Genomic characterization of coxsackievirus type B3 strains associated with acute flaccid paralysis in south-western India

Abstract

Acute flaccid paralysis (AFP) associated with coxsackievirus type B3 (CV-B3) of the species Enterovirus B is an emerging concern worldwide. Although CV-B3-associated AFP in India has been demonstrated previously, the genomic characterization of these strains is unreported. Here, CV-B3 strains detected on the basis of the partial VP1 gene in 10 AFP cases and five asymptomatic contacts identified from different regions of south-western India during 2009-2010 through the Polio Surveillance Project were considered for complete genome sequencing and characterization. Phylogenetic analysis of complete VP1 gene sequences of global CV-B3 strains classified Indian CV-B3 strains into genogroup GVI, along with strains from Uzbekistan and Bangladesh, and into a new genogroup, GVII. Genomic divergence between genogroups of the study strains was 14.4 % with significantly lower divergence (1.8 %) within GVI (n512) than that within GVII (8.5 %) (n53). The strains from both AFP cases and asymptomatic contacts, identified mainly in coastal Karnataka and Kerala, belonged to the dominant genogroup GVI, while the GVII strains were recovered from AFP cases in north interior Karnataka. All study strains carried inter-genotypic recombination with the structural region similar to reference CV-B3 strains, and 59 non-coding regions and non-structural regions closer to other enterovirus B types. Domain II structures of 59 non-coding regions, described to modulate virus replication, were predicted to have varied structural folds in the two genogroups and were attributed to differing recombination patterns. The results indicate two distinct genomic compositions of CV-B3 strains circulating in India and suggest the need for concurrent analysis of viral and host factors to further understand the varied manifestations of their infections.

Surveillance of enteroviruses from paediatric patients attended at a tertiary hospital in Catalonia from 2014 to 2017

“…It is well-known that one EV type can be related to several clinical manifestations, and inversely. CV-A10, E-5, E-30, CV-B3, and EV-C109 were also associated with neurological affections, as previously described [28][29][30][31], in addition to milder diseases. Instead, E-6 was only related to respiratory symptoms or fever, in discordance with previous studies [32].…”

Echovirus plays major roles in the natural recombination of Coxsackievirus B3

“…Recombination event 1, the AH30 strain, was isolated from a patient with encephalitis complications, who was suspected of having enterovirus infection during an outbreak of hand, foot, and mouth disease (HFMD) in China. This strain, in P1 region, was derived from a CVB3 NIV0923491LV157 parent and P2‐3 region from 2005‐29‐1 strain of EcoV 6 (Supplementary Figure S1A, Table , Figures A, and D). In recombination event 2, EcoV6_2005‐29‐1 strain, as the major parent, and CVB3_DH09Y strain, as the minor parent, gave rise to the recombinant virus, CVB3 NIV0923491LV157 strain (Supplementary Figure S1B, Table , Figures A and D).…”

“…This strain, in P1 region, was derived from a CVB3 NIV0923491LV157 parent and P2‐3 region from 2005‐29‐1 strain of EcoV 6 (Supplementary Figure S1A, Table , Figures A, and D). In recombination event 2, EcoV6_2005‐29‐1 strain, as the major parent, and CVB3_DH09Y strain, as the minor parent, gave rise to the recombinant virus, CVB3 NIV0923491LV157 strain (Supplementary Figure S1B, Table , Figures A and D). Also, in recombination event 3, EcoV6_Henan/116 strain, as the major parent, and CVB3 AH30 strain, as the minor parent, led to the recombinant virus, CVB3 11059‐99 strain (Supplementary Figure S1C, Table , Figures A and D).…”

“…RDP analysis revealed that the six recombination events were identified in the ORF2A. The breakpoints of the six recombinant viruses, AH30, 11059‐99, NIV0923491LV157, 18219‐02, 2679, and NIOV09001C3LVH4, were located in the regions from nucleotide positions 3356, 3400, 3355, 3331, 3325, and 3515, respectively. Four recombination events were identified in the 2B region (Table ).…”

“…This finding indicates that six EcoV6 strains act as major parents for CVB3 strains among molecular evolution and recombination events in circulating enteroviruses. Among the EcoV6 serotypes, the most active strain, 2005‐29‐1, as major parent, combined with NIV0923491LV157 strain from India, DH09Y strain from China, and KM06 strain, also from China, to produce recombinants, AH30, NIV0923491LV157 and A103 b , respectively.…”