A regional genomic surveillance program is implemented to monitor the occurrence and emergence of SARS-CoV-2 variants in Yubei District, China

Liu, Fangyuan; Deng, Peng; He, Jiuhong; Chen, Xiaofeng; Jiang, Xinyu; Yan, Qi; Xu, Jing; Hu, Sihan; Yan, Jin

doi:10.1186/s12985-023-02279-6

Cited by 1 publication

(2 citation statements)

References 63 publications

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“…IRMA overcomes these shortcomings and is widely used in recent publications describing new IAV sequences [52][53][54]. However, the databases used in this tool cannot be updated by users.…”

Section: Discussionmentioning

confidence: 99%

“…For the consensus sequences of the new virus generation using the INSaFLU reference sequences, user-defined sequences should be used, eliminating the possibility of fully automated analysis. IRMA overcomes these shortcomings and is widely used in recent publications describing new IAV sequences [ 52 , 53 , 54 ]. However, the databases used in this tool cannot be updated by users.…”

Section: Discussionmentioning

confidence: 99%

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IAVCP (Influenza A Virus Consensus and Phylogeny): Automatic Identification of the Genomic Sequence of the Influenza A Virus from High-Throughput Sequencing Data

Paremskaia,

Volchkov,

Deviatkin

2024

Viruses

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Recently, high-throughput sequencing of influenza A viruses has become a routine test. It should be noted that the extremely high diversity of the influenza A virus complicates the task of determining the sequences of all eight genome segments. For a fast and accurate analysis, it is necessary to select the most suitable reference for each segment. At the same time, there is no standardized method in the field of decoding sequencing results that allows the user to update the sequence databases to which the reads obtained by virus sequencing are compared. The IAVCP (influenza A virus consensus and phylogeny) was developed with the goal of automatically analyzing high-throughput sequencing data of influenza A viruses. Its goals include the extraction of a consensus genome directly from paired raw reads. In addition, the pipeline enables the identification of potential reassortment events in the evolutionary history of the virus of interest by analyzing the topological structure of phylogenetic trees that are automatically reconstructed.

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“…IRMA overcomes these shortcomings and is widely used in recent publications describing new IAV sequences [52][53][54]. However, the databases used in this tool cannot be updated by users.…”

Section: Discussionmentioning

confidence: 99%