key: cord-324892-mg2dziuw authors: Carneiro, João; Gomes, Catarina; Couto, Cátia; Pereira, Filipe title: CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2 date: 2020-06-12 journal: bioRxiv DOI: 10.1101/2020.04.19.048991 sha: doc_id: 324892 cord_uid: mg2dziuw The ability to detect the SARS-CoV-2 in a widespread epidemic is crucial for screening of carriers and for the success of quarantine efforts. Methods based on real-time reverse transcription polymerase chain reaction (RT-qPCR) and sequencing are being used for virus detection and characterization. However, RNA viruses are known for their high genetic diversity which poses a challenge for the design of efficient nucleic acid-based assays. The first SARS-CoV-2 genomic sequences already showed novel mutations, which may affect the efficiency of available screening tests leading to false-negative diagnosis or inefficient therapeutics. Here we describe the CoV2ID (http://covid.portugene.com/), a free database built to facilitate the evaluation of molecular methods for detection of SARS-CoV-2 and treatment of COVID-19. The database evaluates the available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Updated sequences alignments are used to constantly verify the theoretical efficiency of available testing methods. Detailed information on available detection protocols are also available to help laboratories implementing SARS-CoV-2 testing. The SARS-CoV-2 genome consists of a single, positive-stranded RNA with approximately 30 000 nucleotides. Thousands of genomic sequences are now available in public databases as the epidemic progresses. The great adaptability and infection capacity of RNA viruses depends in part from their high mutation rates. 1 As expected, available SARS-CoV-2 genomic sequences already show a large number of polymorphisms. Many techniques use molecules that interact with the virus RNA genome or the reverse transcribed DNA, either for clinical testing, diagnosis or determination of viral loads. 2 For example, PCR primers and RT-qPCR probes are been widely used to detect SARS-CoV-2. 3, 4 It is likely that oligonucleotides complementary to the virus RNA will be tested as possible antiviral agents. 5, 6 However, polymorphisms can be a challenge for the efficiency of available assays since they may lead to false-negative results in detection tests or inefficient therapeutics. The CoV2ID database (http://covid.portugene.com/) uses java graphics and dynamic tables and works with major web browsers (e.g. Internet Explorer, Mozilla Firefox, Chrome). The database provides descriptive webpages for each oligonucleotide and a search engine to access dynamic tables with numeric data and multiple sequence alignments. A SQLite local database is used for data storage and runs on an Apache web server. The dynamic HTML pages were implemented using CGI-Perl and JavaScript and the dataset tables using the JQuery plugin DataTables v1.9.4 (http://datatables.net/). Python and Perl in-house algorithms were written and used to perform identity and pairwise calculations. The oligonucleotides were retrieved from peer reviewed publications [e.g., [7] [8] [9] [10] [11] [12] [13] [14] and protocols provided by the World Health Organization (WHO). Each oligonucleotide has a specific database code (for example, CoV2ID001). The CoV2ID database ranks The 'CoV2ID ranking score' considers the mean value of the three different measures (PIS, 3'PIS and PPI), as previously described. 15, 16 The SARS-CoV-2 'isolate Wuhan-Hu-1' (NC_045512.2) was used as reference. were obtained from the NCBI GenBank (https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/) and the GISAID Initiative The Chan_RdRp_gene_R) has a CoV2ID score of 91.43%, but was designed to target all SARS-related coronaviruses 14 , which explains its high conservation. In general, available SARS-CoV-2 oligonucleotides diverge from other human coronaviruses by several positions, and therefore are unlikely to cause false-positives. If the aim is to choose an oligonucleotide located in a conserved genomic Viral evolution and the emergence of SARS coronavirus COVID-19 diagnostics in context Positive rate of RT-PCR detection of SARS-CoV-2 infection in 4880 cases from one hospital in Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system RNA therapeutics: beyond RNA interference and antisense oligonucleotides Oligonucleotide antiviral therapeutics: antisense and RNA interference for highly pathogenic RNA viruses Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 RT-LAMP for rapid diagnosis of coronavirus SARS-CoV-2. Microbial Biotechnology Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR CRISPR-Cas12-based detection of SARS-CoV-2 Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment The HIV oligonucleotide database (HIVoligoDB) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR assays The establishment of reference sequence for SARS-CoV-2 and variation analysis This research was supported by national funds through FCT -Foundation for Science and Technology within the scope of UIDB/04423/2020 and UIDP/04423/2020. J.C. also acknowledges the FCT funding for his research contract at CIIMAR, established under the transitional rule of Decree Law 57/2016, amended by Law 57/2017. The authors declare that there are no conflict of interests.