Each time a copy is created, it serves as a template for more copies. Using a pair of short DNA strands, called primers, which complement either end of the selected SARS-CoV-2 sequence, and a thermostable enzyme, DNA polymerase, small areas of the viral genome are “amplified” or copied. The next step of the Midnight protocol is the amplification of viral cDNA by the polymerase chain reaction (PCR). To stabilize the sample and prepare it for sequencing, the RNA is converted into its complementary DNA (cDNA) sequence. RNA is extracted instead of DNA because coronaviruses (such as SARS-CoV-2) have a genome made up of RNA. The first step in the Midnight Panel is the extraction of RNA from virus-positive samples. The Midnight Panel, like the ARTIC method, adopts a targeted sequencing approach to increase the speed, quality, and cost-effectiveness of SARS-CoV-2 genome surveillance. Called the Midnight Panel, the method facilitates the global effort to understand COVID-19 epidemiology. 6 Freed and Silander adapted the Ebola surveillance method and ARTIC method to decode the SARS-CoV-2 genome. As such, the ARTIC method employed a portable sequencer-revolutionary at the time-to provide real-time, mobile sequencing. The general ARTIC method was initially developed for the genomic surveillance of the Ebola virus during an outbreak in a region where access to advanced NGS technologies was limited. Targeted approaches also tend to be faster and more cost-effective. First, targeted sequencing increases the read depth for low-quantity samples of RNA, which increases the likelihood of identifying rare variants. There are several advantages to using the targeted sequencing rather than the whole transcriptome sequencing (WTS) approach. 3-5 The SARS-CoV-2 ARTIC method employs a targeted approach, sequencing only the viral genome and not the entire RNA sample, which includes a huge excess of human RNA (the human transcriptome). Since the emergence of COVID-19, several NGS methods have been used to sequence the SARS-CoV-2 virus that causes the disease the most common one is the protocol developed by Joshua Quick and his colleagues in the ARTIC (Advancing Real-Time Infection Control) Network. Viral genomic data also informs the researchers that create diagnostic tests and the research on vaccines and antiviral therapies. Sequencing also enables the determination of evolution rates, identification of transmission routes, contact tracing, and population surveillance. Not only does the sequencing of viruses allow scientists to monitor for changes in their genome, but such detection also facilitates the mapping of the various mutations and their relationships by building phylogenetic trees. A research team led by two of us (Nikki Freed and Olin Silander, at Massey University, New Zealand) have developed a new NGS method, called the Midnight Panel, for the ultrafast sequencing of the SARS-CoV-2 genome, which cuts the sequencing time by more than half compared with more standard methods. Next-generation sequencing (NGS) has been vital for not only the sequencing of the viral genome but for keeping track of changes in it. With more than 12,000 mutations occurring in the SARS-CoV-2 virus since it was discovered, 1 it was perhaps simply a matter of time before the world saw variants emerge that increased the transmission rate of COVID-19. Only 0.8% of people in low-income countries have received a single dose out of 20.8% of the world population which is a big concern for vulnerable groups.By Nikki E. Surveillance and monitoring of the genomic sequence of SARS-CoV-2 is being done on a priority as virus is mutating for development of effective vaccine or therapeutic measures. Presently 15 vaccines were developed based on the SARS-CoV-2 spike protein, of original Wuhan-hu-1 and being administered in different countries. Currently genetic lineages by GISAID, Nextstrain and Pango are in use to code variants detected and being labeled using letters of the Greek Alphabet, i.e., Alpha, Beta, Gamma and Delta etc. WHO is monitoring and assessing the evolution of SARS-CoV-2 and notified Variants of Concern (VOCs) and Variants of Interest (VOIs), in order to prioritise the activities globally on containing COVID-19 pandemic. SARA-CoV-2 is reported to mutate and variants reported to have one specific mutation, D614G which is makes to spread faster. Coronavirus employs a complex gene expression and pathway system unique among RNA viruses. Coronoviruses are large enveloped RNA viruses of Coronaviridae. Globally 17.8 Cr population was effected within a short span of period leading to 38.6 L deaths. COVID-19 virus, SARS-CoV-2 first reported from Wuhan City of Hubei Province of China became pandemic infectious disease of severe respiratory disorder.
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