Complete genomic analysis of uncommon G12P[11] rotavirus causing a nosocomial outbreak of acute diarrhea in the newborns in New Delhi, India.

Rotaviruses (RVs) are the major causative agents of acute gastroenteritis in children, but in neonates, RV infections are generally nosocomial in origin and mostly asymptomatic. However, there have been infrequent reports of nosocomial outbreaks of clinical disease in this population. In this study, we describe uncommon RV genotype; G12P[11] associated with an outbreak of acute gastroenteritis in the neonatal ward and neonatal intensive care unit (NICU) in New Delhi, North India. Full-genome analyses of the pathogenic G12P[11] strain was carried out to map the genotype constellation and further to explore the variations in the antigenic epitopes on the immunodominant VP7 and VP4 proteins, the amino acid sequences were compared with neonatal strains; ROTAVAC® (G9P[11]) and asymptomatic G12P[11] and also other G/P-type matched strains. The study revealed G12-P[11]-I1-R1-C1-M1-A1-N1-T1-E1-H1 human Wa-like genotype constellation and highlights evidence of gene reassortment. No significant differences were observed in the sequences of structural (except VP3) and nonstructural encoding genes of G12P[11] strains recovered from symptomatic and asymptomatic neonates. Presence of additional N-linked glycosylation site was noted in the G12 strains, as a consequence of a change from Asp→Asn at amino acid position 238. Interestingly, only two and four amino acids substitution within the 7-1a and 8-1 antigenic epitope were observed, respectively, compared with asymptomatic G12P[11] strain. The study emphasizes the importance of close monitoring of RV outbreaks in neonates for early alarming of novel strain.

Full genome based sequence and structural characterization of an unusual group A rotavirus G12P[11] isolated from neonates in Pune, western India.

Studies conducted at neonatal intensive care units in Pune, western India, suggested early exposure to rotaviruses and predominance of unusual human-bovine-like G12P[11] strains. The whole genome sequencing and phylogenetic analyses of a naturally attenuated, culture adapted neonatal strain, (NIV-1740121) revealed multiple-gene reassortment events, containing ROTAVAC® vaccine strain, 116E-like VP4, VP6, NSP3, NSP5 genes, VP7 gene of G12 origin and VP3 gene of porcine ancestry in a human Wa-like backbone. Analysis of 3D structure modeling of the VP7 and VP4 proteins with respect to 116E suggested amino acid variations in the major neutralizing epitopes of VP7, contributed to a modified charge density. Visualization of receptor-glycan interaction structures of NIV-1740121 and 116E VP8* showed type I glycan binds with a similar conformation at the same active site as represented in the available crystal structure of G10P[11] VP8*. The study adds to the knowledge of age restricted tropism of P[11] strains in neonates.

Clinical and genetic characteristics of unusual G12P[11] rotavirus strains recovered from neonates: A study from Pune, Western India.

Rotavirus infections in neonates are generally nosocomial, and differ from pediatric infections both clinically and epidemiologically. These infections are predominantly asymptomatic and often associated with unusual strains. Globally, so far limited data is available on rotavirus infections in neonates admitted at Neonatal Intensive Care Unit. The aim of the present study is to determine the prevalence of rotavirus among neonates and to study their genetic characteristics. Stool specimens (n = 701) collected from neonates (n = 621) admitted during April 2016 to March 2018 mainly for prematurity, low birth weight and associated respiratory distress syndrome from two hospitals from Pune were tested for rotavirus, genotyped and representative strains were sequenced for the genes encoding outer capsid proteins, VP7 and VP4. Rotavirus was detected in 24.31% neonates. Majority of rotavirus infected neonates (98.68%) were asymptomatic. Peak rotavirus antigen detection (91.38%) occurred during the first 2 weeks of admission. Low, very low and normal birth weight neonates with gestational age ≥28 weeks had significantly higher rotavirus infection than those with extreme low birth weight with gestational age <28 weeks. Rotaviral infections occurred almost evenly throughout the year without an apparent peak in colder months. Predominance of unusual G12P[11] strains (97.1%) was observed. Phylogenetic analysis of the partial VP7 coding gene revealed all G12 strains clustered in lineage III and shared 96.94%-100% (nucleotide) and 96.26%-100% (amino acid) identities among themselves, and 95.69%-98.98% (nucleotide) and 94.77%-98.98% (amino acid) with other lineage III G12 strains respectively. Similarly VP4 partial gene sequences of P[11] study strains shared 97.5%-100% (nucleotide and amino acid) identities among themselves and highest 93.34%-94.53% (nucleotide) and 93.57%-94.64% (amino acid) identity with vaccine strain 116E, G9P[11]. The study highlights high frequency of unusual G12P[11] strains among neonates for the first time in western India and reaffirms limited strain diversity in this population. The knowledge of neonatal strains is important for estimating the efficacies of rotavirus vaccines.