Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats1–4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans5–7. Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV. Characterization of full-length genome sequences from patients infected with a new coronavirus (2019-nCoV) shows that the sequences are nearly identical and indicates that the virus is related to a bat coronavirus.

/pdf/a-pneumonia-outbreak-associated-with-a-new-coronavirus-of-4uc8p3yu65.pdf

A pneumonia outbreak associated with a new coronavirus of probable bat origin

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.

Accurate identification of bacterial isolates is one of the fundamental tasks in clinical microbiology laboratories. This is critical in providing a microbiological diagnosis to an infectious disease and guiding appropriate antibiotic treatment as well as infection control measures. On the population scale, accurate bacterial identification is important for defining epidemiology of infectious diseases. Traditionally, identification of bacteria in clinical microbiology laboratories is performed using conventional phenotypic tests, including Gram smear, cultural requirements, growth characteristics, and biochemical tests. These tests are relatively inexpensive and accurate for most commonly encountered bacteria in clinical laboratories. However, in certain circumstances, these phenotypic tests may fail to work and more sophisticated methods may be required. For example, accurate identification of anaerobic bacteria and mycobacteria may require special equipment and expertise such as gas chromatography–mass spectrometry. Moreover, phenotypic methods often fail to identify rare bacteria or bacteria which exhibit variable expression of certain traits, and are associated with ambiguity in determining end point reactions. As phenotypic methods rely on the availability of pure culture for the study of growth characteristics and biochemical profiles, it also takes considerable time for slow-growing bacteria to be identified. Furthermore, these methods are not applicable for noncultivable bacteria and in culture-negative infections.

Bacterial Identification Based on Universal Gene Amplification and Sequencing

In vitro susceptibility of Salmonella enterica serovar Typhi to ceftolozane/tazobactam.

Six horses were challenged experimentally with a strain of Burkholderia pseudomallei isolated from a fatal case of the infection in a dromedary camel years earlier in the Emirate of Dubai. Three horses were inoculated subcutaneously and in 3 the bacterium was administered by the oral route. Four of the horses became serologically positive based on reactions to one or more of the OIE described tests for glanders. B. pseudomallei was re-isolated from the 4 serological positive horses. Only one of the subcutaneously infected horses, developed fever for 3 days. The white blood cell values and the neutrophil counts were also elevated. The study confirmed that existing serological test for diagnosing glanders cannot differentiate between glanders and melioidosis in horses.

Evaluation of serological responses in horses challenged with Burkholderia pseudomallei using current diagnostic tests for glanders.

Antimicrobial resistance (AMR) is imposing a global public health threat. Despite its importance, resistance characterization in the native background of clinically isolated resistant pathogens is frequently hindered by the lack of genome editing tools in these “non-model” strains. Pseudomonas aeruginosa is both a prototypical multidrug resistant (MDR) pathogen and a model species for understanding CRISPR-Cas functions. In this study, we report the successful development of the first native type I-F CRISPR-Cas mediated, one-step genome editing technique in a paradigmatic MDR strain PA154197. The technique is readily applicable in additional type I-F CRISPR-containing, clinical/environmental P. aeruginosa isolates. A two-step In-Del strategy is further developed to edit genomic locus lacking an effective PAM (protospacer adjacent motif) or within an essential gene, which together principally allows any type of non-lethal genomic manipulations in these strains. Exploiting these powerful techniques, a series of reverse mutations are constructed and the key resistant determinants of the MDR PA154197 are elucidated which include over-production of two multidrug efflux pumps MexAB-OprM and MexEF-OprN, and a typical fluoroquinolone (FQ) resistance mutation T83I in the drug target gene gyrA. Characterizing antimicrobial susceptibilities in isogenic strains containing various combinations of single, double, or all three key resistance determinants reveal that i) extensive synergy exists between the target mutation and over-production of efflux pumps, and between the two over-produced tripartite efflux pumps to confer clinically significant FQ resistance; ii) while basal level MexAB-OprM confers resistance only to penicillins, its over-production leads to substantial resistance to all antipseudonmonal β-lactams and additional resistance to FQs; iii) despite the acquisition and over-production of multiple resistant mutations, no obvious evolutionary trade-off of collateral sensitivity is developed in PA154197. Together, these results provide new insights into resistance development in clinical MDR P. aeruginosa strains and demonstrate the great potentials of native CRISPR systems in AMR research.

https://www.biorxiv.org/content/biorxiv/early/2019/01/08/496711.full.pdf

Native CRISPR-Cas mediated in situ genome editing reveals the exquisite interplay of resistance mutations in clinical multidrug resistant Pseudomonas aeruginosa

Patrick C. Y. Woo

Papers

Bacterial Identification Based on Universal Gene Amplification and Sequencing

In vitro susceptibility of Salmonella enterica serovar Typhi to ceftolozane/tazobactam.

Evaluation of serological responses in horses challenged with Burkholderia pseudomallei using current diagnostic tests for glanders.

Native CRISPR-Cas mediated in situ genome editing reveals the exquisite interplay of resistance mutations in clinical multidrug resistant Pseudomonas aeruginosa

Diversity of coronaviruses in bats: insights into origin of SARS coronavirus