Diverse Head-to-Tail Sequences in the Circular Genome of Human Bocavirus Genotype 1 among Children with Acute Respiratory Infections Implied the Switch of Template Chain in the Rolling-Circle Replication Model
Abstract
:1. Introduction
2. Materials and Methods
2.1. Clinical Specimens
2.2. Nucleic Acid Extraction
2.3. CEMP Assay for Multiple-Pathogen Screening
2.4. Genotyping of HBoVs by PCR
2.5. Amplification, Cloning, and Sanger Sequencing of Head-to-Tail Sequences and Assembly of the HBoV1 Circular Genome
2.6. Amplicon Sequencing of Nested PCR Amplification Products
2.7. Sequence Analysis of the Head-to-Tail Sequence
2.8. Meta-Genomic Next-Generation Sequencing (mNGS) of Circular Genomes
3. Results
3.1. Pathogen Screening by the CEMP Assay
3.2. The Head-to-Tail Sequences of HBoV1 by TA Cloning and Sanger Sequencing
3.3. The Head-to-Tail Sequences of HBoV1 by Amplicon Sequencing
3.4. Meta-Genomic Next-Generation Sequencing (mNGS)
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Round | Name | Position | Sequences (5′-3′) |
---|---|---|---|
First | HBoV1-F1-Tail (+) | JQ923422:5187-5206 | gcttctgcttacaagttcct |
HBoV1-R1-Head (−) | JQ923422:365-346 | ggaggattgaaagccatagt | |
Second | HBoV1-F2-Tail (+) | JQ923422:5283-5300 | tggtgttaccgtctcgaa |
HBoV1-R2-Head (−) | JQ923422:272-254 | aggaagtgcagcagcttaa |
Type | No. of Sequences | 5′ REH Located on the Position of JQ923422 | Linker Sequences | 3′ LEH Located on the Position of JQ923422 | |
---|---|---|---|---|---|
Sequences | Position on 5′ REH of JQ923422 | ||||
5 | 1 | 5283–5451 | GCGCATGTTATGGATTACATCAT | unknown | 196–272 |
9 | 14 | 5283–5402 | GCTGATATAAAACT | 5467–5480 | 119–272 |
11 | 4 | 5283–5402 | GCTGATATAAAACT | 5467–5480 | 119–272 |
13 | 6 | 5283–5426 | ATGTACAACAACAACACATTAAAAGATAT | 5491–5519 | 139–272 |
14 | 4 | 5283–5402 | GCTGATATAAAACTAAGATGGCGCATGTAC | 5467–5496 | 112–272 |
20 | 1 | 5283–5402 | GCTGATATAAAACTAAGATG | 5467–5486 | 73–272 |
21 | 1 | 5283–5402 | GCTGATATAAAACTAAGATG | 5467–5486 | 71–272 |
23 | 1 | 5283–5426 | ATGTACAA | 5491–5498 | 72–272 |
24 | 2 | 5283–5402 | GCTGATATAAAACTAAGATGGCGCATGTACA | 5467–5497 | 67–272 |
28 | 2 | 5283–5442 | AAAGT | unknown | 69–272 |
29 | 1 | 5283–5429 | TAGATCA | unknown | 56–272 |
31 | 1 | 5283–5444 | GC | 5467–5468 | 48–272 |
32 | 1 | 5283–5402 | GCTGATATAAAACTAAGATGGCG | 5467–5489 | 17–272 |
Variants | Alignment Results between Variants and Reference Sequence | ||
---|---|---|---|
288a | 1–120 5283–5402 | 121–144 5403–5426 | 145–288 129–272 |
288b | 1–120 5283–5402 | 121–144 5420–5397 * | 145–288 129–272 |
304a | 1–120 5283–5402 | 121–149 5403–5431 | 150–304 118–272 |
304b | 1–120 5283–5402 | 121–149 5420–5392 * | 150–304 118–272 |
374a | 1–124 5283–5406 | 125–242 23–140 | 243–374 141–272 |
374b | 1–124 5283–5406 | 125–242 118–1 * | 243–374 141–272 |
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Zhang, K.; De, R.; Xu, Y.; Han, Z.; Zhu, R.; Sun, Y.; Jia, L.; Chen, D.; Zhou, Y.; Guo, Q.; et al. Diverse Head-to-Tail Sequences in the Circular Genome of Human Bocavirus Genotype 1 among Children with Acute Respiratory Infections Implied the Switch of Template Chain in the Rolling-Circle Replication Model. Pathogens 2024, 13, 757. https://doi.org/10.3390/pathogens13090757
Zhang K, De R, Xu Y, Han Z, Zhu R, Sun Y, Jia L, Chen D, Zhou Y, Guo Q, et al. Diverse Head-to-Tail Sequences in the Circular Genome of Human Bocavirus Genotype 1 among Children with Acute Respiratory Infections Implied the Switch of Template Chain in the Rolling-Circle Replication Model. Pathogens. 2024; 13(9):757. https://doi.org/10.3390/pathogens13090757
Chicago/Turabian StyleZhang, Kexiang, Ri De, Yanpeng Xu, Zhenzhi Han, Runan Zhu, Yu Sun, Liping Jia, Dongmei Chen, Yutong Zhou, Qi Guo, and et al. 2024. "Diverse Head-to-Tail Sequences in the Circular Genome of Human Bocavirus Genotype 1 among Children with Acute Respiratory Infections Implied the Switch of Template Chain in the Rolling-Circle Replication Model" Pathogens 13, no. 9: 757. https://doi.org/10.3390/pathogens13090757
APA StyleZhang, K., De, R., Xu, Y., Han, Z., Zhu, R., Sun, Y., Jia, L., Chen, D., Zhou, Y., Guo, Q., Yao, Y., Liu, S., Qu, D., Qian, Y., & Zhao, L. (2024). Diverse Head-to-Tail Sequences in the Circular Genome of Human Bocavirus Genotype 1 among Children with Acute Respiratory Infections Implied the Switch of Template Chain in the Rolling-Circle Replication Model. Pathogens, 13(9), 757. https://doi.org/10.3390/pathogens13090757