Quasispecies Diversity and Amino Acid Variation at the Fusion Protein Cleavage Site of Newcastle Disease Virus Isolated from Cormorants in Central Asia.
- 1Laboratory of Biochemistry of Viruses, Research and Production Center for Microbiology and Virology, 105 Bogenbay batyr str., Almaty 050010, Kazakhstan.
- 2Laboratory of Viral Ecology, Research and Production Center for Microbiology and Virology, 105 Bogenbay batyr str., Almaty 050010, Kazakhstan.
Abstract
Newcastle disease virus (NDV) remains a major threat to poultry production worldwide, and wild waterbirds are recognized as reservoirs of virulent strains. To characterize fine-scale quasispecies diversity at the virulence-determining fusion (F) protein cleavage site, amplicons encompassing the six-amino-acid motif were deep-sequenced from seven egg-passaged cormorant-derived isolates. Fifty-four distinct amino-acid substitutions passed predefined abundance and statistical filters and were detected across all six cleavage-site positions. The cleavage-site quasispecies was dominated by a limited set of recurrent substitutions (R1G, F6L, F6V, F6C, R4G, and several position-2 variants), each supported by hundreds of thousands of reads and occurring at frequencies of 1-26% across samples. Pooled Shannon entropy indicated that positions 1 and 6 were the most variable, whereas positions 3 and 5 showed lower diversity across the dataset. Principal component analysis showed apparent differences in mutation-frequency profiles among the seven egg-passaged isolates; the first two principal components explained 97.9% of the variance (PC1, 87.4%; PC2, 10.5%). Heatmap visualization showed that a subset of variants, including R1G and F6L/V/C, was consistently abundant across samples, whereas others were isolate-specific. These data describe position-specific cleavage-site heterogeneity in seven egg-passaged NDV isolates originally recovered from cormorants. The observed variant frequencies may reflect a combination of diversity present in the original specimens and changes introduced or selected during egg amplification. The coexistence of the predominant velogenic RRQRRF motif with lower-frequency alternative and stop-codon-containing haplotypes documents sequence heterogeneity in outbreak-related material after egg amplification and provides a descriptive basis for future genotype-resolved and phenotype-linked studies.
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BibTeX
@article{karamendin2026quasispecies,
title = {{Quasispecies Diversity and Amino Acid Variation at the Fusion Protein Cleavage Site of Newcastle Disease Virus Isolated from Cormorants in Central Asia.}},
author = {Kobey Karamendin and Sardor Nuralibekov and Temirlan Sabyrzhan and Yermukhammet Kasymbekov and Klara Daulbayeva and Yelizaveta Khan and Marat Kumar and Aidyn Kydyrmanov},
journal = {Pathogens (Basel, Switzerland)},
year = {2026},
month = oct,
doi = {10.3390/pathogens15101059},
url = {https://europepmc.org/article/MED/42931211},
note = {CC BY},
}
RIS
TY - JOUR
TI - Quasispecies Diversity and Amino Acid Variation at the Fusion Protein Cleavage Site of Newcastle Disease Virus Isolated from Cormorants in Central Asia.
AU - Kobey Karamendin
AU - Sardor Nuralibekov
AU - Temirlan Sabyrzhan
AU - Yermukhammet Kasymbekov
AU - Klara Daulbayeva
AU - Yelizaveta Khan
AU - Marat Kumar
AU - Aidyn Kydyrmanov
PY - 2026
DA - 2026/10/08
JO - Pathogens (Basel, Switzerland)
DO - 10.3390/pathogens15101059
UR - https://europepmc.org/article/MED/42931211
AB - Newcastle disease virus (NDV) remains a major threat to poultry production worldwide, and wild waterbirds are recognized as reservoirs of virulent strains. To characterize fine-scale quasispecies diversity at the virulence-determining fusion (F) protein cleavage site, amplicons encompassing the six-amino-acid motif were deep-sequenced from seven egg-passaged cormorant-derived isolates. Fifty-four distinct amino-acid substitutions passed predefined abundance and statistical filters and were detected across all six cleavage-site positions. The cleavage-site quasispecies was dominated by a limited set of recurrent substitutions (R1G, F6L, F6V, F6C, R4G, and several position-2 variants), each supported by hundreds of thousands of reads and occurring at frequencies of 1-26% across samples. Pooled Shannon entropy indicated that positions 1 and 6 were the most variable, whereas positions 3 and 5 showed lower diversity across the dataset. Principal component analysis showed apparent differences in mutation-frequency profiles among the seven egg-passaged isolates; the first two principal components explained 97.9% of the variance (PC1, 87.4%; PC2, 10.5%). Heatmap visualization showed that a subset of variants, including R1G and F6L/V/C, was consistently abundant across samples, whereas others were isolate-specific. These data describe position-specific cleavage-site heterogeneity in seven egg-passaged NDV isolates originally recovered from cormorants. The observed variant frequencies may reflect a combination of diversity present in the original specimens and changes introduced or selected during egg amplification. The coexistence of the predominant velogenic RRQRRF motif with lower-frequency alternative and stop-codon-containing haplotypes documents sequence heterogeneity in outbreak-related material after egg amplification and provides a descriptive basis for future genotype-resolved and phenotype-linked studies.
SN - 2076-0817
ER -