[1]
|
Lu JJ, Xing H, Wang CH, Tang MJ, Wu CC, Ye F, et al. Mpox (formerly monkeypox): pathogenesis, prevention and treatment. Signal Transduct Target Ther 2023;8(1):458. https://doi.org/10.1038/s41392-023-01675-2. |
[2]
|
Ladnyj ID, Ziegler P, Kima E. A human infection caused by monkeypox virus in Basankusu Territory, Democratic Republic of the Congo. Bull World Health Organ 1972;46(5):593-7. https://pubmed.ncbi.nlm.nih.gov/4340218. |
[3]
|
Isidro J, Borges V, Pinto M, Sobral D, Santos JD, Nunes A, et al. Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus. Nat Med 2022;28(8):1569 − 72. https://doi.org/10.1038/s41591-022-01907-y. |
[4]
|
Gigante CM, Korber B, Seabolt MH, Wilkins K, Davidson W, Rao AK, et al. Multiple lineages of monkeypox virus detected in the United States, 2021-2022. Science 2022;378(6619):560 − 5. https://doi.org/10.1126/science.add4153. |
[5]
|
Otieno JR, Ruis C, Onoja AB, Kuppalli K, Hoxha A, Nitsche A, et al. Global genomic surveillance of monkeypox virus. Nat Med 2025;31(1):342 − 50. https://doi.org/10.1038/s41591-024-03370-3. |
[6]
|
Zhao H, Wang WL, Zhao L, Ye S, Song JD, Lu RJ, et al. The first imported case of monkeypox in the mainland of China — Chongqing municipality, China, September 16, 2022. China CDC Wkly 2022;4(38):853 − 4. https://doi.org/10.46234/ccdcw2022.175. |
[7]
|
Wu CC, Ruhan A, Ye S, Ye F, Huo WB, Lu RJ, et al. Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing. Virol Sin 2024;39(1):134 − 43. https://doi.org/10.1016/j.virs.2023.12.002. |
[8]
|
Yu JH, Zhang X, Liu JJ, Xiang LL, Huang S, Xie XT, et al. Phylogeny and molecular evolution of the first local monkeypox virus cluster in Guangdong Province, China. Nat Commun 2023;14(1):8241. https://doi.org/10.1038/s41467-023-44092-3. |
[9]
|
Wu CC, Cui LB, Pan Y, Lv ZQ, Yao MX, Wang WL, et al. Characterization of whole genomes from recently emerging Mpox cases in several regions of China, 2023. Sci China Life Sci 2024;67(5):1079 − 81. https://doi.org/10.1007/s11427-023-2485-8. |
[10]
|
Ren RQ, Li C, Bai WQ, Wang YL, Li D, Ding F, et al. The epidemiological characteristics of mpox cases - China, 2023. China CDC Wkly 2024;6(26):619 − 23. https://doi.org/10.46234/ccdcw2024.118. |
[11]
|
Shan KJ, Wu CC, Tang XL, Lu RJ, Hu YL, Tan WJ, et al. Molecular evolution of protein sequences and codon usage in monkeypox viruses. Genomics Proteomics Bioinf 2024;22(1):qzad003. https://doi.org/10.1093/gpbjnl/qzad003. |
[12]
|
Hatmal MM, Al-Hatamleh MAI, Olaimat AN, Ahmad S, Hasan H, Ahmad Suhaimi NA, et al. Comprehensive literature review of monkeypox. Emerg Microbes Infect 2022;11(1):2600 − 31. https://doi.org/10.1080/22221751.2022.2132882. |
[13]
|
Chen YD, Wu CC, Ruhan A, Zhao L, Zhang ZX, Tan WJ. Perspective on the application of genome sequencing for monkeypox virus surveillance. Virol Sin 2023;38(2):327 − 33. https://doi.org/10.1016/j.virs.2023.03.006. |
[14]
|
Chen SF, Zhou YQ, Chen YR, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018;34(17):i884 − 90. https://doi.org/10.1093/bioinformatics/bty560. |
[15]
|
Li H. New strategies to improve minimap2 alignment accuracy. Bioinformatics 2021;37(23):4572 − 4. https://doi.org/10.1093/bioinformatics/btab705. |
[16]
|
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv:1207.3907 [Preprint] 2012. https://doi.org/10.48550/arXiv.1207.3907. |
[17]
|
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. Gigascience 2021;10(2):giab008. https://doi.org/10.1093/gigascience/giab008. |
[18]
|
Aksamentov I, Roemer C, Hodcroft EB, Neher RA. Nextclade: clade assignment, mutation calling and quality control for viral genomes. J Open Source Softw 2021;6(67):3773. https://doi.org/10.21105/joss.03773. |
[19]
|
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020;37(5):1530 − 4. https://doi.org/10.1093/molbev/msaa015. |
[20]
|
Sagulenko P, Puller V, Neher RA. TreeTime: maximum-likelihood phylodynamic analysis. Virus Evol 2018;4(1):vex042. https://doi.org/10.1093/ve/vex042. |
[21]
|
Chi LJ, Zhang XL, Xue YB, Chen H. fastHaN: a fast and scalable program for constructing haplotype network for large-sample sequences. Mol Ecol Resour 2025;25(5):e13829. https://doi.org/10.1111/1755-0998.13829. |
[22]
|
Tang XL, Wu CC, Li X, Song YH, Yao XM, Wu XK, et al. On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev 2020;7(6):1012 − 23. https://doi.org/10.1093/nsr/nwaa036. |
[23]
|
Xu J, Liu C, Zhang Q, Zhu HN, Cui F, Zhao ZQ, et al. The first detection of mpox virus DNA from wastewater in China. Sci Total Environ 2024;932:172742. https://doi.org/10.1016/j.scitotenv.2024.172742. |
[24]
|
Zhang SJ, Wang FX, Peng Y, Gong XH, Fan GH, Lin YL, et al. Evolutionary trajectory and characteristics of Mpox virus in 2023 based on a large-scale genomic surveillance in Shenzhen, China. Nat Commun 2024;15(1):7452. https://doi.org/10.1038/s41467-024-51737-4. |
[25]
|
Vakaniaki EH, Kacita C, Kinganda-Lusamaki E, O'Toole Á, Wawina-Bokalanga T, Mukadi-Bamuleka D, et al. Sustained human outbreak of a new MPXV clade I lineage in eastern Democratic Republic of the Congo. Nat Med 2024;30(10):2791-5. http://dx.doi.org/10.1038/s41591-024-03130-3. |
[26]
|
de Araujo JC, Carvalho APA, Leal CD, Natividade M, Borin M, Guerra A, et al. Detection of multiple human viruses, including mpox, using a wastewater surveillance approach in brazil. Pathogens 2024;13(7):589. https://doi.org/10.3390/pathogens13070589. |
[27]
|
Tiwari A, Adhikari S, Kaya D, Islam MA, Malla B, Sherchan SP, et al. Monkeypox outbreak: wastewater and environmental surveillance perspective. Sci Total Environ 2023;856(Pt 2):159166. http://dx.doi.org/10.1016/j.scitotenv.2022.159166. |
[28]
|
WHO. Considerations for wastewater and environmental surveillance for monkeypox virus: Interim guidance. 2024. https://www.who.int/publications/i/item/B09178. [2025-7-4]. |