First Polycipivirus and Unmapped RNA Virus Diversity in the Yellow Crazy Ant, Anoplolepis gracilipes

Lee, Chih-Chi; Hsu, Hung-Wei; Lin, Chun-Yi; Gustafson, Nicolas; Matsuura, Kenji; Lee, Chow‐Yang; Yang, Chun‐Pai

doi:10.3390/v14102161

Cited by 2 publications

(4 citation statements)

References 65 publications

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“…Solenopsis invicta virus 7, apis picorna-like virus 5, PNG bee virus 9, Hangzhou Sesamia inferens solinvi-like virus 1, rob180rna1 (YCA-associated virus-like sequence 8 in [34]), HVAC-associated RNA virus 1, apis picorna-like virus 3 , Bundaberg bee virus 8, Milolii virus, lasius picorna-like virus 9…”

Section: Resultsmentioning

confidence: 99%

“…An unclassified group related to Solenopsis invicta virus 7 [33] (), close to the family Acypiviridae (see Fig. S1h in [34]).…”

Section: Resultsmentioning

confidence: 99%

“…Solenopsis invicta virus 7-like group, closely related to the proposed family Acypiviridae (see Fig. S1h in [34]).…”

Section: Proteins From Several Cypoviruses Contain a Divergent Wiv Do...mentioning

confidence: 85%

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WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection

Karlin

2024

Journal of General Virology

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The most powerful approach to detect distant homologues of a protein is based on structure prediction and comparison. Yet this approach is still inapplicable to many viral proteins. Therefore, we applied a powerful sequence-based procedure to identify distant homologues of viral proteins. It relies on three principles: (1) traces of sequence similarity can persist beyond the significance cutoff of homology detection programmes; (2) candidate homologues can be identified among proteins with weak sequence similarity to the query by using ‘contextual’ information, e.g. taxonomy or type of host infected; (3) these candidate homologues can be validated using highly sensitive profile–profile comparison. As a test case, this approach was applied to a protein without known homologues, encoded by ORF4 of Lake Sinai viruses (which infect bees). We discovered that the ORF4 protein contains a domain that has homologues in proteins from >20 taxa of viruses infecting arthropods. We called this domain ‘widespread, intriguing, versatile’ (WIV), because it is found in proteins with a wide variety of functions and within varied domain contexts. For example, WIV is found in the NSs protein of tospoviruses, a global threat to food security, which infect plants as well as their arthropod vectors; in the RNA2 ORF1-encoded protein of chronic bee paralysis virus, a widespread virus of bees; and in various proteins of cypoviruses, which infect the silkworm Bombyx mori. Structural modelling with AlphaFold indicated that the WIV domain has a previously unknown fold, and bibliographical evidence suggests that it facilitates infection of arthropods.

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Section: Resultsmentioning

confidence: 99%

“…An unclassified group related to Solenopsis invicta virus 7 [33] (), close to the family Acypiviridae (see Fig. S1h in [34]).…”

Section: Resultsmentioning

confidence: 99%

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WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection

Karlin

2024

Journal of General Virology

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“…Solenopsis invicta virus 7, Apis-Picorna-like virus 5, PNG bee virus 9, Hangzhou sesamia inferens solinvi-like virus 1, YCA-associated virus-like sequence 8 [34], HVAC-associated RNA virus 1, Apis picorna-like virus 3, Bundaberg bee virus 8, Milolii virus, Lasius picorna-like virus 9…”

Section: The Wiv Domain Is Found In Proteins From Over 20 Viral Taxa ...mentioning

confidence: 99%

An Overlooked Protein Domain, WIV, Is Found a Wide Number of Arthropod Viruses and Probably Facilitates Infection

Karlin¹

2023

Preprint

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Today, the most powerful approach to detect distant homologs of a protein is based on structure prediction and comparison. Yet this approach is still inapplicable to many viral proteins. Therefore, we developed a powerful sequence-based procedure to identify distant homologs of viral proteins. It relies on 3 main principles: 1) Traces of sequence similarity with a protein can persist beyond the significance cutoff of homology detection programs; 2) Candidate homologs can be identified among proteins with weak sequence similarity to the query, by using "contextual" information, e.g. taxonomy or type of host infected; 3) These candidate homologs can be validated using highly sensitive profile-profile comparison.As a test case, we applied our approach to a protein without known homologs, ORF4 of Lake Sinai virus (which infects bees). We discovered that ORF4 is composed of a domain that has homologs in proteins from >20 taxa of viruses infecting arthropods. We called it “Widespread, Intriguing, Versatile” (WIV) domain because it is found in proteins with a wide variety of domain organizations and functions. For example, WIV is encoded by the NSs protein of tospoviruses, a global threat to food security, which infect plants through arthropod vectors; by the protein encoded by RNA2 ORF1 of chronic bee paralysis virus, a widespread virus of bees; and by various proteins of cypoviruses, which infect the silkworm bombyx mori. WIV has a previously unknown structural fold, according to Alphafold predictions. In some viral species, WIV facilitates infection of arthropods, according to bibliographical evidence

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First Polycipivirus and Unmapped RNA Virus Diversity in the Yellow Crazy Ant, Anoplolepis gracilipes

Cited by 2 publications

References 65 publications

WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection

WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection

An Overlooked Protein Domain, WIV, Is Found a Wide Number of Arthropod Viruses and Probably Facilitates Infection

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