“…The SARS-CoV-2 spike protein recognizes host cells and is the main target of the human immune response, and some of the protein mutations have been linked to heightened infectivity and the ability to evade infection-blocking antibodies ( 114 ). During the onset of COVID-19, two major locally transmitted outbreaks occurred in China, one in Wuhan from December 2019 to April 2020, another in Beijing-Xinfadi in June 2020 ( 115 ). Interestingly, SARS-CoV-2 sequences recovered from Beijing-Xinfadi can be distinguished by a single nucleotide at position 241, a conserved pyrimidine nucleotide located in the loop region of stem-loop 5B of the 5′-untranslated region ( 116 ), compared with those collected in Wuhan.…”
Section: Discussionmentioning
confidence: 99%
“…Interestingly, SARS-CoV-2 sequences recovered from Beijing-Xinfadi can be distinguished by a single nucleotide at position 241, a conserved pyrimidine nucleotide located in the loop region of stem-loop 5B of the 5′-untranslated region ( 116 ), compared with those collected in Wuhan. Viral isolates from patients and the environment generally encode uridine, whereas the viruses isolated in Wuhan encode a cytidine nucleotide at the corresponding position ( 115 ). In this study, the C241T variation was observed at all time points.…”
Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals.
“…The SARS-CoV-2 spike protein recognizes host cells and is the main target of the human immune response, and some of the protein mutations have been linked to heightened infectivity and the ability to evade infection-blocking antibodies ( 114 ). During the onset of COVID-19, two major locally transmitted outbreaks occurred in China, one in Wuhan from December 2019 to April 2020, another in Beijing-Xinfadi in June 2020 ( 115 ). Interestingly, SARS-CoV-2 sequences recovered from Beijing-Xinfadi can be distinguished by a single nucleotide at position 241, a conserved pyrimidine nucleotide located in the loop region of stem-loop 5B of the 5′-untranslated region ( 116 ), compared with those collected in Wuhan.…”
Section: Discussionmentioning
confidence: 99%
“…Interestingly, SARS-CoV-2 sequences recovered from Beijing-Xinfadi can be distinguished by a single nucleotide at position 241, a conserved pyrimidine nucleotide located in the loop region of stem-loop 5B of the 5′-untranslated region ( 116 ), compared with those collected in Wuhan. Viral isolates from patients and the environment generally encode uridine, whereas the viruses isolated in Wuhan encode a cytidine nucleotide at the corresponding position ( 115 ). In this study, the C241T variation was observed at all time points.…”
Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals.
“…Besides, Spike-D614G increases virion spike density and infectivity 45 , 46 . Mutation at position 241 is located in the 5’-untranslated region of the virus genome and it was found to be the distinguishing mutation between the two major locally transmitted outbreaks in China, the first one identified in December 2019 in Wuhan and the second one in June 2020 in Beijing-Xinfadi 47 . Figure 1 ( A ) Genome-wide environmental conservation landscape.…”
End-point RT-PCR is a suitable alternative diagnostic technique since it is cheaper than RT-qPCR tests and can be implemented on a massive scale in low- and middle-income countries. In this work, a bioinformatic approach to guide the design of PCR primers was developed, and an alternative diagnostic test based on end-point PCR was designed. End-point PCR primers were designed through conservation analysis based on kmer frequency in SARS-CoV-2 and human respiratory pathogen genomes. Highly conserved regions were identified for primer design, and the resulting PCR primers were used to amplify 871 nasopharyngeal human samples with a previous RT-qPCR based SARS-CoV-2 diagnosis. The diagnostic test showed high accuracy in identifying SARS-CoV-2-positive samples including B.1.1.7, P.1, B.1.427/B.1.429 and B.1.617.2/ AY samples with a detection limit of 7.2 viral copies/µL. In addition, this test could discern SARS-CoV-2 infection from other viral infections with COVID-19-like symptomatology. The designed end-point PCR diagnostic test to detect SARS-CoV-2 is a suitable alternative to RT-qPCR. Since the proposed bioinformatic approach can be easily applied in thousands of viral genomes and over highly divergent strains, it can be used as a PCR design tool as new SARS-CoV-2 variants emerge. Therefore, this end-point PCR test could be employed in epidemiological surveillance to detect new SARS-CoV-2 variants as they emerge and propagate.
Introduction::
Severe Acute Respiratory Syndrome Coronavirus – 2, SARS-CoV-2, is a well-known virus for its fatal infectivity and widespread impact on the health of the worldwide population. Genome sequencing is critical in understanding the virus’s behavior, origin, and genetic variants. This article conducts an extensive literature review on the SARS-CoV-2 genome, including its Genome Structure, Genome Analysis, Evolution, Mutation, and, Genome Computation. It highlights the summary of clinical and evolutionary research along with the applicability of computational methods in the areas. It lucidly presents the structural detail and mutation analysis of SARS-CoV-2 without overwhelming the readers with difficult terms. In the pandemic, machine learning and deep learning emerged as a paradigm change, that when combined with genome analysis, enabled more precise identification and prognosis of the virus's impact. Molecular detailing is crucial in extracting features from the SARS-CoV-2 genome before computation models are applied.
Method::
Further, in this systematic study we investigate the usage of Machine Learning and Deep Learning models mapped to SARS-CoV-2 genome samples to see their applicability in virus detection and disease severity prediction. We searched research articles from various reputed journals explaining the structure, evolution, mutations, and computational methods published until June 2022.
Result::
The paper summarizes significant trends in the research of SARS-COV-2 genomes. Furthermore, this research also identifies the limitations and research gaps that yet have to be explored more and indicates future directions.
Impact Statement: There are few review articles on the SARS-CoV-2 genome; these reviews target various aspects of the SARS-COV2 genome individually. This article considers all the aspects simultaneously and provides in-depth knowledge about the SARS-CoV-2 genome.
Conclusion::
This article provides a detailed description about the type of samples, volumes of selection, processes, and tools used by various researchers in their studies. Further, the computational techniques applied to the SARS-COV2 genome are also discussed and analysed thoroughly.
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