Selected article for: "GenBank accession and maximum likelihood"
Author: Söderman, Martina; Rhedin, Samuel; Tolfvenstam, Thomas; Rotzén-Östlund, Maria; Albert, Jan; Broliden, Kristina; Lindblom, Anna
Title: Frequent Respiratory Viral Infections in Children with Febrile Neutropenia - A Prospective Follow-Up Study
  • Document date: 2016_6_16
    • ID: 1a2u9p4t_6
    Snippet: RV/EV genotyping was performed by VP4/VP2 sequencing for samples that were PCR-positive for RV and/or EV using a recently published method [20] based on a method and primers originally published by Wisdom et al. [21] . Briefly, viral RNA was extracted as described above for most samples, but the RNeasy Lipid Tissue Mini Kit (Qiagen, Sollentuna, Sweden) was used for samples that were negative in the VP4/VP2 PCR after MagAttract extraction. The RNA.....
    Document: RV/EV genotyping was performed by VP4/VP2 sequencing for samples that were PCR-positive for RV and/or EV using a recently published method [20] based on a method and primers originally published by Wisdom et al. [21] . Briefly, viral RNA was extracted as described above for most samples, but the RNeasy Lipid Tissue Mini Kit (Qiagen, Sollentuna, Sweden) was used for samples that were negative in the VP4/VP2 PCR after MagAttract extraction. The RNA was used for the nested reverse transcriptase (RT)-PCR with One-step Superscript-Platinum Taq (Life Technologies, Stockholm, Sweden) for the first (outer) PCR, and Platinum Taq for the second (nested) PCR. Sequencing was done on an ABI 3730 instrument and the RV/EV species and type was determined by maximum likelihood phylogenetic trees constructed using PhyML [22] and the sequences have been deposited in GenBank under accession numbers KX15472-KX154585 for RV-A and KX290514-KX290520 for RV-C. Two of the RV-C samples were not submitted to the GenBank because the sequences were of suboptimal quality due to a probable infection with more than one RV genotype.

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