Genetic Relatedness of Infectious Hypodermal and Hematopoietic Necrosis Virus Isolates, United States, 2019

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Abstract

Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is a nonenveloped, linear, single-stranded DNA virus belonging to the family Parvoviridae and is a World Organisation for Animal Health (OIE)–notifiable crustacean pathogen. During screening of Penaeus vannamei shrimp from 3 commercial shrimp facilities in the United States for a panel of OIE-listed (n = 7) and nonlisted (n = 2) crustacean diseases, shrimp from these facilities tested positive for IHHNV. Nucleotide sequences of PCR amplicons showed 99%–100% similarity to IHHNV isolates from Latin America and Asia. The whole genome of the isolates also showed high similarity to type 2 infectious forms of IHHNV. Phylogenetic analysis using capsid gene and whole-genome sequences demonstrated that the isolates clustered with an IHHNV isolate from Ecuador. The detection of an OIE-listed crustacean pathogen in the United States highlights the need for biosecurity protocols in hatcheries and grow-out ponds to mitigate losses.

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Most cited references 29

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A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.

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Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.

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Is Open Access

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

Matthew Kearse, Richard Moir, Amy Wilson … (2012)

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com

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Author and article information

Journal

Journal ID (nlm-ta): Emerg Infect Dis

Journal ID (iso-abbrev): Emerg Infect Dis

Journal ID (publisher-id): EID

Title: Emerging Infectious Diseases

Publisher: Centers for Disease Control and Prevention

ISSN (Print): 1080-6040

ISSN (Electronic): 1080-6059

Publication date (Print): February 2022

Volume: 28

Issue: 2

Pages: 373-381

Affiliations

[1]The University of Arizona, Tucson, Arizona, USA (A.K. Dhar, R. Cruz-Flores, J. Ramos, M. Garfias, G. Lyons);

[2]US Department of Agriculture National Veterinary Services Laboratories, Ames, Iowa, USA (J. Warg, M.L. Killian);

[3]Molsoft, Inc., San Diego, California, USA (A. Orry)

Author notes

Address for correspondence: Arun K. Dhar, Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, Bldg 90, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA; email: adhar@ 123456email.arizona.edu

Article

Publisher ID: 21-1874

DOI: 10.3201/eid2802.211874

PMC ID: 8798669

PubMed ID: 35075996

SO-VID: a303d5ce-72fd-465b-a853-450967129bcd

License:

Emerging Infectious Diseases is a publication of the U.S. Government. This publication is in the public domain and is therefore without copyright. All text from this work may be reprinted freely. Use of these materials should be properly cited.

Genetic Relatedness of Infectious Hypodermal and Hematopoietic Necrosis Virus Isolates, United States, 2019

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Point-of-Care Testing for Infectious Diseases Super Collection

Most cited references 29

Basic local alignment search tool.

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

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