Molecular detection of a novel totivirus from golden shiner (Notemigonus crysoleucas) baitfish in the USA

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Abstract

During regulatory and routine surveillance sampling of apparently healthy baitfish from the state of Minnesota, a novel totivirus (tentatively named “golden shiner totivirus”, GSTV) was detected in a homogenate of kidney and spleen of golden shiner (Notemigonus crysoleucas). The nearly complete genome is 7788 nt long with a complete 5’ untranslated region (UTR) of 135 nt (1-135 nt position), complete open reading frames (ORFs) and a partial 3’ UTR of 54 nt (7734-7788). The sequence is comprised of two ORFs (ORF1 and ORF2). The larger ORF1 encodes a 1659-aa polypeptide in frame +1 from nt position 136 to 5115 (4980 nt) with a start codon at position 136-138 and a stop codon at position 5113-5115. The ORF1 is 54 aa longer than the 1605-aa ORF1-encoded protein of a reference strain of infectious myonecrosis virus (IMNV), ID-EJ-12-1(AIC34743.1). The predicted ORF1 and ORF2 fusion protein sequence was NFQDGG. Hence, an overlapping region of 99 nt was observed, which is shorter than the 172-nt and 199-nt overlapping regions in Armigeres subalbatus totivirus (AsTV) and IMNV, respectively. GSTV formed a separate lineage based on phylogenetic analysis of ORF1-encoded major capsid protein (MCP) and ORF2-encoded RNA-dependent RNA polymerase (RdRp) sequences. Based on ORF1 MCP sequence analysis, GSTV was most closely related to IMNV, with maximum aa sequence identity of 26.42-27.86 %, followed by 26.59, 22.94 and 21.75 % for Drosophila totivirus (DTV), AsTV and Omono River virus (OMRV), respectively. Similar to ORF1, the ORF2 (RdRp) of GSTV formed a separate clade with maximum identity of 38.10 % and 38.50 % to IMNV and DTV, respectively. The virus identified here differs enough from its closest relative that it may represent a new genus in the family Totiviridae. The disease-causing potential and management impact of this novel virus is unknown at this time.

Original languageEnglish (US)
Pages (from-to)2227-2234
Number of pages8
JournalArchives of Virology
Volume161
Issue number8
DOIs
StatePublished - Aug 1 2016

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Totivirus
Cyprinidae
Viruses
RNA Replicase
Capsid Proteins
Totiviridae
Open Reading Frames
Drosophila
Initiator Codon
Terminator Codon
5' Untranslated Regions
Protein Sequence Analysis
3' Untranslated Regions
Rivers

Cite this

@article{5c996efb6f7e43aba6eb882af77a5baa,
title = "Molecular detection of a novel totivirus from golden shiner (Notemigonus crysoleucas) baitfish in the USA",
abstract = "During regulatory and routine surveillance sampling of apparently healthy baitfish from the state of Minnesota, a novel totivirus (tentatively named “golden shiner totivirus”, GSTV) was detected in a homogenate of kidney and spleen of golden shiner (Notemigonus crysoleucas). The nearly complete genome is 7788 nt long with a complete 5’ untranslated region (UTR) of 135 nt (1-135 nt position), complete open reading frames (ORFs) and a partial 3’ UTR of 54 nt (7734-7788). The sequence is comprised of two ORFs (ORF1 and ORF2). The larger ORF1 encodes a 1659-aa polypeptide in frame +1 from nt position 136 to 5115 (4980 nt) with a start codon at position 136-138 and a stop codon at position 5113-5115. The ORF1 is 54 aa longer than the 1605-aa ORF1-encoded protein of a reference strain of infectious myonecrosis virus (IMNV), ID-EJ-12-1(AIC34743.1). The predicted ORF1 and ORF2 fusion protein sequence was NFQDGG. Hence, an overlapping region of 99 nt was observed, which is shorter than the 172-nt and 199-nt overlapping regions in Armigeres subalbatus totivirus (AsTV) and IMNV, respectively. GSTV formed a separate lineage based on phylogenetic analysis of ORF1-encoded major capsid protein (MCP) and ORF2-encoded RNA-dependent RNA polymerase (RdRp) sequences. Based on ORF1 MCP sequence analysis, GSTV was most closely related to IMNV, with maximum aa sequence identity of 26.42-27.86 {\%}, followed by 26.59, 22.94 and 21.75 {\%} for Drosophila totivirus (DTV), AsTV and Omono River virus (OMRV), respectively. Similar to ORF1, the ORF2 (RdRp) of GSTV formed a separate clade with maximum identity of 38.10 {\%} and 38.50 {\%} to IMNV and DTV, respectively. The virus identified here differs enough from its closest relative that it may represent a new genus in the family Totiviridae. The disease-causing potential and management impact of this novel virus is unknown at this time.",
author = "Mor, {Sunil Kumar} and Phelps, {Nicholas Benjamin Daniel}",
year = "2016",
month = "8",
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doi = "10.1007/s00705-016-2906-8",
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T1 - Molecular detection of a novel totivirus from golden shiner (Notemigonus crysoleucas) baitfish in the USA

AU - Mor, Sunil Kumar

AU - Phelps, Nicholas Benjamin Daniel

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N2 - During regulatory and routine surveillance sampling of apparently healthy baitfish from the state of Minnesota, a novel totivirus (tentatively named “golden shiner totivirus”, GSTV) was detected in a homogenate of kidney and spleen of golden shiner (Notemigonus crysoleucas). The nearly complete genome is 7788 nt long with a complete 5’ untranslated region (UTR) of 135 nt (1-135 nt position), complete open reading frames (ORFs) and a partial 3’ UTR of 54 nt (7734-7788). The sequence is comprised of two ORFs (ORF1 and ORF2). The larger ORF1 encodes a 1659-aa polypeptide in frame +1 from nt position 136 to 5115 (4980 nt) with a start codon at position 136-138 and a stop codon at position 5113-5115. The ORF1 is 54 aa longer than the 1605-aa ORF1-encoded protein of a reference strain of infectious myonecrosis virus (IMNV), ID-EJ-12-1(AIC34743.1). The predicted ORF1 and ORF2 fusion protein sequence was NFQDGG. Hence, an overlapping region of 99 nt was observed, which is shorter than the 172-nt and 199-nt overlapping regions in Armigeres subalbatus totivirus (AsTV) and IMNV, respectively. GSTV formed a separate lineage based on phylogenetic analysis of ORF1-encoded major capsid protein (MCP) and ORF2-encoded RNA-dependent RNA polymerase (RdRp) sequences. Based on ORF1 MCP sequence analysis, GSTV was most closely related to IMNV, with maximum aa sequence identity of 26.42-27.86 %, followed by 26.59, 22.94 and 21.75 % for Drosophila totivirus (DTV), AsTV and Omono River virus (OMRV), respectively. Similar to ORF1, the ORF2 (RdRp) of GSTV formed a separate clade with maximum identity of 38.10 % and 38.50 % to IMNV and DTV, respectively. The virus identified here differs enough from its closest relative that it may represent a new genus in the family Totiviridae. The disease-causing potential and management impact of this novel virus is unknown at this time.

AB - During regulatory and routine surveillance sampling of apparently healthy baitfish from the state of Minnesota, a novel totivirus (tentatively named “golden shiner totivirus”, GSTV) was detected in a homogenate of kidney and spleen of golden shiner (Notemigonus crysoleucas). The nearly complete genome is 7788 nt long with a complete 5’ untranslated region (UTR) of 135 nt (1-135 nt position), complete open reading frames (ORFs) and a partial 3’ UTR of 54 nt (7734-7788). The sequence is comprised of two ORFs (ORF1 and ORF2). The larger ORF1 encodes a 1659-aa polypeptide in frame +1 from nt position 136 to 5115 (4980 nt) with a start codon at position 136-138 and a stop codon at position 5113-5115. The ORF1 is 54 aa longer than the 1605-aa ORF1-encoded protein of a reference strain of infectious myonecrosis virus (IMNV), ID-EJ-12-1(AIC34743.1). The predicted ORF1 and ORF2 fusion protein sequence was NFQDGG. Hence, an overlapping region of 99 nt was observed, which is shorter than the 172-nt and 199-nt overlapping regions in Armigeres subalbatus totivirus (AsTV) and IMNV, respectively. GSTV formed a separate lineage based on phylogenetic analysis of ORF1-encoded major capsid protein (MCP) and ORF2-encoded RNA-dependent RNA polymerase (RdRp) sequences. Based on ORF1 MCP sequence analysis, GSTV was most closely related to IMNV, with maximum aa sequence identity of 26.42-27.86 %, followed by 26.59, 22.94 and 21.75 % for Drosophila totivirus (DTV), AsTV and Omono River virus (OMRV), respectively. Similar to ORF1, the ORF2 (RdRp) of GSTV formed a separate clade with maximum identity of 38.10 % and 38.50 % to IMNV and DTV, respectively. The virus identified here differs enough from its closest relative that it may represent a new genus in the family Totiviridae. The disease-causing potential and management impact of this novel virus is unknown at this time.

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