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. 2023 Oct 9;15(10):2068.
doi: 10.3390/v15102068.

Identification of Multiple Novel Viruses in Fecal Samples of Black-Necked Cranes Using Viral Metagenomic Methods

Qifan Zhao  1 , Ran Zhao  2 , Yijie Sun  1 , Li Ji  1 , Yuan Xi  1 , Xiaochun Wang  1 , Quan Shen  1 , Likai Ji  1 , Yan Wang  1 , Zhenqiang You  3 , Shixing Yang  1 , Wen Zhang  1
Affiliations

Identification of Multiple Novel Viruses in Fecal Samples of Black-Necked Cranes Using Viral Metagenomic Methods

Qifan Zhao et al. Viruses. .

Abstract

The black-necked crane is the only species of crane that lives in the high-altitude region of the Tibet Plateau. At present, there is little research on viral diseases of the black-necked crane (Grus nigricollis). In this study, a viral metagenomic approach was employed to investigate the fecal virome of black-necked cranes in Saga County, Shigatse City, Tibet, China. The identified virus families carried by black-necked cranes mainly include Genomoviridae, Parvoviridae, and Picornaviridae. The percentages of sequence reads belonging to these three virus families were 1.6%, 3.1%, and 93.7%, respectively. Among them, one genome was characterized as a novel species in the genus Grusopivirus of the family Picornaviridae, four new parvovirus genomes were obtained and classified into four different novel species within the genus Chaphamaparvovirus of the subfamily Hamaparvovirinae, and four novel genomovirus genomes were also acquired and identified as members of three different species, including Gemykroznavirus haeme1, Gemycircularvirus ptero6, and Gemycircularvirus ptero10. All of these viruses were firstly detected in fecal samples of black-necked cranes. This study provides valuable information for understanding the viral community composition in the digestive tract of black-necked cranes in Tibet, which can be used for monitoring, preventing, and treating potential viral diseases in black-necked cranes.

Keywords: black-necked crane; genomic structure; phylogenetic analysis; viral metagenomics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Pie chart of the composition of fecal virome detected in black-necked cranes, shown as percentages. The percentage of sequence reads in different viral families refers to all viruses in the same viral family obtained from the library and not just new viruses that were identified.
Figure 2
Figure 2
The genomic organization, conserved motifs, and phylogenetic analysis of the grusopivirus identified in black-necked cranes. (a) The genomic organization of one grusopivirus strain. The ORF- and viral-encoding proteins of grusopivirus are marked with different colors. The conserved motifs are also shown. (b,c) Phylogenetic analysis based on the P1 region and 3CD of grusopivirus, which was identified in this study, and other reference strains belonging to the subfamily Paavivirinae of the family Picornaviridae. Grusopivirus D, which was identified in this study, is highlighted in red.
Figure 3
Figure 3
The genomic organization, conserved helicase domain motifs, and phylogenetic analysis of four chaphamaparvoviruses identified in black-necked cranes. (a) The genomic organization of four chaphamaparvoviruses identified in black-necked cranes. Viral-encoding proteins of four chaphamaparvoviruses are marked with different colors, in which red is used for nonstructural protein 1, pink for nonstructural protein 2, and green for capsid protein. (b) The conserved NTPase/helicase motif (Walker A, B, B’, and C) of these four parvoviruses and other reference strains are shown. The conserved motifs are marked with an orange frame. (c) The phylogenetic analysis was based on NS1 proteins of the mentioned parvoviruses, as well as on their closest viral relatives, which were determined using the best BLASTp hits and other representative strains belonging to the genus Chaphamaparvovirus of the subfamily Hamaparvovirinae. The four chaphamaparvoviruses identified in this study are highlighted in red.
Figure 4
Figure 4
The genomic organization and phylogenetic analysis of genomoviruses identified in black-necked cranes. (a) The genomic organization of four genomoviruses identified in black-necked cranes. Viral-encoding proteins of four genomoviruses are marked with different colors, in which red is used for replication-associated protein and green for capsid protein. (b) Phylogenetic analysis based on the Rep proteins of four genomoviruses identified in this study and on reference strains of other genomoviruses. The four genomoviruses identified in this study are highlighted in red.
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Grants and funding

This research was funded by the National Key Research and Development Programs of China (No. 2022YFC2603801), National Natural Science Foundation of China (No. 32102682), and Science Foundation of Higher Education of Jiangsu Province (No. 21KJB230006).