Vector-borne pathogen surveillance in a metagenomic world

Author: Marla Magaña Cansino


From its inception to its widespread usage, nucleic acid–based assays have become the mainstay tool in infectious disease diagnostics and surveillance. Often reliant on polymerase chain reaction (PCR) or other methods of amplification, they have been adapted for quantitation, high-throughput testing, automation, isothermal, real-time, multiplex, or miniaturized target detection [1]. Nucleic acid sequencing has gone through a slower but steady evolution, from Sanger sequencing to massively parallel or next-generation sequencing (NGS), which has currently become the standard approach for producing microbial genome data [2]. Concomitantly, characterization of microbial genome diversity has been expanding at an unprecedented pace, revealing an abundance of novel microorganisms, and rapidly enhancing public repositories of microbial genomes [3]. This massive accumulation of genomic data necessitates regular inspection and updating of repositories and detection approaches for accurate discrimination of microbial species. Here, we aim to describe some of the current challenges in microbial nucleic acid detection, particularly from vector and environmental sources.


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  2. Chaudhari HG, Prajapati S, Wardah ZH, Raol G, Prajapati V, Patel R, et al. Decoding the microbial universe with metagenomics: a brief insight. Front Genet. 2023;14:1119740. pmid:37197021
  3. Li CX et al. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. Elife. 2015;4. pmid:25633976

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