An efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small RNA deep sequencing data.
This paper explored our hypothesis that sRNA (18 ∼ 30 bp) deep sequencing technique can be used as an efficient strategy to identify microorganisms other than viruses, such as prokaryotic and eukaryotic pathogens. In the study, the clean reads derived from the sRNA deep sequencing data of wild-caugh...
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Public Library of Science (PLoS)
2014
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oai:doaj.org-article:2bb9ff94c9c44689a94a328f015c89f62021-11-18T08:28:49ZAn efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small RNA deep sequencing data.1932-620310.1371/journal.pone.0090831https://doaj.org/article/2bb9ff94c9c44689a94a328f015c89f62014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24618575/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203This paper explored our hypothesis that sRNA (18 ∼ 30 bp) deep sequencing technique can be used as an efficient strategy to identify microorganisms other than viruses, such as prokaryotic and eukaryotic pathogens. In the study, the clean reads derived from the sRNA deep sequencing data of wild-caught ticks and mosquitoes were compared against the NCBI nucleotide collection (non-redundant nt database) using Blastn. The blast results were then analyzed with in-house Python scripts. An empirical formula was proposed to identify the putative pathogens. Results showed that not only viruses but also prokaryotic and eukaryotic species of interest can be screened out and were subsequently confirmed with experiments. Specially, a novel Rickettsia spp. was indicated to exist in Haemaphysalis longicornis ticks collected in Beijing. Our study demonstrated the reuse of sRNA deep sequencing data would have the potential to trace the origin of pathogens or discover novel agents of emerging/re-emerging infectious diseases.Lu ZhuangZhiyi ZhangXiaoping AnHang FanMaijuan MaBenjamin D AndersonJiafu JiangWei LiuWuchun CaoYigang TongPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 3, p e90831 (2014) |
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Medicine R Science Q |
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Medicine R Science Q Lu Zhuang Zhiyi Zhang Xiaoping An Hang Fan Maijuan Ma Benjamin D Anderson Jiafu Jiang Wei Liu Wuchun Cao Yigang Tong An efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small RNA deep sequencing data. |
| description |
This paper explored our hypothesis that sRNA (18 ∼ 30 bp) deep sequencing technique can be used as an efficient strategy to identify microorganisms other than viruses, such as prokaryotic and eukaryotic pathogens. In the study, the clean reads derived from the sRNA deep sequencing data of wild-caught ticks and mosquitoes were compared against the NCBI nucleotide collection (non-redundant nt database) using Blastn. The blast results were then analyzed with in-house Python scripts. An empirical formula was proposed to identify the putative pathogens. Results showed that not only viruses but also prokaryotic and eukaryotic species of interest can be screened out and were subsequently confirmed with experiments. Specially, a novel Rickettsia spp. was indicated to exist in Haemaphysalis longicornis ticks collected in Beijing. Our study demonstrated the reuse of sRNA deep sequencing data would have the potential to trace the origin of pathogens or discover novel agents of emerging/re-emerging infectious diseases. |
| format |
article |
| author |
Lu Zhuang Zhiyi Zhang Xiaoping An Hang Fan Maijuan Ma Benjamin D Anderson Jiafu Jiang Wei Liu Wuchun Cao Yigang Tong |
| author_facet |
Lu Zhuang Zhiyi Zhang Xiaoping An Hang Fan Maijuan Ma Benjamin D Anderson Jiafu Jiang Wei Liu Wuchun Cao Yigang Tong |
| author_sort |
Lu Zhuang |
| title |
An efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small RNA deep sequencing data. |
| title_short |
An efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small RNA deep sequencing data. |
| title_full |
An efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small RNA deep sequencing data. |
| title_fullStr |
An efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small RNA deep sequencing data. |
| title_full_unstemmed |
An efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small RNA deep sequencing data. |
| title_sort |
efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small rna deep sequencing data. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2014 |
| url |
https://doaj.org/article/2bb9ff94c9c44689a94a328f015c89f6 |
| work_keys_str_mv |
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