The phylogenetics and pathogen population dynamics of infectious hypodermal and hematopoietic necrosis virus (IHHNV) in global shrimp populations
Ofori-Amponsah, Emmanuel, Andrade Martinez, Maria, Meehan, Michael T., and Condon, Kelly (2026) The phylogenetics and pathogen population dynamics of infectious hypodermal and hematopoietic necrosis virus (IHHNV) in global shrimp populations. Aquaculture, 616. 743684.
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Abstract
Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV) has posed a persistent threat to global shrimp aquaculture since its emergence in the 1980s, with transmission exacerbated by intensified farming and international trade. While previous studies have focused on regional outbreaks, the global evolutionary dynamics of IHHNV remain poorly understood. Here, we analyse 126 IHHNV capsid protein sequences (107 sequences extracted from GenBank and 19 newly collected sequences from northern Queensland, Australia) and 63 NS1 gene sequences (44 from GenBank and 19 from northern Queensland, Australia) collected from 12 countries between 1986 and 2022. Bayesian coalescent analyses estimate a mean nucleotide substitution rate of 4.5 × 10−4 (95% HPD 2.8 × 10−4, 6.4 × 10−4) substitutions/site/year for the capsid region and 1.9 × 10−4 (95% HPD 1.1 × 10−4, 2.8 × 10−4) for NS1, consistent with earlier region-specific results. The time to the most recent common ancestor was dated to the early 1980s (95% HPD: 1976–1986). Demographic reconstruction revealed periods of exponential growth in the 1990s and early 2000s, followed by a decline in the mid-2010s. Phylogenetic analysis revealed marked genetic diversity and strong geographic structuring, with some evidence of international viral exchange. Distinct regional SNP patterns mirrored the phylogenetic structure, supporting geographically constrained viral evolution and diversification. The high evolutionary rates and structured global distribution of IHHNV underscore the need for continued molecular surveillance and enhanced biosecurity to mitigate the risk of future outbreaks.
| Item ID: | 90693 |
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| Item Type: | Article (Research - C1) |
| ISSN: | 1873-5622 |
| Keywords: | Capsid, IHHNV, NS1, Phylogenetics, Shrimp |
| Copyright Information: | © 2026 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/) |
| Date Deposited: | 10 May 2026 23:19 |
| FoR Codes: | 30 AGRICULTURAL, VETERINARY AND FOOD SCIENCES > 3005 Fisheries sciences > 300501 Aquaculture @ 50% 31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310410 Phylogeny and comparative analysis @ 50% |
| SEO Codes: | 10 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 1002 Fisheries - aquaculture > 100205 Aquaculture prawns @ 80% 28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280101 Expanding knowledge in the agricultural, food and veterinary sciences @ 20% |
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