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《Cell host & microbe》2022,30(4):545-555.e4
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Yang Li Hao-Rui Si Yan Zhu Nan Xie Bei Li Xiang-Ping Zhang Jun-Feng Han Hong-Hong Bao Yong Yang Kai Zhao Zi-Yuan Hou Si-Jia Cheng Shuan-Hu Zhang Zheng-Li Shi Peng Zhou 《中国病毒学》2022,37(2):187-197
The nationwide COVID-19 epidemic ended in 2020, a few months after its outbreak in Wuhan, China at the end of 2019. Most COVID-19 cases occurred in Hubei Province, with a few local outbreaks in other provinces of China. A few studies have reported the early SARS-CoV-2 epidemics in several large cities or provinces of China. However, information regarding the early epidemics in small and medium-sized cities, where there are still traditionally large families and community culture is more strongly maintained and thus, transmission profiles may differ, is limited. In this study, we characterized 60 newly sequenced SARS-CoV-2 genomes from Anyang as a representative of small and medium-sized Chinese cities, compared them with more than 400 reference genomes from the early outbreak, and studied the SARS-CoV-2 transmission profiles. Genomic epidemiology revealed multiple SARS-CoV-2 introductions in Anyang and a large-scale expansion of the epidemic because of the large family size. Moreover, our study revealed two transmission patterns in a single outbreak, which were attributed to different social activities. We observed the complete dynamic process of single-nucleotide polymorphism development during community transmission and found that intrahost variant analysis was an effective approach to studying cluster infections. In summary, our study provided new SARS-CoV-2 transmission profiles representative of small and medium-sized Chinese cities as well as information on the evolution of SARS-CoV-2 strains during the early COVID-19 epidemic in China. 相似文献
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Luis Antonio Moreno Borraz Mercedes Giménez López Patricia Carrera Lasfuentes Emilio González Pérez Concepción Ortíz Domingo José Luis Bonafonte Marteles Carmen Vicente Gaspar Francisco Amorós de la Nieta Alejandro Sastre Heres Ángel Luis García Forcada María Pilar Serrano Herrero Silvia Fernández Doblado María Carmen Espinosa Val María Mar Fernández Adarve Adriana Narvión Carriquiri Fernando Arto Maza Marta Barea Gil Irene Aznar Vázquez Ana Coarasa Lirón de Robles 《Revista espa?ola de geriatría y gerontología》2021,56(2):75-80
Background and goalsThe aim of the study is to know the prevalence of SARS-CoV-2 infection in patients and professional staff of a medium or long-stay hospital during the peak period of the pandemic in Spain, spring 2020.Material and methodsAt the end of February 2020, we developed at the hospital a strategy to diagnose the SARS-CoV-2 infection consisting of complementing the realization of PCR tests at real time with a quick technique of lateral flow immunochromatography to detect IgG and IgM antibodies against the virus. We also developed a protocol to realize those diagnostic tests and considered an infection (current or past) a positive result in any of the above tests.We included 524 participants in the study (230 patients and 294 hospital staff), and divided them into hospital patients and Hemodialysis outpatients. Furthermore, we divided the hospital staff into healthcare and non-healthcare staff. The documented period was from March, 20th to April, 21st, 2020.Results26 out of 230 patients tested positive in any of the diagnostic techniques (PCR, antibodies IgG, IgM) with a 11.30% prevalence. According to patients groups, we got a 14.38% prevalence in hospital patients vs. 5.95% in outpatients, with a significantly higher risk in admitted patients after adjustment for age and gender (OR=3,309, 95%CI: 1,154-9,495).24 out of 294 hospital staff tested positive in any of the diagnostic techniques, with a 8.16% prevalence. According to the groups, we got a 8.91% prevalence in healthcare staff vs. 4.26% in non-healthcare staff. Thus, we do not see any statistically significant differences between hospital staff and patients as far as prevalence is concerned (P=0,391), (OR=2,200, 95%CI: 0,500-9,689).ConclusionsThe result of the study was a quite low prevalence rate of SARS-CoV-2 infection, in both patients and hospital staff, being the hospital patients’ prevalence rate higher than the outpatients’, and the healthcare staff higher than the non-healthcare's. Combining PCR tests (gold standard) with antibodies tests proved useful as a diagnostic strategy. 相似文献
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Yongsen Ruan Mei Hou Xiaolu Tang Xionglei He Xuemei Lu Jian Lu Chung-I Wu Haijun Wen 《Molecular biology and evolution》2022,39(3)
In new epidemics after the host shift, the pathogens may experience accelerated evolution driven by novel selective pressures. When the accelerated evolution enters a positive feedback loop with the expanding epidemics, the pathogen’s runaway evolution may be triggered. To test this possibility in coronavirus disease 2019 (COVID-19), we analyze the extensive databases and identify five major waves of strains, one replacing the previous one in 2020–2021. The mutations differ entirely between waves and the number of mutations continues to increase, from 3-4 to 21-31. The latest wave in the fall of 2021 is the Delta strain which accrues 31 new mutations to become highly prevalent. Interestingly, these new mutations in Delta strain emerge in multiple stages with each stage driven by 6–12 coding mutations that form a fitness group. In short, the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from the oldest to the youngest wave, and from the earlier to the later stages of the Delta wave, is a process of acceleration with more and more mutations. The global increase in the viral population size (M(t), at time t) and the mutation accumulation (R(t)) may have indeed triggered the runaway evolution in late 2020, leading to the highly evolved Alpha and then Delta strain. To suppress the pandemic, it is crucial to break the positive feedback loop between M(t) and R(t), neither of which has yet to be effectively dampened by late 2021. New waves after Delta, hence, should not be surprising. 相似文献
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Shuhui Song Cuiping Li Lu Kang Dongmei Tian Nazish Badar Wentai Ma Shilei Zhao Xuan Jiang Chun Wang Yongqiao Sun Wenjie Li Meng Lei Shuangli Li Qiuhui Qi Aamer Ikram Muhammad Salman Massab Umair Huma Shireen Fatima Batool Bing Zhang Hua Chen Yun-Gui Yang Amir Ali Abbasi Mingkun Li Yongbiao Xue Yiming Bao 《基因组蛋白质组与生物信息学报(英文版)》2021,19(5):727-740
COVID-19 has swept globally and Pakistan is no exception. To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan, we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1, 2020. We identified a total of 347 mutated positions, 31 of which were over-represented in Pakistan. Meanwhile, we found over 1000 intra-host single-nucleotide variants (iSNVs). Several of them occurred concurrently, indicating possible interactions among them or coevolution. Some of the high-frequency iSNVs in Pakistan were not observed in the global population, suggesting strong purifying selections. The genomic epidemiology revealed five distinctive spreading clusters. The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure, indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation (G8371T in ORF1ab) of this cluster. Furthermore, 28 putative international introductions were identified, several of which are consistent with the epidemiological investigations. In all, this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan, which could aid ongoing and future viral surveillance and COVID-19 control. 相似文献
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Allison J. Greaney Tyler N. Starr Pavlo Gilchuk Seth J. Zost Elad Binshtein Andrea N. Loes Sarah K. Hilton John Huddleston Rachel Eguia Katharine H.D. Crawford Adam S. Dingens Rachel S. Nargi Rachel E. Sutton Naveenchandra Suryadevara Paul W. Rothlauf Zhuoming Liu Sean P.J. Whelan Robert H. Carnahan Jesse D. Bloom 《Cell host & microbe》2021,29(1):44-57.e9
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Matteo Chiara David S Horner Carmela Gissi Graziano Pesole 《Molecular biology and evolution》2021,38(6):2547
Effective systems for the analysis of molecular data are fundamental for monitoring the spread of infectious diseases and studying pathogen evolution. The rapid identification of emerging viral strains, and/or genetic variants potentially associated with novel phenotypic features is one of the most important objectives of genomic surveillance of human pathogens and represents one of the first lines of defense for the control of their spread. During the COVID 19 pandemic, several taxonomic frameworks have been proposed for the classification of SARS-Cov-2 isolates. These systems, which are typically based on phylogenetic approaches, represent essential tools for epidemiological studies as well as contributing to the study of the origin of the outbreak. Here, we propose an alternative, reproducible, and transparent phenetic method to study changes in SARS-CoV-2 genomic diversity over time. We suggest that our approach can complement other systems and facilitate the identification of biologically relevant variants in the viral genome. To demonstrate the validity of our approach, we present comparative genomic analyses of more than 175,000 genomes. Our method delineates 22 distinct SARS-CoV-2 haplogroups, which, based on the distribution of high-frequency genetic variants, fall into four major macrohaplogroups. We highlight biased spatiotemporal distributions of SARS-CoV-2 genetic profiles and show that seven of the 22 haplogroups (and of all of the four haplogroup clusters) showed a broad geographic distribution within China by the time the outbreak was widely recognized—suggesting early emergence and widespread cryptic circulation of the virus well before its isolation in January 2020. General patterns of genomic variability are remarkably similar within all major SARS-CoV-2 haplogroups, with UTRs consistently exhibiting the greatest variability, with s2m, a conserved secondary structure element of unknown function in the 3′-UTR of the viral genome showing evidence of a functional shift. Although several polymorphic sites that are specific to one or more haplogroups were predicted to be under positive or negative selection, overall our analyses suggest that the emergence of novel types is unlikely to be driven by convergent evolution and independent fixation of advantageous substitutions, or by selection of recombined strains. In the absence of extensive clinical metadata for most available genome sequences, and in the context of extensive geographic and temporal biases in the sampling, many questions regarding the evolution and clinical characteristics of SARS-CoV-2 isolates remain open. However, our data indicate that the approach outlined here can be usefully employed in the identification of candidate SARS-CoV-2 genetic variants of clinical and epidemiological importance. 相似文献
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Joyce M Ngoi Peter K Quashie Collins M Morang'a Joseph HK Bonney Dominic SY Amuzu Selassie Kumordjie Ivy A Asante Evelyn Y Bonney Miriam Eshun Linda Boatemaa Vanessa Magnusen Erasmus N Kotey Nicaise T Ndam Frederick Tei-Maya Augustina K Arjarquah Evangeline Obodai Isaac D Otchere Yaw Bediako Joe K Mutungi Lucas N Amenga-Etego John K Odoom Abraham K Anang George B Kyei Bright Adu William K Ampofo Gordon A Awandare 《Experimental biology and medicine (Maywood, N.J.)》2021,246(8):960
The confirmed case fatality rate for the coronavirus disease 2019 (COVID-19) in Ghana has dropped from a peak of 2% in March to be consistently below 1% since May 2020. Globally, case fatality rates have been linked to the strains/clades of circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a specific country. Here we present 46 whole genomes of SARS-CoV-2 circulating in Ghana, from two separate sequencing batches: 15 isolates from the early epidemic (March 12–April 1 2020) and 31 from later time-points ( 25–27 May 2020). Sequencing was carried out on an Illumina MiSeq system following an amplicon-based enrichment for SARS-CoV-2 cDNA. After genome assembly and quality control processes, phylogenetic analysis showed that the first batch of 15 genomes clustered into five clades: 19A, 19B, 20A, 20B, and 20C, whereas the second batch of 31 genomes clustered to only three clades 19B, 20A, and 20B. The imported cases (6/46) mapped to circulating viruses in their countries of origin, namely, India, Hungary, Norway, the United Kingdom, and the United States of America. All genomes mapped to the original Wuhan strain with high similarity (99.5–99.8%). All imported strains mapped to the European superclade A, whereas 5/9 locally infected individuals harbored the B4 clade, from the East Asian superclade B. Ghana appears to have 19B and 20B as the two largest circulating clades based on our sequence analyses. In line with global reports, the D614G linked viruses seem to be predominating. Comparison of Ghanaian SARS-CoV-2 genomes with global genomes indicates that Ghanaian strains have not diverged significantly from circulating strains commonly imported into Africa. The low level of diversity in our genomes may indicate lower levels of transmission, even for D614G viruses, which is consistent with the relatively low levels of infection reported in Ghana. 相似文献
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Song Zhi-Gang Chen Yan-Mei Wu Fan Xu Lin Wang Bang-Fang Shi Lei Chen Xiao Dai Fa-Hui She Jia-Lei Chen Jian-Min Holmes Edward C. Zhu Tong-Yu Zhang Yong-Zhen 《中国病毒学》2020,35(6):785-792
Virologica Sinica - Healthcare workers (HCWs) are at high risk of occupational exposure to the new pandemic human coronavirus, SARS-CoV-2, and are a source of nosocomial transmission in airborne... 相似文献
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Erik Volz Verity Hill John T. McCrone Anna Price David Jorgensen Áine O’Toole Joel Southgate Robert Johnson Ben Jackson Fabricia F. Nascimento Sara M. Rey Samuel M. Nicholls Rachel M. Colquhoun Ana da Silva Filipe James Shepherd David J. Pascall Rajiv Shah Natasha Jesudason Thomas R. Connor 《Cell》2021,184(1):64-75.e11
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《遗传》2024,47(2)
由严重急性呼吸综合征冠状病毒2 (severe acute respiratory syndrome coronavirus 2;SARS-CoV-2)引起的2019冠状病毒病(coronavirus disease 2019;COVID-19)大流行给人类生命安全和全球经济造成了巨大冲击。SARS-CoV-2基因组的快速变异引起了广泛关注;基因组中几乎每个位点都发生过单核苷酸变异(single nucleotide variants;SNVs);其中刺突蛋白上的变异在病毒的适应性进化和传播中起着尤为关键的作用。本文综述了SARS-CoV-2及非人类动物中相关冠状病毒的系统发生关系;并深入分析了SARS-CoV-2的谱系划分以及关键氨基酸变异对病毒生物学特性的影响。此外;本文还概述了当前面临的挑战;并展望了深度突变扫描(deep mutational scanning;DMS)结合人工智能方法在预测新冠病毒变异株流行趋势中的广阔应用前景。 相似文献
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Nighat Perveen Sabir Bin Muzaffar Mohammad Ali Al-Deeb 《Saudi Journal of Biological Sciences》2021,28(2):1417-1425
The novel coronavirus disease (COVID-19) that emerged in December 2019 had caused substantial morbidity and mortality at the global level within few months. It affected economies, stopped travel, and isolated individuals and populations around the world. Wildlife, especially bats, serve as reservoirs of coronaviruses from which the variant Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged that causes COVID-19. In this review, we describe the current knowledge on COVID-19 and the significance of wildlife hosts in its emergence. Mammalian and avian coronaviruses have diverse host ranges with distinct lineages of coronaviruses. Recombination and reassortments occur more frequently in mixed-animal markets where diverse viral genotypes intermingle. Human coronaviruses have evolved through gene gains and losses primarily in interfaces where wildlife and humans come in frequent contact. There is a gap in our understanding of bats as reservoirs of coronaviruses and there is a misconception that bats periodically transmit coronaviruses to humans. Future research should investigate bat viral diversity and loads at interfaces between humans and bats. Furthermore, there is an urgent need to evaluate viral strains circulating in mixed animal markets, where the coronaviruses circulated before becoming adapted to humans. We propose and discuss a management intervention plan for COVID-19 and raise questions on the suitability of current containment plans. We anticipate that more virulent coronaviruses could emerge unless proper measures are taken to limit interactions between diverse wildlife and humans in wild animal markets. 相似文献
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基因组学技术, 特别是宏基因组测序在未知病毒的鉴定与溯源中起到了重要作用。相较于传统的病毒分离培养方法, 宏基因组技术可以从混合样本中获得病毒的核酸序列, 极大加速了未知病毒的鉴定与溯源, 在针对高流行性、高致病性的病毒研究中发挥了重要作用。基于宏基因组技术对未知病毒进行鉴定和溯源, 其准确性很大程度上依赖于取样及已知宿主的病毒库的完整性。然而, 当前病毒多样性的基础研究相对薄弱, 病毒的宿主信息则更加匮乏。野生动物和畜禽是人畜共患病致病病毒的重要中间宿主, 构建广泛的动物-病毒关联数据库对于准确、快速地鉴定和预防致病性病毒具有重要意义。本综述以SARS-CoV-2为例, 总结了基因组学技术在病毒的鉴定与溯源上的应用, 并针对当前动物病毒库完整性低的现状, 对构建野生和家养动物携带病毒的关联数据库的可行性提出依据与建议。 相似文献
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新型冠状病毒(SARS-CoV-2)自2019年底流行至今,已进化出多个不同的亚型或分支并在全球共同传播。2020年12月14日,英国报道了一种新的SARS-CoV-2 variants of concern 202012/01(VOC 202012/01)变异株,其刺突(spike,S)蛋白累积了10个氨基酸突变,传播力增强。为分析SARS-CoV-2 VOC 202012/01变异株的全球传播与进化规律,本研究对截至到2020年12月31日的GISAID数据库中符合VOC 202012/01变异株特征的全基因组序列进行了时空分布及S蛋白进化特征分析。结果表明,VOC 202012/01变异株自2020年9月20日于英国首次出现后,在英国境内迅速蔓延,毒株数量逐月增多,并逐步扩散到全球4个大洲22个国家。在2020年9~12月传播期间,VOC 202012/01变异株的S蛋白除10个特征性位点稳定突变以外,均呈随机突变,仅有2个氨基酸突变位点存在于50条以上的序列中,行成小的分支。本文初步阐明了SARS-CoV-2 VOC 202012/01变异株的在全球早期流行中的传播与S蛋白的进化特征,为我国应对VOC 202012/01变异株的监测与防控提供科学依据。 相似文献
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新型冠状病毒肺炎疫情的全球大流行,对全球公共健康、社会和经济运转造成了重大影响。在药物研发迟滞及疫苗有效性未得到充分验证的情况下,对人群进行大规模的快速筛查,寻找潜在的感染者(尤其是轻症和无症状患者),并进行集中隔离,切断传播途径和保护易感人群是首要的任务。因此对于SARS-CoV-2感染,早期诊断尤为重要。总结现有市场上的新冠病毒抗原快速检测产品,对全球抗原快速检测市场进行分析,概述其研发的动向并展望了我国在新冠抗原检测新方法、新技术方面的自主创新能力。 相似文献
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《蛋白质与细胞》2024,15(6)
Intensive selection pressure constrains the evolutionary trajectory of SARS-CoV-2 genomes and results in vari-ous novel variants with distinct mutation profiles.Point mutations,particularly those within the receptor binding domain(RBD)of SARS-CoV-2 spike(S)protein,lead to the functional alteration in both receptor engagement and monoclonal antibody(mAb)recognition.Here,we review the data of the RBD point mutations possessed by major SARS-CoV-2 variants and discuss their individual effects on ACE2 affinity and immune evasion.Many single amino acid substitutions within RBD epitopes crucial for the antibody evasion capacity may conversely weaken ACE2 binding affinity.However,this weakened effect could be largely compensated by specific epistatic mutations,such as N501Y,thus maintaining the overall ACE2 affinity for the spike protein of all major variants.The predominant direction of SARS-CoV-2 evolution lies neither in promoting ACE2 affinity nor evading mAb neutralization but in maintaining a delicate balance between these two dimensions.Together,this review interprets how RBD mutations efficiently resist antibody neutralization and meanwhile how the affinity between ACE2 and spike protein is main-tained,emphasizing the significance of comprehensive assessment of spike mutations. 相似文献