meat_metageonics
metagenomics-derived viral sequences found in beef, pork, chicken purchased from supermarkets in San Francisco
All samples were collected in sterile zippered plastic bags and frozen the same day at -80°C until further processing. Meat samples (~25 mg) were frozen and thawed on dry ice three times, homogenized, filtered, and nuclease treated as previously described to enrich for nucleic acids within viral particles. Remaining total nucleic acid was then isolated using MagMAX™ Viral RNA Isolation Kits (Qiagen) according to manufacturer's protocol. A library of randomly amplified PCR products from viral RNA and DNA was prepared by using a Nextera DNA Sample Prep Kit and sequenced on the MiSeq Illumina platform (Illumina, San Diego, CA, USA). Six separate pools of nucleic acids from the 30 meat specimens were generated, each pool contained 5 specimens from the same farm animal species. The viral nucleic acid pools, containing both DNA and RNA viral sequences, were subjected to reverse transcription reactions with SuperScript III reverse transcriptase (Invitrogen) and 100 picomoles of a random hexamer primer, followed by a single round of DNA synthesis using Klenow fragment polymerase (New England BioLabs). A library was then constructed using Nextera XT DNA Sample Preparation Kit (Illumina) and then sequenced using the Miseq Illumina platform with 250 bases paired ends with a distinct molecular tag for each pool.
meat
BSRI
meat_metageonics