Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2

Since 2002, the world has witnessed major outbreaks of acute respiratory illness by three zoonotic coronaviruses (CoVs), which differ from each other in pathogenicity. Reasons for the lower pathogenicity of SARS-CoV-2 than the other two zoonotic coronaviruses, SARS-CoV and MERS-CoV, are not well understood. We herein compared the codon usage patterns of the three zoonotic CoVs causing severe acute respiratory syndromes and four human-specific CoVs (NL63, 229E, OC43, and HKU1) causing mild diseases. We found that the seven viruses have different codon usages, with SARS-CoV-2 having the lowest effective number of codons (ENC) among the zoonotic CoVs. Human codon adaptation index (CAI) analysis revealed that the CAI value of SARS-CoV-2 is the lowest among the zoonotic CoVs. The ENC and CAI values of SARS-CoV-2 were more similar to those of the less-pathogenic human-specific CoVs. To further investigate adaptive evolution within SARS-CoV-2, we examined codon usage patterns in 3573 genomes of SARS-CoV-2 collected over the initial 4 months of the pandemic. We showed that the ENC values and the CAI values of SARS-CoV-2 were decreasing over the period. The low ENC and CAI values could be responsible for the lower pathogenicity of SARS-CoV-2. While mutational pressure appears to shape codon adaptation in the overall genomes of SARS-CoV-2 and other zoonotic CoVs, the E gene of SARS-CoV-2, which has the highest codon usage bias, appears to be under strong natural selection. Data from the study contribute to our understanding of the pathogenicity and evolution of SARS-CoV-2 in humans.     

Deciphering the co-adaptation of codon usage between respiratory coronaviruses and their human host uncovers candidate therapeutics for COVID-19

Coronavirus disease 2019 (COVID-19) has caused thousands of deaths worldwide and has become an urgent public health concern. The extraordinary interhuman transmission of this disease has urged scientists to examine the various facets of its pathogenic agent, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, based on publicly available genomic data, we analyzed the codon usage co-adaptation profiles of SARS-CoV-2 and other respiratory coronaviruses (CoVs) with their human host, identified CoV-responsive human genes and their functional roles on the basis of both the relative synonymous codon usage (RSCU)-based correlation of viral genes with human genes and differential gene expression analysis, and predicted potential drugs for COVID-19 treatment based on these genes. The relatively high codon adaptation index (CAI) values (>0.70) signposted the gene expressivity efficiency of CoVs in human. The ENc-GC3 plot indicated that SARS-CoV-2 genome was under strict selection pressure while SARS-CoV and MERS-CoV were under selection and mutational pressures. The RSCU-based correlation analysis indicated that the viral genomes shared similar codons with a panoply of human genes. The merging of RSCU-based correlation data and SARS-CoV-2-responsive differentially expressed genes allowed the identification of human genes potentially affected by SARS-CoV-2 infection. Functional enrichment analysis indicated that these genes were enriched in biological processes and pathways related to host response to viral infection and immune response. Using the drug-gene interaction database, we screened a list of drugs that could target these genes as potential COVID-19 therapeutics. Our findings not only will contribute in vaccine development but also provide a useful set of drugs that could guide practitioners in strategical monitoring of COVID-19. We recommend practitioners to scrupulously screen this list of predicted drugs in order to authenticate those qualified for treating COVID-19 symptoms.     

2017年泰州市重点职业病危害因素接触人员职业健康风险评估分析

依据《江苏省重点职业病监测与职业健康风险评估工作实施方案》要求，分析泰州市职业健康检查、职业病诊断与鉴定、职业病患者工伤保险待遇落实及职业病报告信息。结果显示，2017年职业健康检查共16759人，检出职业病10例，疑似职业病23例，职业禁忌证22人。职业病患者均已享受工伤保险待遇。泰州市重点职业病危害因素为电焊烟尘、矽尘和噪声，应进一步加强职业健康监护工作。     

Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host

Rotavirus infection is a worldwide problem, with occurrence of highly divergent viruses classified in 8 species (A–H). We report here the evolution assessment of codon usage patterns in virus–host system in avian rotavirus (AvRV) of species RVA, RVD, RVF and RVG (preferentially affecting birds). The nucleotide contents, codon usage bias (CUB), relative synonymous codon usage (RSCU), and effective number of codons (ENCs) values were investigated targeting overexpressing major inner capsid viral protein (VP6) of these AvRV species. The results confirm that the evolutionary characteristics influences the rotavirus (RV) genetic diversity and impact of host’s natural selection on the AvRVs codons. Synonymous codon usage patterns were evaluated following multivariate statistical procedures on all available AvRV coding gene sequences. RSCU trees accommodated all AvRV species and preferred host sequences in one topology confirming greater imminence of AvRVs with the host chicken cell genes. Similarly, the codon adaptation index (CAI) results also displayed a higher adaptation of AvRVs to its chicken host. The codon preference analysis of RVs revealed that VP6 gene express more proficiently in the yeast system, whereas, codon optimization might be required for the effectual expression in Escherichia coli and Homo sapiens. The findings provide basic evidence on the dynamics of AvRV evolution and its host adaptation, which could be exploited for additional research on avian species in future.     

The characteristic of codon usage pattern and its evolution of hepatitis C virus

To give a new perspective on the codon usage of the hepatitis C virus (HCV) and the factors accounting for shaping the codon usage pattern of the virus, the relative synonymous codon usage (RSCU) values, aromaticity and hydrophobicity of each polyprotein of the virus, effective number of codons (ENC) values and nucleotide contents were calculated to implement a comparative analysis to evaluate the dynamics of the virus evolution. The RSCU values of each codon of 144 HCV ORFs indicated that all abundant codons were C/G-ended codons. The plots of principal component analysis based on sub-genotype of HCV indicated that sub-genotype 1a and 1b separated clearly on the axis of f2 suggesting that the codon usage bias between sub-genotype 1a and 1b strains was different. By comparing the codon usage between HCV and human cells, we found that the synonymous codon usage pattern of HCV was a mixture of coincidence and antagonism to that of host cells. The characteristics of the synonymous codon usage patterns and nucleotide contents of HCV, and the correlation analysis between GC(3s), GC(1,2s), GC% (ORF), GC% (5'-UTR), GC% (3'-UTR), aromaticity, hydrophobicity and ENC value, respectively, indicated that mutational pressure was the dominant factor accounting for the codon usage variation and selection pressure also accounted for HCV codon usage pattern.     

Clustering of low usage codons in the translation initiation region of hepatitis C virus

The adaptation of the overall codon usage pattern of hepatitis C virus (HCV) to that of human is estimated by the synonymous codon usage value (RSCU). The synonymous codon usage biases for the translation initiation region (TIR) of this virus are also analyzed by calculation of usage fluctuation of each synonymous codon along the TIR (the first 30 codon sites of the whole coding sequence of HCV). As for the overall codon usage pattern of HCV, this virus has a significant tendency to delete the codons with CpG or TpA dinucleotides. Turning to the adaptation of the overall codon usage of HCV to that of human, over half part of codons has a similar usage pattern between this virus and human, suggesting that the host cellular environment of the overall codon usage pattern influences the formation of codon usage for HCV. In addition, there is no obvious phenomenon that the codons with relatively low energy tend to be highly selected in the TIR of HCV, suggesting that the synonymous codon usage patterns for the TIR of HCV might be not affected by the secondary structure of nucleotide sequence, however, the formation of synonymous codons usage in the TIR of HCV is influenced by the overall codon usage patterns of human to some degree.     

Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection

Severe acute respiratory syndrome (SARS) is a highly contagious infectious disease which first emerged in late 2002, caused by a then novel human coronavirus, SARS coronavirus (SARS-CoV). The virus is believed to have originated from bats and transmitted to human through intermediate animals such as civet cats. The re-emergence of SARS-CoV remains a valid concern due to the continual persistence of zoonotic SARS-CoVs and SARS-like CoVs (SL-CoVs) in bat reservoirs. In this study, the screening for the presence of SARS-specific T cells in a cohort of three SARS-recovered individuals at 9 and 11 years post-infection was carried out, and all memory T cell responses detected target the SARS-CoV structural proteins. Two CD8⁺ T cell responses targeting the SARS-CoV membrane (M) and nucleocapsid (N) proteins were characterized by determining their HLA restriction and minimal T cell epitope regions. Furthermore, these responses were found to persist up to 11 years post-infection. An absence of cross-reactivity of these CD8⁺ T cell responses against the newly-emerged Middle East respiratory syndrome coronavirus (MERS-CoV) was also demonstrated. The knowledge of the persistence of SARS-specific celullar immunity targeting the viral structural proteins in SARS-recovered individuals is important in the design and development of SARS vaccines, which are currently unavailable.     

The effects of synonymous codon usages on genotypic formation of open reading frames in hepatitis E virus

Hepatitis E virus (HEV) infection has emerged as an important public health issue. As a zoonotic RNA virus, new strains are continuously discovered from human or various animal species. However, the capability of cross-species infection varies largely among different strains. Because the classical nucleotide-based genotyping system provides little functional insight, this study aimed to comprehensively investigate codon usage of the HEV coding regions for better understanding the evolutional orientation, virus-host interaction and cross-species transmission. We observed significant differences of the four nucleotide usages in the three open reading frames, indicating that the evolutional tendency of HEV caused by mutation pressure is modified by the evolutional dynamic related to positive selection. Furthermore, significant differences of nucleotide usages were found among HEV isolated from different host species, suggesting an important role of natural selection related to the host. Analysis of effective number of codons revealed distinct degrees of biased codon usage caused by mutation pressure or the host. Finally, we have mapped the similarity levels of the overall codon usage between the virus and the host to assess the potential of cross-species infection. Thus, this study has provided a novel aspect for better understanding the HEV genetic orientation and the zoonotic nature.     

新型冠状病毒感染者核酸和抗体检测结果分析

目的 了解新型冠状病毒(novel coronavirus 2019,2019-nCoV)感染者不同时期、不同类型标本中病毒核酸和抗体的检测情况,为完善新型冠状病毒肺炎(简称新冠肺炎)诊疗和防控方案提供科学依据。 方法 2020年2月26—27日采集娄底市71例新冠肺炎确诊病例和25例无症状感染者的粪便、血液和咽拭子,应用RT-PCR方法开展2019-nCoV核酸检测,采用胶体金方法开展2019-nCoV抗体检测,分析检测结果。 结果 共采集96份粪便,95份咽拭子,83份血液标本,粪便2019-nCoV核酸检出率不同年龄组差异有统计学意义;无症状感染者阳性率(47.06%)高于确诊病例(12.70%),＜40岁患者的阳性率(37.5%)高于≥40岁患者的阳性率(8.33%);咽拭子的阳性率无症状感染者(12.5%)和确诊病例(11.3%)差异无统计学意义;血液标本2019-nCoV 抗体检出率为94.0%。 结论 出院患者咽拭子、粪便标本均不同程度检出2019-nCoV核酸,无症状感染者粪便标本核酸检出率高于确诊病例,提示应重点关注无症状感染者在疫情传播中的作用,需加强对无症状感染者、出院患者的持续追踪和管理,综合多个指标进一步评估传染性。     

Synonymous codon usage analysis of hand,foot and mouth disease viruses: A comparative study on coxsackievirus A6, A10, A16, and enterovirus 71 from 2008 to 2015

Enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) have been considered major pathogens of hand, foot and mouth disease (HFMD) throughout the world for decades. In recent years, coxsackievirus A6 (CVA6) and coxsackievirus A10 (CVA10) have raised attention as two other serious pathogens of HFMD. The present study focused on the synonymous codon usage of four viruses isolated from 2008 to 2015, with particular attention on P1 (encoding capsid proteins) and P2-P3 regions (both encoding non-structural proteins) in the genomic RNA. Relative synonymous codon usage, effective number of codons, neutrality and correspondence were analyzed. The results indicated that these viruses prefer A/T at the third position in codons rather than G/C. The most frequent codons of 4 essential and 2 semi-essential amino acids, as well as a key amino acid of metabolic junctions (Glu) used in the four viruses are also the most frequently used in humans. Effective number of codons (ENC) values indicated weak codon usage bias in all the viruses. Relatively, the force of mutation pressure in the P1 region was found to be stronger than that in the P2-P3 region, and this force in the P1 region of CVA6 and EV71 was stronger than that of CVA10 and A16. The neutrality analysis results implied that mutation pressure plays a minor role in shaping codon bias of these viruses. Correspondence analysis indicated that the codon usage of EV71 strains varied much more than that of other viruses. In conclusion, the present study provides novel and comparative insight into the evolution of HFMD pathogens at the codon level.     

双抗原夹心免疫层析法在新型冠状病毒感染诊断中的应用

目的:探讨双抗原夹心免疫层析法抗体检测在新型冠状病毒(2019-nCoV)感染中的诊断价值。方法:选取在医院就诊的179例新型冠状病毒肺炎(COVID-19)患者为临床诊断阳性病例,另选同期就诊的85例确诊未感染2019-nCoV患者为临床诊断阴性病例。采用基于双抗原夹心法的胶体金免疫层析法和上转发光免疫层析法进行血清总抗体(IgG、IgM和IgA)检测,分析两种方法2019-nCoV总抗体(IgG、IgM和IgA)检测结果与临床诊断的灵敏度、特异度和总符合率。结果:建立针对2019-nCoV抗体检测的双抗原夹心免疫层析方法,胶体金免疫层析法检测血清2019-nCoV总抗体(IgG、IgM和IgA)与临床诊断的灵敏度、特异度和总符合率分别为97.77%、100%和98.48%;上转发光免疫层析法分别为98.88%、100%和99.24%。两种检测方法检测血清2019-nCoV总抗体(IgG、IgM和IgA)的总符合率与临床诊断结果比较,差异有统计学意义(χ²=246.5,χ²=225.0;P<0.05)。结论:双抗原夹心法对于2019-nCoV抗体检测具有重要应用价值。     

新型冠状病毒(2019-nCoV)相关研究进展

 

自2019年12月底，湖北武汉暴发新型冠状病毒（2019-nCoV）感染疫情，截至2020年2月20日全国发现感染病例累计7万余例，2019-nCoV传播速度快，影响大。为尽快了解2019-nCoV感染的发生、发展进程，本文对2019-nCoV相关研究进行综述，以进一步了解其致病机制，科学、合理的采取诊疗措施，积极预防和控制疫情。

     

Review of bats and SARS

Bats have been identified as a natural reservoir for an increasing number of emerging zoonotic viruses, including henipaviruses and variants of rabies viruses. Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Our current research focused on the identification of the reservoir species for the progenitor virus of the SARS coronaviruses responsible for outbreaks during 2002-2003 and 2003-2004. In addition to SARS-like coronaviruses, many other novel bat coronaviruses, which belong to groups 1 and 2 of the 3 existing coronavirus groups, have been detected by PCR. The discovery of bat SARS-like coronaviruses and the great genetic diversity of coronaviruses in bats have shed new light on the origin and transmission of SARS coronaviruses.     

WHO《新型冠状病毒感染暴发时社区、家庭和医疗卫生机构照护中医用口罩的使用指南》解读

 

有效预防和控制新型冠状病毒的暴发流行是政府、公众及每位卫生专业人员面临的严峻挑战。在新型冠状病毒暴发时期,世界卫生组织（WHO）发布《新型冠状病毒暴发时社区、家庭和医疗卫生机构照护中医用口罩的使用指南》,对从事公共卫生、感染的预防和控制的卫生专业人员、卫生管理人员、卫生保健和社区卫生工作人员医用口罩的使用提出了指导性的建议。本文对该指南进行解读,了解在社区、家庭和医疗卫生机构照护中医用口罩 佩戴和管理的建议,旨在为口罩的正确佩戴,合理使用,避免资源浪费提供科学依据。

     

2019 Novel coronavirus (COVID-19) overview

Novel coronaviruses (CoVs) are zoonotic pathogens, but the first human-to-human transmission has been reported. CoVs have the best known genome of all RNA viruses, and mutations in the genome have now been found. A pneumonia of unknown cause detected in Wuhan, China, was first reported to the WHO Country Office in China on 31 December 2019. This study aims to report early findings related to COVID-19 and provide methods to prevent and treat it. 

     

Analysis of codon usage patterns and influencing factors in rice tungro bacilliform virus

Rice tungro bacilliform virus (RTBV) belongs to genus Tungrovirus within the family Caulimoviridae harbors circular double-stranded DNA (dsDNA). Rice tungro disease (RTD) caused by RTBV, responsible for severe rice yield losses in South and Southeast Asia. Here, we performed a systematic evolutionary and codon usage bias (CUB) analysis of RTBV genome sequences. We analysed different bioinformatics techniques to calculate the nucleotide compositions, the relative synonymous codon usage (RSCU), and other indices. The results indicated slightly or low codon usage bias in RTBV isolates. Mutation and natural selection pressures have equally contributed to this low codon usage bias. Additionally, multiple factors such as host, geographical distribution also affect codon usage patterns in RTBV genomes. RSCU analysis revealed that RTBV shows mutation bias and prefers A and U ended codons to code amino acids. Codon usage patterns of RTBV were also found to be influenced by its host. This indicates that RTBV have evolved codon usage patterns that are specific to its host. The findings from this study are expected to increase our understanding of factors leading to viral evolution and fitness with respect to hosts and the environment.     

Genomic Analysis of Influenza A Viruses, including Avian Flu (H5N1) Strains

This study was designed to conduct genomic analysis in two steps, such as the overall relative synonymous codon usage (RSCU) analysis of the five virus species in the orthomyxoviridae family, and more intensive pattern analysis of the four subtypes of influenza A virus (H1N1, H2N2, H3N2, and H5N1) which were isolated from human population. All the subtypes were categorized by their isolated regions, including Asia, Europe, and Africa, and most of the synonymous codon usage patterns were analyzed by correspondence analysis (CA). As a result, influenza A virus showed the lowest synonymous codon usage bias among the virus species of the orthomyxoviridae family, and influenza B and influenza C virus were followed, while suggesting that influenza A virus might have an advantage in transmitting across the species barrier due to their low codon usage bias. The ENC values of the host-specific HA and NA genes represented their different HA and NA types very well, and this reveals that each influenza A virus subtype uses different codon usage patterns as well as the amino acid compositions. In NP, PA and PB2 genes, most of the virus subtypes showed similar RSCU patterns except for H5N1 and H3N2 (A/HK/1774/1999) subtypes which were suspected to be transmitted across the species barrier, from avian and porcine species to human beings, respectively. This distinguishable synonymous codon usage patterns in non-human origin viruses might be useful in determining the origin of influenza A viruses in genomic levels as well as the serological tests. In this study, all the process, including extracting sequences from GenBank flat file and calculating codon usage values, was conducted by Java codes, and these bioinformatics-related methods may be useful in predicting the evolutionary patterns of pandemic viruses.     

微滴式数字PCR和实时荧光定量PCR对新型冠状病毒肺炎患者不同时间血便尿中核酸检测结果初步探讨

目的 分析微滴式数字PCR(droplet digital PCR, ddPCR)和实时荧光定量PCR(quantitative real-time PCR,qPCR)的核酸检测结果,比较两种方法检测各类样本的差异性,为改进新型冠状病毒核酸检测方案提供数据支持。 方法 利用ddPCR和qPCR技术对已经确诊的3例新型冠状病毒肺炎患者发病不同时间的全血、尿液、粪便共22份标本进行新型冠状病毒核酸检测。 结果 两种方法对人保守区域基因扩增结果一致:全血标本信号最强,尿液次之,粪便最少;ddPCR在1份全血,1份尿液,5份粪便中检出ORF-1ab和N基因的阳性微滴,qPCR仅在3份粪便中检出上述基因,漏检的3个标本基因拷贝数平均浓度为128 copies/ml;ddPCR在发病<5、5~15、>15 d的各类标本中都有检出,qPCR检出以中晚期为主;重症病例用ddPCR均可测到阳性微滴,qPCR检测的各类标本均为阴性;轻症病例的各类标本中qPCR只有粪便核酸检测阳性,ddPCR检出率高于qPCR。 结论 ddPCR可以有效克服qPCR 灵敏度不足的难题,是对qPCR 的有益补充,尤其是针对病毒载量比较低的血液、尿液和可疑的粪便或肛拭子标本,适用于早期感染的判断及患者治愈后出院诊断。