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Coronavirus disease 2019 (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with a limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13324X. We identified 564 high-quality SARS-CoV-2 variants. A total of 18 variants mapped to reverse transcription polymerase chain reaction primer/probe sites, and four variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (20A, 20B and 20C) (94%), whereas 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.
Six distinct biotypes of the Asian rice gall midge, Orseolia oryzae (Wood-Mason), have been characterized so far from different parts of India and their geographical distribution has been well mapped and monitored annually through the national gall midge biotype studies. These studies have been showing minor changes in the virulence pattern of the pest population at Warangal in Andhra Pradesh state since 2000. Hence, a sample of the pest population from the site was collected during 2003 and selected subsequently in a greenhouse through 13 successive generations for virulence against diverse sources of plant resistance. This Warangal-derived population (WDP) was tested to record reactions of two sets of differential rice varieties used for biotype detection and known to carry one of the 10 known gall midge-resistance genes. The results revealed that WDP has acquired virulence against CR-MR1523, one of the biotype differential rice varieties, which derived resistance from the source Ptb21 cultivar. Since the virulence pattern noted for WDP was different from that noted for the six characterized biotypes, it is proposed to designate this new biotype, tentatively, as biotype 4M. Only three of the resistance genes, viz. Gm3Gm4 and Gm8 confer resistance against this biotype.
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