High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing

Abstract

The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.

Understanding the SARS-CoV-2 to Manage COVID-19

“…Variety in the viral genome also determines the efficiency of vaccines or drugs on each of these populations. Our genome analysis efforts along with others in the country show two major clades of virus 42,43 (►Fig. 3a).…”

Testing and surveillance strategies in the context of COVID-19 in India

“…Over the last 6 months, we have developed some understanding of the dynamics of the virus with two major clades observed in Indian samples. The A3i clade had emerged as the dominant variant early on in the pandemic in the country [19,20]. Later, the globally prevalent A2a subtype became predominant as the pandemic swept across India (( Figure 3) [21].…”

“…Currently, the global repository Nextstrain has over 90,000 genome submissions of this virus, categorised into 10 known viral variants, based on their genomic differences from each other [22]. Comparison of viral genomes from India and other parts of the world reveals encouraging insights into the presence of a single predominant A2a strain [20]. This is a strong premise to expect that vaccines and drugs developed against the virus will work equally well across the world.…”

Consensus Scientific Statement on Advisory Working Guidelines and Recommendations for the Female Population in COVID-19 Era by WINCARS

“…The disparity in COVID-19 manifestation in the severity of the disease or mortality does not seem to be because of the difference in the virus. [143][144][145][146][147] SARS-CoV-2 enters host cells through binding ACE-2 receptors expressed on the cell surfaces. Men have shown to express higher levels of ACE2 on lung epithelial cells and in soluble form.…”