key: cord-0695836-hyrke6j2 authors: Ithete, Ndapewa Laudika; Stoffberg, Samantha; Corman, Victor Max; Cottontail, Veronika M.; Richards, Leigh Rosanne; Schoeman, M. Corrie; Drosten, Christian; Drexler, Jan Felix; Preiser, Wolfgang title: Close Relative of Human Middle East Respiratory Syndrome Coronavirus in Bat, South Africa date: 2013-10-03 journal: Emerg Infect Dis DOI: 10.3201/eid1910.130946 sha: e6721f956795bb264b2a66d30e5e6f2145a09193 doc_id: 695836 cord_uid: hyrke6j2 nan Respiratory Syndrome Coronavirus in Bat, South Africa To the Editor: The severe acute respiratory syndrome (SARS) outbreak of 2002-03 and the subsequent implication of bats as reservoir hosts of the causative agent, a coronavirus (CoV), prompted numerous studies of bats and the viruses they harbor. A novel clade 2c betacoronavirus, termed Middle East respiratory syndrome (MERS)-CoV, was recently identified as the causative agent of a severe respiratory disease that is mainly affecting humans on the Arabian Peninsula (1) . Extending on previous work (2), we described European Pipistrellus bat-derived CoVs that are closely related to MERS-CoV (3) . We now report the identification of a South Africa bat derived CoV that has an even closer phylogenetic relationship with MERS-CoV. During 2011-2012, fecal pellets were collected from 62 bats representing 13 different species in the KwaZulu-Natal and Western Cape Provinces of South Africa and stored in RNAlater solution (Life Technologies, Carlsbad, CA, USA). Details about the bat sample are available in the online Technical Appendix Table ( wwwnc. cdc.gov/EID/article/19/10/13-0946-Techapp1.pdf). RNA was extracted by using the QIAamp Viral RNA Mini Kit (QIAGEN, Hilden, Germany). Screening for CoVs was done by nested reverse transcription PCR using broadly reactive oligonucleotide primers targeting a conserved region in the RNA-dependent RNA polymerase (RdRp) gene (online Technical Appendix). PCR results were positive for 5 (8%) of the 62 specimens. PCR amplicons for 4 positive specimens yielded alphacoronavirus sequences related to recently described bat alphacoronaviruses from South Africa (4) . The other positive specimen, termed PML/2011, was from an adult female Neoromicia cf. zuluensis bat sampled in 2011; the specimen yielded a novel betacoronavirus (GenBank accession no. KC869678). Online Technical Appendix Figure 1 shows the distribution of this bat species. To obtain better phylogenetic resolution, we extended the 398-nt RdRp fragment generated by the screening PCR to 816 nt, as described (5). PML/2011 differed from MERS-CoV by only 1 aa exchange (0.3%) in the translated 816-nt RdRp gene fragment. Thus, PML/2011 was much more related to MERS-CoV than any other known virus. The amino acid sequence of the next closest known relatives of MERS-CoV, from European Pipistrellus bats (3), differed from MERS-CoV by 1.8%. The amino acid sequences of viruses from Nycteris bats in Ghana (3) and the 2c prototype bat CoVs, HKU4 and HKU5, from China (6) differed by 5.5%-7.7% from MERS-CoV. The smaller 152to 396-nt RdRp fragments of 2c bat CoVs from a Hypsugo savii bat in Spain (7), bat guano in Thailand (8), and a Nyctinomops bat in Mexico (9) showed no or only partial overlap with the 816-nt fragment generated in this study; thus, a direct comparison could not be done. However, in their respective RdRp fragments, these CoVs yielded amino acid sequence distances of 3.5%-8.0% and were thus probably more distant from MERS-CoV than the virus described here. A Bayesian phylogenetic analysis of the 816-nt RdRp sequence confirmed the close relationship between PML/2011 and MERS-CoV (Figure) . Their phylogenetic relatedness was as close as that of SARS-CoV and the most closely related bat coronavirus known, Rs672 from a Rhinolophus sinicus bat (Figure) . Like PML/2011 and MERS-CoV, Rs672 and SARS-CoV showed only 1 aa exchange in the translated 816-nt RdRp fragment. To confirm this relatedness, we amplified and sequenced a short 269-nt sequence encompassing the 3′-terminus of the spike gene for PML/2011 (oligonucleotide primers available upon request from the authors). A partial spike gene-based phylogeny using this sequence yielded the same topology as that using the partial RdRp sequence (online Technical Appendix Figure 2 ). Again, PML/2011 was most closely related to MERS-CoV, showing only a 10.9% aa sequence distance in this gene, which encodes the glycoprotein responsible for CoV attachment and cellular entry. This distance was less than the 13.3% aa sequence distance between MERS-CoV and the European Pipistrellus CoVs (3) and less than the 20.5%-27.3% aa sequence distance between MERS-CoV and HKU5 and between MERS-CoV and HKU4 (6) in the same sequence fragment. Our results further support the hypothesis that, like human CoV-229E and SARS-CoV, ancestors of MERS-CoV might exist in Old World insectivorous bats belonging to the family Vespertilionidae, to which the genera To the Editor: Extraintestinal pathogenic Escherichai coli (ExPEC) bacteria have the ability to cause diverse and serious diseases, such as urinary tract infections (UTIs) and bacteremia (1-3); incidence of bacteremia is increasing globally (4) . The emergence of multidrug resistance in E. coli is also becoming a global concern, with particular emphasis on E. coli sequence type (ST) 131, which is being increasingly reported in UTIs. Drug resistance is mediated by extended-spectrum β-lactamases (ES-BLs), mainly of the CTX-M family, particularly CTX-M-15 and 14, and less frequently of the SHV and OXA families (5, 6) . Few studies are available regarding the characterization of E. coli strains causing bacteremia. We characterized 140 E. coli isolates from bacteremia patients treated at Nottingham University Hospital (Nottingham, UK) over a 5-month period, with the aim of developing an epidemiologic profile of the population of ExPEC that causes bacteremia. For context, we compared the isolates with 125 E. coli isolates from urine samples collected during the same period. Cases were selected to include isolates from a diverse patient group: patient ages ranged from 1 month to 90 years; patient sex was evenly divided between male and female; infections were community-and hospitalassociated; and suspected sources of infection varied. Antimicrobial drug susceptibility tests, PCR detection of ESBL genes , multilocus sequence typing using the Achtman scheme (http:// mlst.ucc.ie/mlst/dbs/Ecoli), and virulence-associated gene (VAG) carriage screening by PCR were performed on isolates as described (7). Significantly more bacteremia E. coli isolates than urine E. coli isolates were resistant to ciprofloxacin (25.7% Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Circulation of group 2 coronaviruses in a bat species common to urban areas in Western Europe Human betacoronavirus 2c EMC/2012-related viruses in bats, Ghana and Europe Coronaviruses in South African bats Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features Detection of alpha and betacoronaviruses in multiple Iberian bat species Group C betacoronavirus in bat guano fertilizer Coronaviruses in bats from Mexico Complete genome analysis of 33 ecologically and biologically diverse Rift Valley fever virus strains reveals widespread virus movement and low genetic diversity due to recent common ancestry We thank Tobias Bleicker, Sebastian Brünink, and Monika Eschbach-Bludau for technical assistance; Thomas Seifert, Sonja Matthee, and Conrad Mathee for invaluable help; and Anna-Marie Corman for assistance with geographic information processing.