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Primary assessment of the diversity of Omicron sublineages and the epidemiologic features of autumn/winter 2022 COVID-19 wave in Chinese mainland

Frontiers of Medicine   Pages 758-767 doi: 10.1007/s11684-022-0981-7

Abstract: With the recent ongoing autumn/winter 2022 COVID-19 wave and the adjustment of public health control measures, there have been widespread SARS-CoV-2 infections in Chinese mainland. Here we have analyzed 369 viral genomes from recently diagnosed COVID-19 patients in Shanghai, identifying a large number of sublineages of the SARS-CoV-2 Omicron family. Phylogenetic analysis, coupled with contact history tracing, revealed simultaneous community transmission of two Omicron sublineages dominating the infections in some areas of China (BA.5.2 mainly in Guangzhou and Shanghai, and BF.7 mainly in Beijing) and two highly infectious sublineages recently imported from abroad (XBB and BQ.1). Publicly available data from August 31 to November 29, 2022 indicated an overall severe/critical case rate of 0.035% nationwide, while analysis of 5706 symptomatic patients treated at the Shanghai Public Health Center between September 1 and December 26, 2022 showed that 20 cases (0.35%) without comorbidities progressed into severe/critical conditions and 153 cases (2.68%) with COVID-19-exacerbated comorbidities progressed into severe/critical conditions. These observations shall alert healthcare providers to place more resources for the treatment of severe/critical cases. Furthermore, mathematical modeling predicts this autumn/winter wave might pass through major cities in China by the end of the year, whereas some middle and western provinces and rural areas would be hit by the upcoming infection wave in mid-to-late January 2023, and the duration and magnitude of upcoming outbreak could be dramatically enhanced by the extensive travels during the Spring Festival (January 21, 2023). Altogether, these preliminary data highlight the needs to allocate resources to early diagnosis and effective treatment of severe cases and the protection of vulnerable population, especially in the rural areas, to ensure the country’s smooth exit from the ongoing pandemic and accelerate socio-economic recovery.

Keywords： SARS-CoV-2     COVID-19     Omicron     genomic epidemiology    

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Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the trace

Biao Kan, Haijian Zhou, Pengcheng Du, Wen Zhang, Xin Lu, Tian Qin, Jianguo Xu

Frontiers of Medicine 2018, Volume 12, Issue 1,   Pages 23-33 doi: 10.1007/s11684-017-0607-7

Abstract:

Two decades have passed since the first bacterial whole-genome sequencing, which provides new opportunity for microbial genome. Consequently, considerable genetic diversity encoded by bacterial genomes and among the strains in the same species has been revealed. In recent years, genome sequencing techniques and bioinformatics have developed rapidly, which has resulted in transformation and expedited the application of strategy and methodology for bacterial genome comparison used in dissection of infectious disease epidemics. Bacterial whole-genome sequencing and bioinformatic computing allow genotyping to satisfy the requirements of epidemiological study in disease control. In this review, we outline the significance and summarize the roles of bacterial genome sequencing in the context of bacterial disease control and prevention. We discuss the applications of bacterial genome sequencing in outbreak detection, source tracing, transmission mode discovery, and new epidemic clone identification. Wide applications of genome sequencing and data sharing in infectious disease surveillance networks will considerably promote outbreak detection and early warning to prevent the dissemination of bacterial diseases.

Keywords： genome sequencing     genomic epidemiology     bacteria     surveillance     infectious diseases    

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Statistical considerations for genomic selection

Huimin KANG, Lei ZHOU, Jianfeng LIU

Frontiers of Agricultural Science and Engineering 2017, Volume 4, Issue 3,   Pages 268-278 doi: 10.15302/J-FASE-2017164

Abstract: Genomic selection is becoming increasingly important in animal and plant breeding, and is attractingthe most commonly used statistical methods and some extensions of them, i.e., ridge regression and genomicIn simulation studies where true breeding values are available, accuracy of genomic estimated breedingFactors influencing the accuracy of genomic selection include linkage disequilibrium between markersGenomic selection has been implemented in the breeding programs of dairy cattle, beef cattle, pigs and

Keywords： genomic estimated breeding value     genomic selection     linkage disequilibrium     statistical methods    

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Recent transmission of Mycobacterium tuberculosis in China: the implication of molecular epidemiology

Chongguang Yang, Qian Gao

Frontiers of Medicine 2018, Volume 12, Issue 1,   Pages 76-83 doi: 10.1007/s11684-017-0609-5

Abstract: Evidence from molecular epidemiology studies has delineated the recent transmission of ( ) strains inWe reviewed the implementations of molecular epidemiology of TB in China, the estimated disease burden

Keywords： tuberculosis     recent transmission     molecular epidemiology     China    

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Chronic hepatitis B virus infection: epidemiology, prevention, and treatment in China

Rui Yu,Rong Fan,Jinlin Hou

Frontiers of Medicine 2014, Volume 8, Issue 2,   Pages 135-144 doi: 10.1007/s11684-014-0331-5

Abstract: The universal vaccination program since 1992 has changed the epidemiology of hepatitis B virus infection

Keywords： chronic hepatitis B     epidemiology     prevention     treatment    

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The epidemiology of norovirus gastroenteritis in China: disease burden and distribution of genotypes

Honglu Zhou, Songmei Wang, Lorenz von Seidlein, Xuanyi Wang

Frontiers of Medicine 2020, Volume 14, Issue 1,   Pages 1-7 doi: 10.1007/s11684-019-0733-5

Abstract: With the improvements of sanitation and nationwide safe water supply the occurrence of bacterial diarrhea declined remarkably, while viruses became the leading causes of acute gastroenteritis (AGE). Of these viruses, noroviruses (NoVs) are responsible for a considerable burden of gastroenteritis, especially in children<2 years and elderly≥65 years. NoVs circulating in the Chinese population are antigenically highly diverse with the genotype GII.4 being the dominant strain followed by GII.3. Given the widespread contamination in environmental sources, and highly infectious nature of NoVs, vaccination would be the desirable strategy for the control of NoV infections. However, a better understanding of acquired immunity after infection, and a reliable immunological surrogate marker are urgently needed, since two vaccine candidates based on virus-like particles (VLPs) are currently moving into clinical evaluations in China.

Keywords： molecular epidemiology     norovirus     disease burden     genotype     China    

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GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

Frontiers of Agricultural Science and Engineering 2021, Volume 8, Issue 2,

Abstract:

Horticultural crops are a major source of high value nutritious food, and new improved cultivars developed through breeding are required for sustainable production in the face of abiotic and biotic stresses, and to deliver novel, premium products to consumers. However, grower confidence in the performance of new germplasm, particularly across environmental variability, is important for commercial adoption and germplasm-environment matching to optimize production.

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GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

Craig HARDNER, Satish KUMAR, Dorrie MAIN, Cameron PEACE

Frontiers of Agricultural Science and Engineering   Pages 353-355 doi: 10.15302/J-FASE-2021387

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Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer

Frontiers of Medicine doi: 10.1007/s11684-023-1008-8

Abstract: Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequentHowever, knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely

Keywords： 3D genome     cancer     TADs     loop     gene regulation    

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Genomic Epidemiology of ST34 Monophasic Salmonella enterica Serovar Typhimurium from Clinical Patients Article

Yujiao Mu, Ruichao Li, Pengcheng Du, Pei Zhang, Yan Li, Shenghui Cui, Séamus Fanning, Li Bai

Engineering 2022, Volume 15, Issue 8,   Pages 34-44 doi: 10.1016/j.eng.2022.05.006

Abstract: To date, the epidemiology and genomic characterization of this pathogen in China have not been well described

Keywords： Salmonella Typhimurium monophasic variant     ST34     Prevalence     Phylogenetic analysis     Chinese lineages    

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Tumor growth and metastasis can be inhibited by maintaining genomic stability in cancer cells

Yi Liang,Qisheng Feng,Jian Hong,Futuo Feng,Yi Sang,Wenrong Hu,Miao Xu,Roujun Peng,Tiebang Kang,Jinxin Bei,Yixin Zeng

Frontiers of Medicine 2015, Volume 9, Issue 1,   Pages 57-62 doi: 10.1007/s11684-015-0389-8

Abstract: Our previous research demonstrates that SLCCs are inducible by increasing genomic instability in cancerradicals and is used to protect patients from radioactive exposure, was used as an agent that maintains genomicFurthermore, MMC alone enhanced genomic instability, but MMC combined with AET attenuated the extentof genomic instability in primary VX2 tumor tissue.Taken together, our data suggest that the genomic protector AET can inhibit the induction of SLCCs, and

Keywords： rabbit VX2 liver tumor     mitomycin C     AET     stem-like cancer cells     genomic instability    

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Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

Frontiers of Medicine doi: 10.1007/s11684-023-0994-x

Abstract: Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples, whose genomic characteristicsCollectively, this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs

Keywords： primary central nervous system lymphoma     whole-genome sequencing     TMSB4X     copy number variation     gene mutation    

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Genomic variations in the counterpart normal controls of lung squamous cell carcinomas

Dalin Zhang, Liwei Qu, Bo Zhou, Guizhen Wang, Guangbiao Zhou

Frontiers of Medicine 2018, Volume 12, Issue 3,   Pages 280-288 doi: 10.1007/s11684-017-0580-1

Abstract: occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomicHowever, few studies have investigated the genomic variations that occur only in normal tissues thatWe then called genomic variations specific to the normal lung tissues through filtering the genomic sequenceSixteen genomic variations were called in the three normal lung tissues.Our results uncovered previously unreported genomic variations in CNCs, rather than LUSCs, that may be

Keywords： lung cancer     counterpart normal control     genomic variations    

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Detection of genomic signatures for pig hairlessness using high-density SNP data

Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 4,   Pages 307-313 doi: 10.15302/J-FASE-2014039

Abstract: We conducted a genomic scan for genetically differentiated regions between hairy and hairless pigs usingA total of 38405 SNPs in 498 animals from 36 diverse breeds were used to detect genomic signatures for

Keywords： hairlessness     pig     selective sweeping    

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Epidemiology of fungal infections in China

Min Chen, Yuan Xu, Nan Hong, Yali Yang, Wenzhi Lei, Lin Du, Jingjun Zhao, Xia Lei, Lin Xiong, Langqi Cai, Hui Xu, Weihua Pan, Wanqing Liao

Frontiers of Medicine 2018, Volume 12, Issue 1,   Pages 58-75 doi: 10.1007/s11684-017-0601-0

Abstract:

With the increasing number of immunocompromised hosts, the epidemiological characteristics of fungal infections have undergone enormous changes worldwide, including in China. In this paper, we reviewed the existing data on mycosis across China to summarize available epidemiological profiles. We found that the general incidence of superficial fungal infections in China has been stable, but the incidence of tinea capitis has decreased and the transmission route has changed. By contrast, the overall incidence of invasive fungal infections has continued to rise. The occurrence of candidemia caused by species other than and including some uncommon species has increased recently in China. Infections caused by have also propagated in recent years, particularly with the emergence of azole-resistant . An increasing trend of cryptococcosis has been noted in China, with var. ST 5 genotype isolates as the predominant pathogen. Retrospective studies have suggested that the epidemiological characteristics of pneumonia in China may be similar to those in other developing countries. Endemic fungal infections, such as sporotrichosis in Northeastern China, must arouse research, diagnostic, and treatment vigilance. Currently, the epidemiological data on mycosis in China are variable and fragmentary. Thus, a nationwide epidemiological research on fungal infections in China is an important need for improving the country’s health.

Keywords： fungi     infection     epidemiology     China    

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Title Author Date Type Operation

Primary assessment of the diversity of Omicron sublineages and the epidemiologic features of autumn/winter 2022 COVID-19 wave in Chinese mainland

Journal Article

Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the trace

Biao Kan, Haijian Zhou, Pengcheng Du, Wen Zhang, Xin Lu, Tian Qin, Jianguo Xu

Journal Article

Statistical considerations for genomic selection

Huimin KANG, Lei ZHOU, Jianfeng LIU

Journal Article

Recent transmission of Mycobacterium tuberculosis in China: the implication of molecular epidemiology

Chongguang Yang, Qian Gao

Journal Article

Chronic hepatitis B virus infection: epidemiology, prevention, and treatment in China

Rui Yu,Rong Fan,Jinlin Hou

Journal Article

The epidemiology of norovirus gastroenteritis in China: disease burden and distribution of genotypes

Honglu Zhou, Songmei Wang, Lorenz von Seidlein, Xuanyi Wang

Journal Article

GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

Journal Article

GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

Craig HARDNER, Satish KUMAR, Dorrie MAIN, Cameron PEACE

Journal Article

Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer

Journal Article

Genomic Epidemiology of ST34 Monophasic Salmonella enterica Serovar Typhimurium from Clinical Patients

Yujiao Mu, Ruichao Li, Pengcheng Du, Pei Zhang, Yan Li, Shenghui Cui, Séamus Fanning, Li Bai

Journal Article

Tumor growth and metastasis can be inhibited by maintaining genomic stability in cancer cells

Yi Liang,Qisheng Feng,Jian Hong,Futuo Feng,Yi Sang,Wenrong Hu,Miao Xu,Roujun Peng,Tiebang Kang,Jinxin Bei,Yixin Zeng

Journal Article

Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

Journal Article

Genomic variations in the counterpart normal controls of lung squamous cell carcinomas

Dalin Zhang, Liwei Qu, Bo Zhou, Guizhen Wang, Guangbiao Zhou

Journal Article

Detection of genomic signatures for pig hairlessness using high-density SNP data

Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING

Journal Article

Epidemiology of fungal infections in China

Min Chen, Yuan Xu, Nan Hong, Yali Yang, Wenzhi Lei, Lin Du, Jingjun Zhao, Xia Lei, Lin Xiong, Langqi Cai, Hui Xu, Weihua Pan, Wanqing Liao

Journal Article