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Masters Degrees (Virology)

Permanent URI for this collectionhttps://hdl.handle.net/10413/7018

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Browsing Masters Degrees (Virology) by Author "De Oliveira, Tulio Paiva N Andrade."

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    Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq.
    (2022) Tshiabuila, Derek Kalala.; De Oliveira, Tulio Paiva N Andrade.
    Corona Virus Disease 2019 (COVID-19) is an ongoing pandemic that has spread rapidly around the world and has seen over 431 000 000 identified cases and 5 930 000 deaths caused by this disease by the end of January 2022. Many viral lineages have arisen from Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) as public health measures from numerous countries have failed to contain the spread of the virus. Sequencing of SARS-CoV-2 has enabled the identification and classification of the viral lineages, while real-time tracking of the emergence and spread of these lineages has been facilitated by the open sharing of genomic surveillance data and collaborative online platforms. Several studies have suggested that various mutations may have a functional effect on the virus, such as a substitution in the spike protein (D614G) may result in increased transmissibility whilst an N439K substitution in the receptor-binding domain (RBD) may assist in neutralizing monoclonal antibodies. It is therefore necessary that a fast and reliable sequencing technology be used to rapidly and correctly produce SARS-CoV-2 genomes that can be used to identify viral lineages. Many sequencing laboratories have begun using Nanopore sequencing as it promises high throughput, realtime sequencing, at an affordable cost and many of their sequencing platforms allow for portability. The sequencing technology has, however, not been verified to produce consensus SARS-CoV-2 genomes that are comparable to Illumina Sequencing which is currently the gold standard Next Generation Sequencing (NGS) technology for SARS-CoV-2 sequencing. In this study, we compared the Illumina and Nanopore sequencing platforms by comparing the SARS-CoV-2 genomes produced by the Illumina MiSeq and Oxford Nanopore Technology (ONT) GridION X5. The results show that the GridION is currently unsuitable for SARS-CoV-2 genomic surveillance as consensus genomes produced by the platform have a lower quality than those produced by the MiSeq which reduces the reliability of the data obtained from the genomes. These results can be used to better understand the Nanopore sequencing technology and how it differs from the Illumina technology which will help in updating the Nanopore technology to produce consensus genomes at a faster rate than the Illumina technology whilst still having a similar quality.
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    Implementation of an efficient sample pooling strategy for high throughput diagnostic testing of Severe Acute Respiratory Syndrome Corona Virus-2.
    (2022) Anyaneji, Ugochukwu Jacob.; De Oliveira, Tulio Paiva N Andrade.; Petruccione, Francesco.; Giandhari, Jennifer.; Lessells, Richard John.; Singh, Lavanya.
    The rapid identification and isolation of infected individuals remains a key strategy for controlling the spread of SARS-CoV-2. Frequent testing of populations to detect infection early in asymptomatic or presymptomatic individuals can be a powerful tool for intercepting transmission, especially when the viral prevalence is low. However, RT-PCR testing – the gold standard of SARS-CoV-2 diagnosis – is expensive, making regular testing of every individual unfeasible. Sample pooling is one approach to lowering costs. By combining samples and testing them in groups the number of tests required is reduced, substantially lowering costs. Here we report on the implementation of pooling strategies using 3-d and 4-d hypercubes to test a professional sports team in South Africa. We have shown that infected samples can be reliably detected in groups of 27 and 81, with minimal loss of assay sensitivity for samples with individual Ct values of up to 32. We report on the automation of sample pooling, using a liquid-handling robot and an automated web interface to identify positive samples. We conclude that hypercube pooling allows for the reliable RT-PCR detection of SARS-CoV-2 infection, at significantly lower costs than lateral flow antigen tests.