Universal transport media utm

Naso-oro-pharyngeal samples were collected using nasal and oropharyngeal (NPOP) swabs (Copan Diagnostics, USA) and were eluted in 3 ml of Universal Transport Media (UTM, Copan Diagnostics, USA) that had been supplemented with 500ul of a protein/DNA/RNA preservative, Allprotect (Qiagen, Germany). Upon collection, samples were stored at −80 °C. The study population consisted a total of 93 infants and young children admitted to Kilifi County hospital, in coastal Kenya, with respiratory infections and control infants who were sampled from home and did not exhibit any respiratory symptoms (Protocol A: n = 6, Protocol B: n = 4, Protocol C: n = 83). Diagnosis of respiratory infections was done using a multiplex PCR that was designed to detect 15 respiratory pathogens: respiratory syncytial virus (RSV - A & B), rhinovirus, parainfluenza virus (1, 2, 3 & 4) adenovirus, influenza (A, B & C), coronavirus (OC43 & e229), human metapneumovirus and Mycoplasma pneumoniae. Written informed consent was sought from the parents or legal guardians of the recruits prior to sampling while ethical clearance for the conduct of this study was provided by the Kenya Medical Research Institute (KEMRI) Scientific and Ethical Review Committee (SERU). All methods were performed in accordance with good clinical laboratory practice (GCLP) guidelines.

Oropharyngeal swabs collected with flocked swabs (Jiangsu Hanheng Medical Technology, Copan) from patients were dissolved directly into either 1 ml SIBA lysis/reaction buffer (Aidian/Qlife), 1 ml PBS (Gibco), 1 ml Universal Transport Media (UTM) (Copan), 1 ml Virus Transport Media (VTM) (Nest Biotechnology) or 1 ml VTM (Mole Bioscience). To release virus from the flocked swabs and the sample collection tubes were incubated for 10 min at room temperature. Samples dissolved in PBS, UTM, VTM or antigen buffers (GenSure COVID-19 Antigen Rapid Test, Acro 2019-nCoV IgG/IgM Rapid Test, Biosynex Covid-19 Ag BSS Rapid Test, SD Biosensor COVID-19 Ag Test were diluted 10-fold in SIBA lysis/reaction buffer (containing mild detergents and 80 mM Mg-acetate) before being applied to the SARS-CoV-2 RT-SIBA Mastermix (Qlife). Samples undergoing SARS-CoV-2 testing by RT-PCR on the Corbas Liat System at Nordsjællands Hospital were used without further preparation according to the manufactures instructions. Samples undergoing SARS-CoV-2 testing by RT-PCR on the BGI system at Hvidovre Hospital were total NA purified on a MGISP-960 using the MGIEasy Magnetic Beads Virus DNA/RNA Extraction Kit (MGI Tech Co., Ltd.). The sample extraction amount was 180 µl and total NA was eluted in 33 µl.

Sample collection (n=1160) was conducted between February and September 2015 in a LAM in Medellin, Colombia; (February, n=90; March, n=226; April, n=112; May, n=142; June, n=150; July, n= 72; August, n=209 and September, n=159). This is the only LAM that is consistently open to the public and a traditional place for people to obtain poultry and other groceries. There are five regularly established poultry sellers at the LAM and around 2500 birds are available for sale at any given time. New birds are brought to the market weekly to bi-weekly, the majority of which are supplied by backyard poultry farmers. Poultry are sold mostly alive, but can be slaughtered, de-feathered and eviscerated at the LAM upon request. Fresh environmental feces and cloacal samples were collected from individual birds and cages using single-use sterile swabs and placed in cryovials containing 1 mL Universal Transport Media, UTM (Copan Italia SPA, Brescia, Italy). Samples were kept at 4 °C for a maximum of four days then stored at −80 °C until analysis.