TASK DEFINITION: In this task, you're given a paragraph from the research paper and your task is to generate a suitable title for the research paper based on the given paper. Under 100 words is a good title length.
PROBLEM: A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient's sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/ Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events. T he ability of coronaviruses (CoVs) to infect multiple species and to rapidly change through recombination presents a continuing human health threat. The epidemic of severe acute respiratory syndrome (SARS) during 2003-2004 during which a CoV transmitted from bats to civet cats and then to humans demonstrated this potential (reviewed in [1, 2] ). Recently, a novel human betacoronavirus (betaCoV) was found to be associated with at least 13 human infections, 7 of which were fatal (3-7). One of the viruses, EMC/2012, has been sequenced, and its sequence similarity to several bat CoVs suggested an animal origin, but a definitive bat species of origin has not yet been identified (3). Additional genome sequences from this virus are needed to aid diagnostics, monitor population dynamics, identify the animal source, and characterize mechanisms of pathogenesis. The large size (30,000 nt) and high variability of CoV RNA genomes present a challenge for sequencing. We describe a strategy for rapidly designing the primers necessary for reverse transcription and cDNA amplification of such diverse RNA viruses and report the full-genome determination of the novel CoV directly from patient sputum using next-generation short-read sequencing. Full genomes from 2 epidemiologically unlinked novel CoV infections separated in time by >2 months were analyzed to gain clues to 2 major questions: what are the precursors of the virus, and how long has the virus been circulating in its current form? Materials and Methods Fifteen betaCoV full genomes with the closest homology to EMC/2012 (GenBank accession no. JX869059) were analyzed to identify all possible primer-like sequences (melting temperature 58C-60C, guanine plus cytosine content 35%-60%) yielding 357,198 potential primers. The 30-kb JX869059 CoV genome was divided into fifteen 2.5-kb overlapping amplicons, and the 2 highest frequency sequences mapping in the 5 and 3 250 bp of each amplicon were selected. Reverse complements of the 3 mapping sequences were prepared, resulting in a set of 60 primers for the 15 amplicons (4 primers/amplicon). Three additional primers were added for the extreme termini of the genome. The algorithm also prepared a virtual PCR map of the predicted binding and amplicon size for the primer set on CoV genomes. A map of the primer mapping positions

SOLUTION: Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus

PROBLEM: In this paper, we analyze a delayed SEIR epidemic model in which the latent and infected states are infective. The model has a globally asymptotically stable disease-free equilibrium whenever a certain epidemiological threshold, known as the basic reproduction number R 0 , is less than or equal to unity. We investigate the effect of the time delay on the stability of endemic equilibrium when R 0 > 1. We give criteria that ensure that endemic equilibrium is asymptotically stable for all time delays and a Hopf bifurcation occurs as time delay exceeds the critical value. We give formulae for the direction of Hopf bifurcations and the stability of bifurcated periodic solutions by applying the normal form theory and the center manifold reduction for functional differential equations. Numerical simulations are presented to illustrate the analytical results.

SOLUTION: Hopf bifurcation analysis of a delayed SEIR epidemic model with infectious force in latent and infected period

PROBLEM: ABSTRCT 29 Given the scale and rapid spread of severe acute respiratory syndrome coronavirus 2 30 (SARS-CoV-2, known as 2019-nCov) infection , the ongoing global 31 SARS-CoV-2 outbreak has become a huge public health issue. Rapid and precise 32 diagnostic methods are thus immediately needed for diagnosing COVID-19, 33 providing timely treatment and facilitating infection control. A one-step reverse 34 transcription loop-mediated isothermal amplification (RT-LAMP) coupled with 35 nanoparticles-based biosensor (NBS) assay (RT-LAMP-NBS) was successfully 36 established for rapidly and accurately diagnosing COVID-19. A simple equipment 37 (such as heating block) was required for maintaining a constant temperature (63C) 38 for only 40 min. Using two designed LAMP primer sets, F1ab (opening reading frame 39 1a/b) and np (nucleoprotein) genes of SARS-CoV-2 were simultaneously amplified 40 and detected in a 'one-step' and 'single-tube' reaction, and the detection results were 41 easily interpreted by NBS. The sensitivity of SARS-CoV-2 RT-LAMP-NBS was 12 42 copies (each of detection target) per reaction, and no cross-reactivity was generated 43 from non-SARS-CoV-2 templates. Among clinically diagnosed COVID-19 patients, 44 the analytical sensitivity of SARS-CoV-2 was 100% (33/33) in the oropharynx swab 45 samples, and the assay's specificity was also 100% (96/96) when analyzed the clinical 46 samples collected from non-COVID-19 patients. The total diagnosis test from sample 47 collection to result interpretation only takes approximately 1 h. In sum, the 48 RT-LAMP-NBS is a promising tool for diagnosing the current SARS-CoV-2 49 infection in first line field, public health and clinical laboratories, especially for 50 resource-challenged regions. 51

SOLUTION:
Title Page: 1 Reverse transcription loop-mediated isothermal amplification combined with 2 nanoparticles-based biosensor for diagnosis of COVID-19 3 4 Laboratory of Pediatric Respiratory Infection Disease, National Clinical Research