About: Laboratory Investigation and Phylogenetic Analysis of an Imported Middle East Respiratory Syndrome Coronavirus Case in Greece

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Laboratory Investigation and Phylogenetic Analysis of an Imported Middle East Respiratory Syndrome Coronavirus Case in Greece
Creator	Tong, Suxiang Tsiodras, Sotirios Lu, Xiaoyan Erdman, Dean Tao, Ying Antoniadis, Antonios Emmanouil, Mary Kossyvakis, Athanasios Pogka, Vasiliki Mentis, Andreas
source	Medline; PMC
abstract	Rapid and reliable laboratory diagnosis of persons suspected of Middle East respiratory syndrome coronavirus (MERS-CoV) infection is important for timely implementation of infection control practices and disease management. In addition, monitoring molecular changes in the virus can help elucidate chains of transmission and identify mutations that might influence virus transmission efficiency. This was illustrated by a recent laboratory investigation we conducted on an imported MERS-CoV case in Greece. Two oropharyngeal swab specimens were collected on the 1(st) and 2(nd) day of patient hospitalization and tested using two real-time RT-PCR (rRT-PCR) assays targeting the UpE and Orf-1a regions of the MERS-CoV genome and RT-PCR and partial sequencing of RNA-dependent RNA polymerase and nucleocapsid genes. Serum specimens were also collected and serological test were performed. Results from the first swab sample were inconclusive while the second swab was strongly positive for MERS-CoV RNA by rRT-PCR and confirmed positive by RT-PCR and partial gene sequencing. Positive serologic test results further confirmed MERS-CoV infection. Full-length nucleocapsid and spike gene coding sequences were later obtained from the positive swab sample. Phylogenetic analysis revealed that the virus was closely related to recent human-derived MERS-CoV strains obtained in Jeddah and Makkah, Saudi Arabia, in April 2014 and dromedary camels in Saudi Arabia and Qatar. These findings were consistent with the patient’s history. We also identified a unique amino acid substitution in the spike receptor binding domain that may have implications for receptor binding efficiency. Our initial inconclusive rRT-PCR results highlight the importance of collecting multiple specimens from suspect MERS-CoV cases and particularly specimens from the lower respiratory tract.
has issue date	2015-04-28(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0125809
bibo:pmid	25919137
has license	cc0
sha1sum (hex)	4eca3df95a8bf82f07ba51b6978bd4049f8df827
schema:url	https://doi.org/10.1371/journal.pone.0125809
resource representing a document's title	Laboratory Investigation and Phylogenetic Analysis of an Imported Middle East Respiratory Syndrome Coronavirus Case in Greece
has PubMed Central identifier	PMC4412533
has PubMed identifier	25919137
schema:publication	PLoS One
resource representing a document's body	covid:4eca3df95a8bf82f07ba51b6978bd4049f8df827#body_text
is schema:about of	named entity 'specimens' named entity 'MERS-CoV' named entity 'persons' named entity 'spike' named entity 'sequencing' named entity 'collected' named entity 'Rapid' named entity 'gene' named entity 'Phylogenetic analysis' named entity 'April' named entity 'Greece' named entity 'tested' named entity 'Phylogenetic' named entity 'LABORATORY' named entity 'DROMEDARY' named entity 'INFECTION CONTROL' named entity 'EFFICIENCY' named entity 'RAPID' named entity 'PERFORMED' named entity 'IDENTIFIED' named entity 'INVESTIGATION' named entity 'SWAB' named entity 'STRONGLY POSITIVE' named entity 'MULTIPLE' named entity 'MOLECULAR' named entity 'GENES' named entity 'SEROLOGIC TEST' named entity 'INFECTION' named entity 'SERUM' named entity 'POSITIVE' named entity 'QATAR' named entity 'APRIL' named entity 'RECEPTOR BINDING' named entity 'HUMAN' named entity 'OUR' named entity 'DAY' named entity 'SAMPLE' named entity 'TIMELY' named entity 'MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS' named entity 'OBTAINED' named entity 'SUSPECT' named entity 'UPE' named entity 'INITIAL' named entity 'USING' named entity 'LENGTH' named entity 'TESTED' named entity 'TEST RESULTS' named entity 'IMPLEMENTATION' named entity 'REVEALED' named entity 'CASE' named entity 'PHYLOGENETIC ANALYSIS' named entity 'IMPORTED' named entity 'LABORATORY' named entity 'INCONCLUSIVE' named entity 'TRANSMISSION' named entity 'HOSPITALIZATION' named entity 'PARTIAL' named entity 'TARGETING' named entity 'ADDITION' named entity 'IMPORTANT' named entity 'LABORATORY DIAGNOSIS' named entity 'GREECE' named entity 'RT-PCR' named entity 'SPECIMENS' named entity 'HISTORY' named entity 'AMINO ACID SUBSTITUTION' named entity '27S' named entity 'PERSONS' named entity 'CODING' named entity 'REAL-TIME RT-PCR' named entity 'CHAINS' named entity 'RNA-DEPENDENT RNA POLYMERASE'

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