In addition, it collaborates with the CSIR institute to use a new virus diagnostic protocol with great confidence.

The VRDL at Kurnool Medical College is the first laboratory in South India to collaborate using a new protocol – “ COVIDSeq Next-Generation Sequencing ” – for the diagnosis and phylogenetic analysis of SARS nCoV-2 samples ( COVID-19).

This is the next-generation confirmatory test for COVID-19 performed at the CSIR Institute of Genomics and Integrative Biology, and will be useful for other viruses in the future.

The sequencing approach also provided information on the evolution and genetic epidemiology of SARS-CoV-2 samples, in addition to detecting a new variant N440K responsible for re-infection.

Results

In a research article published in the German Scientific Journal, “ Plos One, ” on February 17, the authors said that seven institutions in India authorized by the CSIR Institute of Genomics and Integrative Biology to use the protocol (approved for clinical trials by the United States Food & Drug Administration) was able to discover two lines of nCOV-2 from SARS (B.1.112 and B.1.99), 73 new variants and 1143 unique single-nucleotide variants.

Pallavalli Rojarani, one of the authors and microbiologist, who was appointed by the state government for a temporary one-year period during the COVID-19 pandemic at Kurnool Medical College, said The Hindu that the KMC-VRDL was the only institution participating from southern India.

“We used the approach on 752 duplicate clinical samples (1,536 in total), which could be sequenced on a single S4 sequencing flow cell on a NovaSeq 6000 machine. Our analysis suggests a high agreement between technical duplicates and High concordance of detection of SARS-CoV-2 between the COVIDSeq and RT-PCR approaches, ”said Ms. Rojarani.

COVIDSeq was able to detect SARS-CoV-2 in six samples with high confidence, which tested negative in the RT-PCR which was considered the gold standard so far.

Ms Rojarani explained that the test could also detect SARS-CoV-2 in a set of 21 samples and in 16 other samples classified as inconclusive and Pan Sarbeco positive, suggesting that COVIDSeq could be used as a confirmatory test.

She thanked KMC Principal and Additional DME P. Chandrasekhar for their support in securing this facility by convincing the government.

The microbiologist said she also worked on 272 samples from June 20, 2020 to September 2020, when the spread was rapid and large numbers of deaths were recorded in the PA.

The N440K strain from Kurnool was found to have spread throughout the PA and some neighboring states. This was another achievement of the lab.

Wide utility

“Using this NGS, we can know the behavior of various bacteria, fungi, viral diseases, genetics of the fetus,” she said while explaining the benefits of having the machine.

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