species. The extensive characterization of key factors and signaling pathways in the immune and nervous systems has shown that tree shrews possess both conserved and unique features relative to primates. Hitherto, the tree shrew has been successfully used to create animal models for myopia, depression, breast cancer, alcohol-induced or non-alcoholic fatty liver diseases, herpes simplex virus type 1 (HSV-1) and hepatitis C virus (HCV) infections, to name a few. The recent successful genetic manipulation of the tree shrew has opened a new avenue for the wider usage of this animal in biomedical research. In this opinion paper, I attempt to summarize the recent research advances that have used the Chinese tree shrew, with a focus on the new knowledge obtained by using the biological properties identified using the tree shrew genome, a proposal for the genome-based approach for creating animal models, and the genetic manipulation of the tree shrew. With more studies using this species and the application of cutting-edge gene editing techniques, the tree shrew will continue to be under the spot light as a viable animal model for investigating the basis of many different human diseases.
6
Zoonotic origins of human coronavirus 2019 (HCoV-19 / SARS-CoV-2): why is this work important?
Gary Wong, Yu-Hai Bi, Qi-Hui Wang, Xin-Wen Chen, Zhi-Gang Zhang, Yong-Gang Yao
2020, 41(3): 213-219. doi: 10.24272/j.issn.2095-8137.2020.031

The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by infection with human coronavirus 2019 (HCoV-19 / SARS-CoV-2 / 2019-nCoV), is a global threat to the human population. Here, we briefly summarize the available data for the zoonotic origins of HCoV-19, with reference to the other two epidemics of highly virulent coronaviruses, SARS-CoV and MERS-CoV, which cause severe pneumonia in humans. We propose to intensify future efforts for tracing the origins of HCoV-19, which is a very important scientific question for the control and prevention of the pandemic.

7
Antimicrobial peptides: new hope in the war against multidrug resistance
James Mwangi, Xue Hao, Ren Lai, Zhi-Ye Zhang
2019, 40(6): 488-505. doi: 10.24272/j.issn.2095-8137.2019.062
+ 摘要 (4174) PDF (843KB) (1697)
The discovery of antibiotics marked a golden age in the revolution of human medicine. However, decades later, bacterial infections remain a global healthcare threat, and a return to the pre-antibiotic era seems inevitable if stringent measures are not adopted to curb the rapid emergence and spread of multidrug resistance and the indiscriminate use of antibiotics. In hospital settings, multidrug resistant (MDR) pathogens, including carbapenem-resistant Pseudomonas aeruginosa, vancomycin-resistant enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA), and extended-spectrum β-lactamases (ESBL) bearing Acinetobacter baumannii, Escherichia coli, and Klebsiella pneumoniae are amongst the most problematic due to the paucity of treatment options, increased hospital stay, and exorbitant medical costs. Antimicrobial peptides (AMPs) provide an excellent potential strategy for combating these threats. Compared to empirical antibiotics, they show low tendency to select for resistance, rapid killing action, broad-spectrum activity, and extraordinary clinical efficacy against several MDR strains. Therefore, this review highlights multidrug resistance among nosocomial bacterial pathogens and its implications and reiterates the importance of AMPs as next-generation antibiotics for combating MDR superbugs.
8
Tree shrew (Tupaia belangeri) as a novel laboratory disease animal model
Ji Xiao, Rong Liu, Ce-Shi Chen
2017, 38(3): 127-137. doi: 10.24272/j.issn.2095-8137.2017.033
+ 摘要 (1747) PDF (224KB) (1366)
The tree shrew (Tupaia belangeri) is a promising laboratory animal that possesses a closer genetic relationship to primates than to rodents. In addition, advantages such as small size, easy breeding, and rapid reproduction make the tree shrew an ideal subject for the study of human disease. Numerous tree shrew disease models have been generated in biological and medical studies in recent years. Here we summarize current tree shrew disease models, including models of infectious diseases, cancers, depressive disorders, drug addiction, myopia, metabolic diseases, and immune-related diseases. With the success of tree shrew transgenic technology, this species will be increasingly used in biological and medical studies in the future.
9
Animal models for filovirus infections
Vinayakumar Siragam, Gary Wong, Xiang-Guo Qiu
2018, 39(1): 15-24. doi: 10.24272/j.issn.2095-8137.2017.053
+ 摘要 (1350) PDF (337KB) (892)
The family Filoviridae, which includes the genera Marburgvirus and Ebolavirus, contains some of the most pathogenic viruses in humans and non-human primates (NHPs), causing severe hemorrhagic fevers with high fatality rates. Small animal models against filoviruses using mice, guinea pigs, hamsters, and ferrets have been developed with the goal of screening candidate vaccines and antivirals, before testing in the gold standard NHP models. In this review, we summarize the different animal models used to understand filovirus pathogenesis, and discuss the advantages and disadvantages of each model with respect to filovirus disease research.
10
Current understanding on the roles of gut microbiota in fish disease and immunity
Jin-Bo Xiong, Li Nie, Jiong Chen
2019, 40(2): 70-76. doi: 10.24272/j.issn.2095-8137.2018.069
+ 摘要 (2335) PDF (86KB) (1891)
Intensive aquaculture has increased the severity and frequency of fish diseases. Given the functional importance of gut microbiota in various facets of host physiology, modulation of this microbiota is a feasible strategy to mitigate emerging diseases in aquaculture. To achieve this, a fundamental understanding of the interplay among fish health, microbiota, and invading pathogens is required. This mini-review focuses on current knowledge regarding the associations between fish diseases, dysbiosis of gut microbiota, and immune responses. Furthermore, updated research on fish disease from an ecological perspective is discussed, including colonization resistance imposed by commensals and strategies used by pathogens to overcome resistance. We also propose several directions for future research, such as exploration of the causal links between fish diseases and specific taxa, and identification of universal gut microbial biomarkers for rapid disease diagnosis.
11
Chromosomal level assembly and population sequencing of the Chinese tree shrew genome
Yu Fan, Mao-Sen Ye, Jin-Yan Zhang, Ling Xu, Dan-Dan Yu, Tian-Le Gu, Yu-Lin Yao, Jia-Qi Chen, Long-Bao Lv, Ping Zheng, Dong-Dong Wu, Guo-Jie Zhang, Yong-Gang Yao
2019, 40(6): 506-521. doi: 10.24272/j.issn.2095-8137.2019.063
+ 摘要 (2944) PDF (4103KB) (687)
Chinese tree shrews (Tupaia belangeri chinensis) have become an increasingly important experimental animal in biomedical research due to their close relationship to primates. An accurately sequenced and assembled genome is essential for understanding the genetic features and biology of this animal. In this study, we used long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C) technology to obtain a high-qualitychromosome-scale scaffolding of the Chinese tree shrew genome. The new reference genome (KIZ version 2: TS_2.0) resolved problems in presently available tree shrew genomes and enabled accurate identification of large and complex repeat regions, gene structures, and species-specific genomic structural variants. In addition, by sequencing the genomes of six Chinese tree shrew individuals, we produced a comprehensive map of 12.8 M single nucleotide polymorphisms and confirmed that the major histocompatibility complex (MHC) loci and immunoglobulin gene family exhibited high nucleotide diversity in the tree shrew genome. We updated the tree shrew genome database (TreeshrewDB v2.0: http://www.treeshrewdb.org) to include the genome annotation information and genetic variations. The new high-quality reference genome of the Chinese tree shrew and the updated TreeshrewDB will facilitate the use of this animal in many different fields of research.
12
Delayed severe cytokine storm and immune cell infiltration in SARS-CoV-2-infected aged Chinese rhesus macaques
Tian-Zhang Song, Hong-Yi Zheng, Jian-Bao Han, Lin Jin, Xiang Yang, Feng-Liang Liu, Rong-Hua Luo, Ren-Rong Tian, Hou-Rong Cai, Xiao-Li Feng, Chao Liu, Ming-Hua Li, Yong-Tang Zheng
2020, 41(5): 503-516. doi: 10.24272/j.issn.2095-8137.2020.202
As of June 2020, Coronavirus Disease 2019 (COVID-19) has killed an estimated 440 000 people worldwide, 74% of whom were aged ≥65 years, making age the most significant risk factor for death caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To examine the effect of age on death, we established a SARS-CoV-2 infection model in Chinese rhesus macaques (Macaca mulatta) of varied ages. Results indicated that infected young macaques manifested impaired respiratory function, active viral replication, severe lung damage, and infiltration of CD11b+ and CD8+ cells in lungs at one-week post infection (wpi), but also recovered rapidly at 2 wpi. In contrast, aged macaques demonstrated delayed immune responses with a more severe cytokine storm, increased infiltration of CD11b+ cells, and persistent infiltration of CD8+ cells in the lungs at 2 wpi. In addition, peripheral blood T cells from aged macaques showed greater inflammation and chemotaxis, but weaker antiviral functions than that in cells from young macaques. Thus, the delayed but more severe cytokine storm and higher immune cell infiltration may explain the poorer prognosis of older aged patients suffering SARS-CoV-2 infection.
13
COVID-19-like symptoms observed in Chinese tree shrews infected with SARS-CoV-2
Ling Xu, Dan-Dan Yu, Yu-Hua Ma, Yu-Lin Yao, Rong-Hua Luo, Xiao-Li Feng, Hou-Rong Cai, Jian-Bao Han, Xue-Hui Wang, Ming-Hua Li, Chang-Wen Ke, Yong-Tang Zheng, Yong-Gang Yao
2020, 41(5): 517-526. doi: 10.24272/j.issn.2095-8137.2020.053
The coronavirus disease 2019 (COVID-19) pandemic continues to pose a global threat to the human population. Identifying animal species susceptible to infection with the SARS-CoV-2/ HCoV-19 pathogen is essential for controlling the outbreak and for testing valid prophylactics or therapeutics based on animal model studies. Here, different aged Chinese tree shrews (adult group, 1 year old; old group, 5–6 years old), which are close relatives to primates, were infected with SARS-CoV-2. X-ray, viral shedding, laboratory, and histological analyses were performed on different days post-inoculation (dpi). Results showed that Chinese tree shrews could be infected by SARS-CoV-2. Lung infiltrates were visible in X-ray radiographs in most infected animals. Viral RNA was consistently detected in lung tissues from infected animals at 3, 5, and 7 dpi, along with alterations in related parameters from routine blood tests and serum biochemistry, including increased levels of aspartate aminotransferase (AST) and blood urea nitrogen (BUN). Histological analysis of lung tissues from animals at 3 dpi (adult group) and 7 dpi (old group) showed thickened alveolar septa and interstitial hemorrhage. Several differences were found between the two different aged groups in regard to viral shedding peak. Our results indicate that Chinese tree shrews have the potential to be used as animal models for SARS-CoV-2 infection.
14
Application of the genome editing tool CRISPR/Cas9 in non-human primates
Xin LUO, Min LI, Bing SU
2016, 37(4): 214-219. doi: 10.13918/j.issn.2095-8137.2016.4.214
+ 摘要 (1769) PDF (1280KB) (2015)
In the past three years, RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system has been used to facilitate efficient genome editing in many model and non-model animals. However, its application in nonhuman primates is still at the early stage, though in view of the similarities in anatomy, physiology, behavior and genetics, closely related nonhuman primates serve as optimal models for human biology and disease studies. In this review, we summarize the current proceedings of gene editing using CRISPR/Cas9 in nonhuman primates.
15
FasParser: a package for manipulating sequence data
Yan-Bo Sun
2017, 38(2): 110-112. doi: 10.24272/j.issn.2095-8137.2017.017
+ 摘要 (1965) PDF (526KB) (1445)
A computer software package called ‘FasParser’ was developed for manipulating sequence data. It can be used on personal computers to perform series of analyses, including counting and viewing differences between two sequences at both DNA and codon levels, identifying overlapping regions between two alignments, sorting of sequences according to their IDs or lengths, concatenating sequences of multiple loci for a particular set of samples, translating nucleotide sequences to amino acids, and constructing alignments in several different formats, as well as some extracting and filtrating of data for a particular FASTA file. Majority of these functions can be run in a batch mode, which is very useful for analyzing large data sets. This package can be used by a broad audience, and is designed for researchers that do not have programming experience in sequence analyses. The GUI version of FasParser can be downloaded from https://github.com/Sun-Yanbo/FasParser, free of charge.
16
An online coronavirus analysis platform from the National Genomics Data Center
Zheng Gong, Jun-Wei Zhu, Cui-Ping Li, Shuai Jiang, Li-Na Ma, Bi-Xia Tang, Dong Zou, Mei-Li Chen, Yu-Bin Sun, Shu-Hui Song, Zhang Zhang, Jing-Fa Xiao, Yong-Biao Xue, Yi-Ming Bao, Zheng-Lin Du, Wen-Ming Zhao
2020, 41(6): 705-708. doi: 10.24272/j.issn.2095-8137.2020.065
17
Taxonomy is the cornerstone of biodiversity conservation-SEABRI reports on biological surveys in Southeast Asia
Shu-Qiang Li, Rui-Chang Quan
2017, 38(5): 213-214. doi: 10.24272/j.issn.2095-8137.2017.061
+ 摘要 (892) PDF (116KB) (444)
18
 Animal models for the study of hepatitis B virus infection
Wei-Na Guo, Bin Zhu, Ling Ai, Dong-Liang Yang, Bao-Ju Wang
2018, 39(1): 25-31. doi: 10.24272/j.issn.2095-8137.2018.013
+ 摘要 (1744) PDF (98KB) (1111)
Even with an effective vaccine, an estimated 240 million people are chronically infected with hepatitis B virus (HBV) worldwide. Current antiviral therapies, including interferon and nucleot(s)ide analogues, rarely cure chronic hepatitis B. Animal models are very crucial for understanding the pathogenesis of chronic hepatitis B and developing new therapeutic drugs or strategies. HBV can only infect humans and chimpanzees, with the use of chimpanzees in HBV research strongly restricted. Thus, most advances in HBV research have been gained using mouse models with HBV replication or infection or models with HBV-related hepadnaviral infection. This review summarizes the animal models currently available for the study of HBV infection.
19
Lamprey: a model for vertebrate evolutionary research
Yang XU, Si-Wei ZHU, Qing-Wei LI
2016, 37(5): 263-269. doi: 10.13918/j.issn.2095-8137.2016.5.263
+ 摘要 (1267) PDF (1085KB) (1081)
Lampreys belong to the superclass Cyclostomata and represent the most ancient group of vertebrates. Existing for over 360 million years, they are known as living fossils due to their many evolutionally conserved features. They are not only a keystone species for studying the origin and evolution of vertebrates, but also one of the best models for researching vertebrate embryonic development and organ differentiation. From the perspective of genetic information, the lamprey genome remains primitive compared with that of other higher vertebrates, and possesses abundant functional genes. Through scientific and technological progress, scientists have conducted in-depth studies on the nervous, endocrine, and immune systems of lampreys. Such research has significance for understanding and revealing the origin and evolution of vertebrates, and could contribute to a greater understanding of human diseases and treatments. This review presents the current progress and significance of lamprey research.
20
Genomic and transcriptomic analyses reveal selection of genes for puberty in Bama Xiang pigs
Yang Yang, Adeniyi C. Adeola, Hai-Bing Xie, Ya-Ping Zhang
2018, 39(6): 424-430. doi: 10.24272/j.issn.2095-8137.2018.068
+ 摘要 (1210) PDF (3071KB) (791)
The Bama Xiang pig (BMX) is a famous early-maturing Chinese indigenous breed with a two-end black coat. To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.
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