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Filippi M, Demoliner M, Gularte JS, de Abreu Goes Pereira VM, da Silva MS, Girardi V, Hansen AW, Spilki FR. Relative frequency of genomic mutations in SARS-CoV-2 recovered from southern Brazilian cases of COVID-19 through the Gamma, Delta and Omicron waves. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 120:105590. [PMID: 38574833 DOI: 10.1016/j.meegid.2024.105590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/06/2024]
Abstract
The presence of different mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can be related to changes in coronavirus disease (COVID-19) infection. Besides, these viral alterations associated with factors such as massive number of positive cases, vaccination and reinfections can be important in the viral evolution process. As well as, mutations found at low frequencies may have a more neutral action and consequently be less inclined to negative selection, facilitating their spread through the population. Related to that, we aimed to present mutations that are possibly relevant in the process of viral evolution found in 115 SARS-CoV-2 sequences from samples of individuals residing in the metropolitan region of Porto Alegre in the state of Rio Grande do Sul, Brazil. The genome from clinical samples was sequenced using High-Throughput Sequencing (HTS) and analyzed using a workflow to map reads and find variations/SNPs. The samples were separated into 3 groups considering the sample lineage. Of the total number of analyzed sequences, 35 were from the Gamma lineage, 35 from Delta and 45 from Omicron. Amino acid changes present in frequencies lower than 80% of the reads in the sequences were evaluated. 11 common mutations among the samples were found in the Gamma lineage, 1 in the ORF1ab gene, 7 in the S gene, 2 in the ORF6 gene and 1 in the ORF7a gene. While in the Delta lineage, a total of 11 mutations distributed in the ORF1ab, S, ORF7a and N genes, 2, 7, 1 and 1 mutation were found in each gene, respectively. And finally, in the Omicron, 16 mutations were identified, 2 in the ORF1ab gene, 12 in the S gene and 2 in the M gene. In conclusion, we emphasize that genomic surveillance can be a useful tool to assess how mutations play a key role in virus adaptation, and its process of susceptibility to new hosts showing the possible signs of viral evolution.
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Affiliation(s)
- Micheli Filippi
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil.
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Viviane Girardi
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
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Kogoj R, Grašek M, Suljič A, Zakotnik S, Vlaj D, Kotnik Koman K, Fafangel M, Petrovec M, Avšič-Županc T, Korva M. Sequencing analysis of SARS-CoV-2 cases in Slovenian long-term care facilities to support outbreak control. Front Public Health 2024; 12:1406777. [PMID: 38813418 PMCID: PMC11133669 DOI: 10.3389/fpubh.2024.1406777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction Residents of long-term care facilities (LTCFs) are at high risk of morbidity and mortality due to COVID-19, especially when new variants of concern (VOC) emerge. To provide intradisciplinary data in order to tailor public health interventions during future epidemics, available epidemiologic and genomic data from Slovenian LTCFs during the initial phases of the COVID-19 pandemic was analyzed. Methods The first part of the study included SARS-CoV-2 reverse-transcription Real-Time PCR (rtRT-PCR) positive LTCF residents, from 21 facilities with COVID-19 outbreaks occurring in October 2020. The second part of the study included SARS-CoV-2 rtRT-PCR positive LTCF residents and staff between January and April 2021, when VOC Alpha emerged in Slovenia. Next-generation sequencing (NGS) was used to acquire SARS-CoV-2 genomes, and lineage determination. In-depth phylogenetic and mutational profile analysis were performed and coupled with available field epidemiological data to assess the dynamics of SARS-CoV-2 introduction and transmission. Results 370/498 SARS-CoV-2 positive residents as well as 558/699 SARS-CoV-2 positive residents and 301/358 staff were successfully sequenced in the first and second part of the study, respectively. In October 2020, COVID-19 outbreaks in the 21 LTCFs were caused by intra-facility transmission as well as multiple independent SARS-CoV-2 introductions. The Alpha variant was confirmed in the first LTCF resident approximately 1.5 months after the first Alpha case was identified in Slovenia. The data also showed a slower replacement of existing variants by Alpha in residents compared to staff and the general population. Discussion Multiple SARS CoV-2 introductions as well as intra-facility spreading impacted disease transmission in Slovenian LTCFs. Timely implementation of control measures aimed at limiting new introductions while controlling in-facility transmission are of paramount importance, especially as new VOCs emerge. Sequencing, in conjunction with epidemiological data, can facilitate the determination of the need for future improvements in control measures to protect LTCF residents from COVID-19 or other respiratory infections.
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Affiliation(s)
- Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Manja Grašek
- Communicable Diseases Center, National Institute of Public Health, Ljubljana, Slovenia
| | - Alen Suljič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Samo Zakotnik
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Doroteja Vlaj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Kaja Kotnik Koman
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Fafangel
- Communicable Diseases Center, National Institute of Public Health, Ljubljana, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Misa Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Duchen D, Clipman SJ, Vergara C, Thio CL, Thomas DL, Duggal P, Wojcik GL. A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction. PLoS One 2024; 19:e0301069. [PMID: 38669259 PMCID: PMC11051683 DOI: 10.1371/journal.pone.0301069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/09/2024] [Indexed: 04/28/2024] Open
Abstract
Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved methods to characterize this diversity could aid drug development efforts. Conventionally, viral sequencing data are mapped/aligned to a reference genome, and only the aligned sequences are retained for analysis. Thus, reference selection is critical, yet selecting the most representative reference a priori remains difficult. We investigate an alternative pangenome approach which can combine multiple reference sequences into a graph which can be used during alignment. Using simulated short-read sequencing data generated from publicly available HBV genomes and real sequencing data from an individual living with CHB, we demonstrate alignment to a phylogenetically representative 'genome graph' can improve alignment, avoid issues of reference ambiguity, and facilitate the construction of sample-specific consensus sequences more genetically similar to the individual's infection. Graph-based methods can, therefore, improve efforts to characterize the genetics of viral pathogens, including HBV, and have broader implications in host-pathogen research.
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Affiliation(s)
- Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Center for Biomedical Data Science, Yale School of Medicine, New Haven, CT, United States of America
| | - Steven J. Clipman
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Candelaria Vergara
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Chloe L. Thio
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David L. Thomas
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Genevieve L. Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
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Tran DH, Do HDK, Tran HT, Pham TNM, Nguyen HD, Linh HT, Cuong HQ, Vu MT, Phung HTT. Rapid identification of SARS-CoV-2 strains via isothermal enzymatic recombinase amplification and nanopore sequencing. Arch Virol 2024; 169:87. [PMID: 38565796 DOI: 10.1007/s00705-024-06012-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/28/2024] [Indexed: 04/04/2024]
Abstract
Surveillance of the SARS-CoV-2 genome has become a crucial technique in the management of COVID-19, aiding the pandemic response and supporting effective public health interventions. Typically, whole-genomic sequencing is used along with PCR-based target enrichment techniques to identify SARS-CoV-2 variants, which is a complicated and time-consuming process that requires central laboratory facilities. Thus, there is an urgent need to develop rapid and cost-effective tools for precise on-site detection and identification of SARS-CoV-2 strains. In this study, we demonstrate the rapid diagnosis of COVID-19 and identification of SARS-CoV-2 variants by amplification and sequencing of the entire SARS-CoV-2 S gene using isothermal enzymatic recombinase amplification combined with the advanced Oxford nanopore sequencing technique. The entire procedure, from sampling to sequencing, takes less than 8 hours and can be performed with limited resources. The newly developed method has noteworthy implications for examining the transmission dynamics of the virus, detecting novel genetic variants, and assessing the effect of mutations on diagnostic approaches, antiviral treatments, and vaccines.
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Affiliation(s)
- Diem Hong Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hau Thi Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | | | - Hoang Danh Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hoang Thuy Linh
- Medical Device Testing Center, Pasteur Institute, Ho Chi Minh City, Vietnam
- University Medical Center, Ho Chi Minh City, Vietnam
| | - Hoang Quoc Cuong
- Directorial Board, Pasteur Institute, Ho Chi Minh City, Vietnam
- Department of Health, Can Tho City, Vietnam
| | - Minh Thiet Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam.
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam.
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Nayak SS, Panigrahi M, Rajawat D, Ghildiyal K, Sharma A, Parida S, Bhushan B, Mishra BP, Dutt T. Comprehensive selection signature analyses in dairy cattle exploiting purebred and crossbred genomic data. Mamm Genome 2023; 34:615-631. [PMID: 37843569 DOI: 10.1007/s00335-023-10021-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/24/2023] [Indexed: 10/17/2023]
Abstract
The main objective of the current research was to locate, annotate, and highlight specific areas of the bovine genome that are undergoing intense positive selection. Here, we are analyzing selection signatures in crossbred (Bos taurus X Bos indicus), taurine (Bos taurus), and indicine (Bos indicus) cattle breeds. Indicine cattle breeds found throughout India are known for their higher heat tolerance and disease resilience. More breeds and more methods can provide a better understanding of the selection signature. So, we have worked on nine distinct cattle breeds utilizing seven different summary statistics, which is a fairly extensive approach. In this study, we carried out a thorough genome-wide investigation of selection signatures using bovine 50K SNP data. We have included the genotyped data of two taurine, two crossbreds, and five indicine cattle breeds, for a total of 320 animals. During the 1950s, these indicine (cebuine) cattle breeds were exported with the aim of enhancing the resilience of taurine breeds in Western countries. For this study, we employed seven summary statistics, including intra-population, i.e., Tajima's D, CLR, iHS, and ROH and inter-population statistics, i.e., FST, XP-EHH, and Rsb. The NCBI database, PANTHER 17.0, and CattleQTL database were used for annotation after finding the important areas under selection. Some genes, including EPHA6, CTNNA2, NPFFR2, HS6ST3, NPR3, KCNIP4, LIPK, SDCBP, CYP7A1, NSMAF, UBXN2B, UGDH, UBE2K, and DAB1, were shown to be shared by three or more different approaches. Therefore, it gives evidence of the most intense selection in these areas. These genes are mostly linked to milk production and adaptability traits. This study also reveals selection regions that contain genes which are crucial to numerous biological functions, including those associated with milk production, coat color, glucose metabolism, oxidative stress response, immunity and circadian rhythms.
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Affiliation(s)
- Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Anurodh Sharma
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - B P Mishra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
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Kohler C, King J, Stacker L, Goller KV, Moritz J, Pohlmann A, Nath N, Tzvetkova A, Rieck M, Paraskevopoulou S, Beslic D, Hölzer M, Fuchs S, Ziemann J, Kaderali L, Beer M, Hübner NO, Becker K. Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020-2022. Emerg Microbes Infect 2023; 12:2245916. [PMID: 37585712 PMCID: PMC10446807 DOI: 10.1080/22221751.2023.2245916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/03/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023]
Abstract
ABSTRACTGlobal and even national genome surveillance approaches do not provide the resolution necessary for rapid and accurate direct response by local public health authorities. Hence, a regional network of microbiological laboratories in collaboration with the health departments of all districts of the German federal state of Mecklenburg-Western Pomerania (M-V) was formed to investigate the regional molecular epidemiology of circulating SARS-CoV-2 lineages between 11/2020 and 03/2022. More than 4750 samples from all M-V counties were sequenced using Illumina and Nanopore technologies. Overall, 3493 (73.5%) sequences fulfilled quality criteria for time-resolved and/or spatially-resolved maximum likelihood phylogenic analyses and k-mean/ median clustering (KMC). We identified 116 different Pangolin virus lineages that can be assigned to 16 Nextstrain clades. The ten most frequently detected virus lineages belonged to B.1.1.7, AY.122, AY.43, BA.1, B.1.617.2, BA.1.1, AY.9.2, AY.4, P.1 and AY.126. Time-resolved phylogenetic analyses showed the occurrence of virus clades as determined worldwide, but with a substantial delay of one to two months. Further spatio-temporal phylogenetic analyses revealed a regional outbreak of a Gamma variant limited to western M-V counties. Finally, KMC elucidated a successive introduction of the various virus lineages into M-V, possibly triggered by vacation periods with increased (inter-) national travel activities. The COVID-19 pandemic in M-V was shaped by a combination of several SARS-CoV-2 introductions, lockdown measures, restrictive quarantine of patients and the lineage specific replication rate. Complementing global and national surveillance, regional surveillance adds value by providing a higher level of surveillance resolution tailored to local health authorities.
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Affiliation(s)
- Christian Kohler
- Friedrich-Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Lina Stacker
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Katja V. Goller
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Juliane Moritz
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Neetika Nath
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Ana Tzvetkova
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Maximilian Rieck
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | | | - Denis Beslic
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Stephan Fuchs
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Janine Ziemann
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Nils-Olaf Hübner
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich-Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
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Rajawat D, Panigrahi M, Nayak SS, Ghildiyal K, Sharma A, Kumar H, Parida S, Bhushan B, Gaur GK, Mishra BP, Dutt T. Uncovering genes underlying coat color variation in indigenous cattle breeds through genome-wide positive selection. Anim Biotechnol 2023; 34:3920-3933. [PMID: 37493405 DOI: 10.1080/10495398.2023.2240387] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima's D, CLR, iHS, varLD, ROH, and FST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Subhashree Parida
- Pharmacology and Toxicology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - G K Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - B P Mishra
- Animal Biotechnology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
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Zhang C, Xu J, Tang R, Yang J, Wang W, Yu X, Shi S. Novel research and future prospects of artificial intelligence in cancer diagnosis and treatment. J Hematol Oncol 2023; 16:114. [PMID: 38012673 PMCID: PMC10680201 DOI: 10.1186/s13045-023-01514-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
Research into the potential benefits of artificial intelligence for comprehending the intricate biology of cancer has grown as a result of the widespread use of deep learning and machine learning in the healthcare sector and the availability of highly specialized cancer datasets. Here, we review new artificial intelligence approaches and how they are being used in oncology. We describe how artificial intelligence might be used in the detection, prognosis, and administration of cancer treatments and introduce the use of the latest large language models such as ChatGPT in oncology clinics. We highlight artificial intelligence applications for omics data types, and we offer perspectives on how the various data types might be combined to create decision-support tools. We also evaluate the present constraints and challenges to applying artificial intelligence in precision oncology. Finally, we discuss how current challenges may be surmounted to make artificial intelligence useful in clinical settings in the future.
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Affiliation(s)
- Chaoyi Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Pancreatic Cancer Institute, No. 399 Lingling Road, Shanghai, 200032, People's Republic of China
- Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, People's Republic of China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Pancreatic Cancer Institute, No. 399 Lingling Road, Shanghai, 200032, People's Republic of China
- Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, People's Republic of China
| | - Rong Tang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Pancreatic Cancer Institute, No. 399 Lingling Road, Shanghai, 200032, People's Republic of China
- Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, People's Republic of China
| | - Jianhui Yang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Pancreatic Cancer Institute, No. 399 Lingling Road, Shanghai, 200032, People's Republic of China
- Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, People's Republic of China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Pancreatic Cancer Institute, No. 399 Lingling Road, Shanghai, 200032, People's Republic of China
- Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, People's Republic of China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, People's Republic of China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
- Shanghai Pancreatic Cancer Institute, No. 399 Lingling Road, Shanghai, 200032, People's Republic of China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, People's Republic of China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
- Shanghai Pancreatic Cancer Institute, No. 399 Lingling Road, Shanghai, 200032, People's Republic of China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, People's Republic of China.
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Loguercio S, Calverley BC, Wang C, Shak D, Zhao P, Sun S, Budinger GS, Balch WE. Understanding the host-pathogen evolutionary balance through Gaussian process modeling of SARS-CoV-2. PATTERNS (NEW YORK, N.Y.) 2023; 4:100800. [PMID: 37602209 PMCID: PMC10436005 DOI: 10.1016/j.patter.2023.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/22/2023] [Accepted: 06/22/2023] [Indexed: 08/22/2023]
Abstract
We have developed a machine learning (ML) approach using Gaussian process (GP)-based spatial covariance (SCV) to track the impact of spatial-temporal mutational events driving host-pathogen balance in biology. We show how SCV can be applied to understanding the response of evolving covariant relationships linking the variant pattern of virus spread to pathology for the entire SARS-CoV-2 genome on a daily basis. We show that GP-based SCV relationships in conjunction with genome-wide co-occurrence analysis provides an early warning anomaly detection (EWAD) system for the emergence of variants of concern (VOCs). EWAD can anticipate changes in the pattern of performance of spread and pathology weeks in advance, identifying signatures destined to become VOCs. GP-based analyses of variation across entire viral genomes can be used to monitor micro and macro features responsible for host-pathogen balance. The versatility of GP-based SCV defines starting point for understanding nature's evolutionary path to complexity through natural selection.
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Affiliation(s)
| | - Ben C. Calverley
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Daniel Shak
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - G.R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL, USA
| | - William E. Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
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10
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Ewart G, Bobardt M, Bentzen BH, Yan Y, Thomson A, Klumpp K, Becker S, Rosenkilde MM, Miller M, Gallay P. Post-infection treatment with the E protein inhibitor BIT225 reduces disease severity and increases survival of K18-hACE2 transgenic mice infected with a lethal dose of SARS-CoV-2. PLoS Pathog 2023; 19:e1011328. [PMID: 37549173 PMCID: PMC10434922 DOI: 10.1371/journal.ppat.1011328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/17/2023] [Accepted: 07/06/2023] [Indexed: 08/09/2023] Open
Abstract
The Coronavirus envelope (E) protein is a small structural protein with ion channel activity that plays an important role in virus assembly, budding, immunopathogenesis and disease severity. The viroporin E is also located in Golgi and ER membranes of infected cells and is associated with inflammasome activation and immune dysregulation. Here we evaluated in vitro antiviral activity, mechanism of action and in vivo efficacy of BIT225 for the treatment of SARS-CoV-2 infection. BIT225 showed broad-spectrum direct-acting antiviral activity against SARS-CoV-2 in Calu3 and Vero cells with similar potency across 6 different virus strains. BIT225 inhibited ion channel activity of E protein but did not inhibit endogenous currents or calcium-induced ion channel activity of TMEM16A in Xenopus oocytes. BIT225 administered by oral gavage for 12 days starting 12 hours before infection completely prevented body weight loss and mortality in SARS-CoV-2 infected K18 mice (100% survival, n = 12), while all vehicle-dosed animals reached a mortality endpoint by Day 9 across two studies (n = 12). When treatment started at 24 hours after infection, body weight loss, and mortality were also prevented (100% survival, n = 5), while 4 of 5 mice maintained and increased body weight and survived when treatment started 48 hours after infection. Treatment efficacy was dependent on BIT225 dose and was associated with significant reductions in lung viral load (3.5 log10), virus titer (4000 pfu/ml) and lung and serum cytokine levels. These results validate viroporin E as a viable antiviral target and support the clinical study of BIT225 for treatment and prophylaxis of SARS-CoV-2 infection.
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Affiliation(s)
- Gary Ewart
- Biotron Limited, North Ryde, New South Wales, Australia
| | - Michael Bobardt
- The Scripps Institute, Immunology and Microbiology, La Jolla, California, United States of America
| | - Bo Hjorth Bentzen
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Yannan Yan
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark
| | | | - Klaus Klumpp
- Biotron Limited, North Ryde, New South Wales, Australia
| | | | - Mette M. Rosenkilde
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark
| | | | - Philippe Gallay
- The Scripps Institute, Immunology and Microbiology, La Jolla, California, United States of America
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11
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Moros Z, Loureiro C, Jaspe R, Sulbarán Y, Delgado M, Aristimuño OC, Franco C, Garzaro D, Rodríguez M, Rangel H, Liprandi F, Pujol F, Zambrano JL. Web-tools for the genomic analysis of the 2022 Monkeypox virus global outbreak. INVESTIGACIÓN CLÍNICA 2023. [DOI: 10.54817/ic.v64n1a06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The resources and platforms available on the internet for collect-ing and sharing information and performing genomic sequence analysis have made it possible to follow closely the evolution the evolution of SARS-CoV-2. However, the current monkeypox outbreak in the world brings us back to the need to use these resources to appraise the extent of this outbreak. The ob-jective of this work was an analysis of the information presented so far in the genomic database GISAID EpiPox™, using various tools available on the web. The results indicate that the monkeypox outbreak is referred as MPXV clade II B.1 lineage and sub-lineages, isolated from male patients mainly from the Euro-pean and American continents. In the current scenario, the access to genomic sequences, epidemiological information, and tools available to the scientific community is of great importance for global public health in order to follow the evolution of pathogens.
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Affiliation(s)
- Zoila Moros
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Carmen Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Rossana Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Yoneira Sulbarán
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Mariangel Delgado
- Unidad de Microscopía Electrónica y Confocal, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Olga Carolina Aristimuño
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Christopher Franco
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Domingo Garzaro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Mariajosé Rodríguez
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Héctor Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - Flor Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
| | - José Luis Zambrano
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Miranda, Venezuela
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12
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Forero DA, Chand V. Methods in molecular biology and genetics: looking to the future. BMC Res Notes 2023; 16:26. [PMID: 36864454 PMCID: PMC9980850 DOI: 10.1186/s13104-023-06298-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
In recent decades, advances in methods in molecular biology and genetics have revolutionized multiple areas of the life and health sciences. However, there remains a global need for the development of more refined and effective methods across these fields of research. In this current Collection, we aim to showcase articles presenting novel molecular biology and genetics techniques developed by scientists from around the world.
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Affiliation(s)
- Diego A. Forero
- grid.442076.30000 0000 9574 5136School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Vaibhav Chand
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, USA.
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13
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Duchen D, Clipman S, Vergara C, Thio CL, Thomas DL, Duggal P, Wojcik GL. A hepatitis B virus (HBV) sequence variation graph improves sequence alignment and sample-specific consensus sequence construction for genetic analysis of HBV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523611. [PMID: 36711598 PMCID: PMC9882026 DOI: 10.1101/2023.01.11.523611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Hepatitis B virus (HBV) remains a global public health concern, with over 250 million individuals living with chronic HBV infection (CHB) and no curative therapy currently available. Viral diversity is associated with CHB pathogenesis and immunological control of infection. Improved methods to characterize the viral genome at both the population and intra-host level could aid drug development efforts. Conventionally, HBV sequencing data are aligned to a linear reference genome and only sequences capable of aligning to the reference are captured for analysis. Reference selection has additional consequences, including sample-specific 'consensus' sequence construction. It remains unclear how to select a reference from available sequences and whether a single reference is sufficient for genetic analyses. Using simulated short-read sequencing data generated from full-length publicly available HBV genome sequences and HBV sequencing data from a longitudinally sampled individual with CHB, we investigate alternative graph-based alignment approaches. We demonstrate that using a phylogenetically representative 'genome graph' for alignment, rather than linear reference sequences, avoids issues of reference ambiguity, improves alignment, and facilitates the construction of sample-specific consensus sequences genetically similar to an individual's infection. Graph-based methods can therefore improve efforts to characterize the genetics of viral pathogens, including HBV, and may have broad implications in host pathogen research.
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Affiliation(s)
- Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Steven Clipman
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Candelaria Vergara
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Chloe L Thio
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - David L Thomas
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
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14
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Moyo E, Moyo P, Mashe T, Dzobo M, Chitungo I, Dzinamarira T. Implementation of Public Health Genomics in Africa: Lessons from the COVID-19 pandemic, challenges, and recommendations. J Med Virol 2023; 95:e28295. [PMID: 36366938 PMCID: PMC9877907 DOI: 10.1002/jmv.28295] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/18/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Public Health Genomics (PHG) is a relatively new field. The wide application of genomic technologies played a pivotal role in elucidating the full genomic sequence of the SARS-CoV-2 virus. This breakthrough proved to be the starting point in the manufacture of diagnostic kits and the subsequent making of vaccines. Beyond the COVID-19 pandemic, many African countries can take advantage of the various investments in genomic technologies to introduce and intensify the use of genomics for public health gain. Public Health Genomics effectively monitors, prevents, and manages non-communicable and infectious diseases. However, there are several challenges to implementing PHG in Africa. In this perspective article, we discuss the utilization of PHG during the COVID-19 pandemic, the lessons learned from using PHG to manage and contain the COVID-19 pandemic, as well as potential challenges Africa may face when putting PHG into practice compared to challenges of other regions. We also discuss our recommendations for overcoming these challenges.
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Affiliation(s)
- Enos Moyo
- Medical Centre OshakatiOshakatiNamibia
| | | | | | - Mathias Dzobo
- School of Health Systems and Public HealthUniversity of PretoriaPretoriaSouth Africa
| | - Itai Chitungo
- College of Medicine and Health SciencesUniversity of ZimbabweHarareZimbabwe
| | - Tafadzwa Dzinamarira
- School of Health Systems and Public HealthUniversity of PretoriaPretoriaSouth Africa
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15
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Suster CJE, Arnott A, Blackwell G, Gall M, Draper J, Martinez E, Drew AP, Rockett RJ, Chen SCA, Kok J, Dwyer DE, Sintchenko V. Guiding the design of SARS-CoV-2 genomic surveillance by estimating the resolution of outbreak detection. Front Public Health 2022; 10:1004201. [PMID: 36276383 PMCID: PMC9581317 DOI: 10.3389/fpubh.2022.1004201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/16/2022] [Indexed: 01/27/2023] Open
Abstract
Genomic surveillance of SARS-CoV-2 has been essential to inform public health response to outbreaks. The high incidence of infection has resulted in a smaller proportion of cases undergoing whole genome sequencing due to finite resources. We present a framework for estimating the impact of reduced depths of genomic surveillance on the resolution of outbreaks, based on a clustering approach using pairwise genetic and temporal distances. We apply the framework to simulated outbreak data to show that outbreaks are detected less frequently when fewer cases are subjected to whole genome sequencing. The impact of sequencing fewer cases depends on the size of the outbreaks, and on the genetic and temporal similarity of the index cases of the outbreaks. We also apply the framework to an outbreak of the SARS-CoV-2 Delta variant in New South Wales, Australia. We find that the detection of clusters in the outbreak would have been delayed if fewer cases had been sequenced. Existing recommendations for genomic surveillance estimate the minimum number of cases to sequence in order to detect and monitor new virus variants, assuming representative sampling of cases. Our method instead measures the resolution of clustering, which is important for genomic epidemiology, and accommodates sampling biases.
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Affiliation(s)
- Carl J. E. Suster
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
| | - Alicia Arnott
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Grace Blackwell
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Mailie Gall
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Jenny Draper
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Elena Martinez
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Alexander P. Drew
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Dominic E. Dwyer
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
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16
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Panigrahi M, Kumar H, Saravanan KA, Rajawat D, Sonejita Nayak S, Ghildiyal K, Kaisa K, Parida S, Bhushan B, Dutt T. Trajectory of livestock genomics in South Asia: A comprehensive review. Gene 2022; 843:146808. [PMID: 35973570 DOI: 10.1016/j.gene.2022.146808] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kaiho Kaisa
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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17
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Chen Z. Precision Public Health in China: Opportunities and Challenges. China CDC Wkly 2022; 4:695-696. [PMID: 36060442 PMCID: PMC9433756 DOI: 10.46234/ccdcw2022.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/01/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhuo Chen
- College of Public Health, The University of Georgia, GA, USA,The University of Nottingham Ningbo China, Zhejiang Province, China,Chen Zhuo,
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18
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Mayor A, da Silva C, Rovira-Vallbona E, Roca-Feltrer A, Bonnington C, Wharton-Smith A, Greenhouse B, Bever C, Chidimatembue A, Guinovart C, Proctor JL, Rodrigues M, Canana N, Arnaldo P, Boene S, Aide P, Enosse S, Saute F, Candrinho B. Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol. BMJ Open 2022; 12:e063456. [PMID: 35820756 PMCID: PMC9274532 DOI: 10.1136/bmjopen-2022-063456] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION Genomic data constitute a valuable adjunct to routine surveillance that can guide programmatic decisions to reduce the burden of infectious diseases. However, genomic capacities remain low in Africa. This study aims to operationalise a functional malaria molecular surveillance system in Mozambique for guiding malaria control and elimination. METHODS AND ANALYSES This prospective surveillance study seeks to generate Plasmodium falciparum genetic data to (1) monitor molecular markers of drug resistance and deletions in rapid diagnostic test targets; (2) characterise transmission sources in low transmission settings and (3) quantify transmission levels and the effectiveness of antimalarial interventions. The study will take place across 19 districts in nine provinces (Maputo city, Maputo, Gaza, Inhambane, Niassa, Manica, Nampula, Zambézia and Sofala) which span a range of transmission strata, geographies and malaria intervention types. Dried blood spot samples and rapid diagnostic tests will be collected across the study districts in 2022 and 2023 through a combination of dense (all malaria clinical cases) and targeted (a selection of malaria clinical cases) sampling. Pregnant women attending their first antenatal care visit will also be included to assess their value for molecular surveillance. We will use a multiplex amplicon-based next-generation sequencing approach targeting informative single nucleotide polymorphisms, gene deletions and microhaplotypes. Genetic data will be incorporated into epidemiological and transmission models to identify the most informative relationship between genetic features, sources of malaria transmission and programmatic effectiveness of new malaria interventions. Strategic genomic information will be ultimately integrated into the national malaria information and surveillance system to improve the use of the genetic information for programmatic decision-making. ETHICS AND DISSEMINATION The protocol was reviewed and approved by the institutional (CISM) and national ethics committees of Mozambique (Comité Nacional de Bioética para Saúde) and Spain (Hospital Clinic of Barcelona). Project results will be presented to all stakeholders and published in open-access journals. TRIAL REGISTRATION NUMBER NCT05306067.
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Affiliation(s)
- Alfredo Mayor
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Clemente da Silva
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
| | - Eduard Rovira-Vallbona
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | | | | | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Caitlin Bever
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | | | - Caterina Guinovart
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | | | | | | | - Simone Boene
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Francisco Saute
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
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19
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Whole-Genome Sequencing of a Potential Ester-Synthesizing Bacterium Isolated from Fermented Golden Pomfret and Identification of Its Lipase Encoding Genes. Foods 2022; 11:foods11131954. [PMID: 35804769 PMCID: PMC9266206 DOI: 10.3390/foods11131954] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/20/2022] [Accepted: 06/25/2022] [Indexed: 12/17/2022] Open
Abstract
Microbial ester synthases are regarded as valuable catalysts in the food industry. Here, one strain of Acinetobacter venetianus with ester synthase-production capacity, SCSMX-3, was isolated from traditional fermented golden pomfret. It exhibited good growth in mesophilic, low salt, and slightly alkaline environments. The ester synthase produced by SCSMX-3 displayed maximum activity at pH 8.0 and 35 °C. Genome sequencing revealed that the strain contains one circular chromosome of 336313 bp and two circular plasmids (plasmid A-14424 bp and plasmid B-11249 bp). Six CRISPR structures enhance the genomic stability of SCSMX-3 and provide the opportunity to create new functional strains. Gene function analysis indicated that SCSMX-3 produces the necessary enzymes for survival under different conditions and for flavor substance synthesis. Furthermore, 49 genes encoding enzymes associated with lipid metabolism, including three triacylglycerol lipases and two esterases, were identified through the NCBI Non-Redundant Protein Database. The lipase encoded by gene0302 belongs to the GX group and the abH15.02 (Burkholderia cepacia lipase) homolog of the abH15 superfamily. Our results shed light on the genomic diversity of and lipid metabolism in A. venetianus isolated from fermented golden pomfret, laying a foundation for the exploration of new ester synthases to improve the flavor of fermented fish products.
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