Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

Abstract

The mulberry silkworm, Bombyx mori (L.), is a model organism of lepidopteran insects with high economic importance. The viral diseases of the silkworm caused by Bombyx mori nucleopolyhedrovirus (BmNPV) and Bombyx mori bidensovirus (BmBDV) inflict huge economic losses and significantly impact the sericulture industry of India and other countries. To understand the distribution of Indian isolates of the BmNPV and to investigate their genetic composition, an in-depth population structure analysis was conducted using comprehensive and newly developed genomic analysis methods. The seven new Indian BmNPV isolates from Anantapur, Dehradun, Ghumarwin, Jammu, Kashmir, Mysore and Salem grouped in the BmNPV clade, and are most closely related to Autographa californica multiple nucleopolyhedrovirus and Rachiplusia ou multiple nucleopolyhedrovirus on the basis of gene sequencing and phylogenetic analyses of the partial polh, lef-8 and lef-9 gene fragments. The whole genome sequencing of three Indian BmNPV isolates from Mysore (-My), Jammu (-Ja) and Dehradun (-De) was conducted, and intra-isolate genetic variability was analyzed on the basis of variable SNP positions and the frequencies of alternative nucleotides. The results revealed that the BmNPV-De and BmNPV-Ja isolates are highly similar in their genotypic composition, whereas the population structure of BmNPV-My appeared rather pure and homogenous, with almost no or few genetic variations. The BmNPV-De and BmNPV-Ja samples further contained a significant amount of BmBDV belonging to the Bidnaviridae family. We elucidated the genotype composition within Indian BmNPV and BmBDV isolates, and the results presented have broad implications for our understanding of the genetic diversity and evolution of BmNPV and co-occurring BmBDV isolates.

Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants

“…Different dots represent different specificities: blue dots=My+De+Ja, red dots=De+Ja; black dots=De+My and Ja+My, black triangles=My. The 1785 SNV positions and their specificities were determined previously from Illumina short-read sequencing data [28].…”

“…Here, reads are mapped against a consensus sequence and the frequency of alternative nucleotides is determined [25,26]. In addition, SNV positions can also be specifically assigned to baculovirus isolates to distinguish and quantify them based on their prevalence [27][28][29]. The use of a common reference sequence is critical in this approach since it allows the determination of specificities of SNV positions and ultimately inter-isolate variation or presence of haplotypes across isolates [29].…”

“…Alphabaculovirus bomori comprises BmNPV as well as the Bombyx mandarina nucleopolyhedrovirus (BomaNPV) [10,12,36]. So far, at least 15 isolates of BmNPV and BomaNPV have been Illumina-sequenced with a genome length ranging between 125 and 130 kb [28,[37][38][39][40]. Several isolates of BmNPV have already been sequenced from India [28,38].…”

Studies on Natural and Experimental Nucleopolyhedrovirus Infection of the Silkworm, Bombyx mori (Race: PMCSR2(SL)) by PCR

“…PCR analysis for the viral DNA which was completely isolated from the polyhedral occlusion bodies (OBs) was performed following standard laboratory protocols (Alletti et al, 2017;Gani et al, 2021). The natural and experimental infected fifth instar larvae of silkworm were homogenized separately in NTE buffer (0.2 M NaCl, 0.02 M Tris-HCl and 0.02 M EDTA, pH 7.4), and 10% tissue suspension was made.…”

Identification of long noncoding RNAs of silkworm at the early stage of Bombyx mori bidensovirus infection

“…Bombyx mori bidensovirus (BmBDV) classified as the only species in the genus Bidensovirus of the Bidnaviridae family, is a small, single‐stranded, bipartite DNA virus, which has been isolated in China, Japan, and India from silkworm (Gani et al, 2021; Seki & Iwashita, 1983; Wang et al, 2007). BmBDV specifically infects columnar cells of the midgut epitheliuma and disturb the digestion and absorption of the midgut (Ito et al, 2016; Kumar et al, 2019), causing loss of appetite and physical decline with obvious clinical symptoms, such as anorexia, diarrhea, and flaccidity.…”