Role of genomics in combating COVID-19 pandemic

Saravanan, K.A.; Panigrahi, Manjit; Kumar, Harshit; Rajawat, Divya; Nayak, Sonali Sonejita; Bhushan, Bharat; Dutt, Triveni

doi:10.1016/j.gene.2022.146387

Cited by 33 publications

(24 citation statements)

References 131 publications

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“… 48 49 Genomic surveillance and phylogenetic analyses have enabled the near real-time estimation of transmission chains of non-sexually recombining, rapidly evolving pathogens such as Ebola, 50 influenza 51 and COVID-19. 52 However, molecular and analytic advancements are still required to characterise transmission patterns of pathogens such as P. falciparum with a sexually recombining stage. 49 Third, the project will assess the value of P. falciparum genetic diversity measures to supplement traditional surveillance for improving stratification, monitoring and impact evaluations in different epidemiological contexts, especially where surveillance data are sparse.…”

Section: Discussionmentioning

confidence: 99%

“…Second, the project will help to target the reservoirs sustaining transmission by quantifying parasite importation, identifying sources and characterising local transmission in near-elimination settings 48 49. Genomic surveillance and phylogenetic analyses have enabled the near real-time estimation of transmission chains of non-sexually recombining, rapidly evolving pathogens such as Ebola,50 influenza51 and COVID-19 52. However, molecular and analytic advancements are still required to characterise transmission patterns of pathogens such as P. falciparum with a sexually recombining stage 49.…”

Section: Discussionmentioning

confidence: 99%

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Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol

et al. 2022

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IntroductionGenomic 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 analysesThis 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 disseminationThe 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 numberNCT05306067.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol

et al. 2022

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“…It was employed in the determination of the causal agent and its source, comprehension of SAR‐CoV‐2 characteristics, surveillance, and the development of molecular diagnostics, treatments, and vaccines. 18 Interindividual variability regarding the incidence, severity and mortality rate of COVID‐19 was recently recorded. Different genetic polymorphisms of specific genes might account for higher susceptibility and unexpected outcomes of COVID‐19 infections in different populations.…”

Section: Uses Of Phg During the Covid‐19 Pandemicmentioning

confidence: 99%

“… 25 Genomic sequencing was utilized to identify the virus causing the outbreaks more quickly and accurately, which enabled quick responses to the outbreaks and more effective surveillance. 18 …”

Section: Uses Of Phg During the Covid‐19 Pandemicmentioning

confidence: 99%

Implementation of Public Health Genomics in Africa: Lessons from the COVID‐19 pandemic, challenges, and recommendations

Moyo

Mashe

et al. 2022

Journal of Medical Virology

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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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“…Genomics, as a branch of biology, includes several sub-disciplines, such as comparative genomics, functional genomics, and macrogenomics. Information about the structure, function, and evolution of a species can be acquired by exploring its genomic features with the support of bioinformatic and computational tools [17]. More importantly, the genes encoding specific biosynthetic enzymes can be excavated from the genome sequence and modified by altering their physical properties, while preserving the necessary coding information, in biocatalytic applications [18,19].…”

Section: Introductionmentioning

confidence: 99%

Whole-Genome Sequencing of a Potential Ester-Synthesizing Bacterium Isolated from Fermented Golden Pomfret and Identification of Its Lipase Encoding Genes

Wang

2022

Foods

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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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Role of genomics in combating COVID-19 pandemic

Cited by 33 publications

References 131 publications

Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol

Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol

Implementation of Public Health Genomics in Africa: Lessons from the COVID‐19 pandemic, challenges, and recommendations

Whole-Genome Sequencing of a Potential Ester-Synthesizing Bacterium Isolated from Fermented Golden Pomfret and Identification of Its Lipase Encoding Genes

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