Increase in rotavirus prevalence with the emergence of genotype G9P[8] in replacement of genotype G12P[6] in Sabah, Malaysia

Abstract

Rotaviruses are major causative agents of acute diarrhea in children under 5 years of age in Malaysia. However, a rotavirus vaccine has not been included in the national vaccination program. To date, only two studies have been carried out in the state of Sabah, Malaysia, although children in this state are at risk of diarrheal diseases. Previous studies showed that 16%-17% of cases of diarrhea were caused by rotaviruses and that equine-like G3 rotavirus strains are predominant. Because the prevalence of rotaviruses and their genotype distribution vary over time, this study was conducted at four government healthcare facilities from September 2019 through February 2020. Our study revealed that the proportion of rotavirus diarrhea increased significantly to 37.2% (51/137) after the emergence of the G9P[8] genotype in replacement of the G12P[8] genotype. Although equine-like G3P[8] strains remain the predominant rotaviruses circulating among children, the Sabahan G9P[8] strain belonged to lineage VI and was phylogenetically related to strains from other countries. A comparison of the Sabahan G9 strains with the G9 vaccine strains used in the RotaSiil and Rotavac vaccines revealed several mismatches in neutralizing epitopes, indicating that these vaccines might not be effective in Sabahan children. However, a vaccine trial may be necessary to understand the precise effects of vaccination.

Fig. 1

Electropherotypes of rotaviruses identified in Sabah. In total, four electropherotypes were identified, four long (L1–L4) and one short (S1) electropherotype patterns were identified. L1 and L2 were detected in genotype G9 and G3 strains, respectively. L3 and L4 were detected in untypable strains. S1 was identified in G3 strains. Images of the original gels are presented in Supplementary Figure S1

Fig. 2

Phylogenetic tree based on nucleotide sequences of the VP7 gene of G1 strains. The human rotavirus strain L116 (genotype G3) was used as an outgroup. Numbers at nodes represent the bootstrap value, and values higher than 70% are shown. The scale bar shows the genetic distance, expressed as nucleotide substitutions per site. Strains from the present study (indicated by a filled circle) belong to lineage Ic and are clustered with strains detected in Sabah in a previous study. The GenBank accession number is shown before each strain name

Fig. 3

Phylogenetic tree based on the VP7 gene of G2 strains. The human rotavirus strain L116 (genotype G3) was used as an outgroup. Numbers at nodes represent the bootstrap value, and values higher than 70% are shown. The scale bar shows the genetic distance, expressed as nucleotide substitutions per site. The strain identified in this study (indicated by a filled circle) belongs to lineage IV. The GenBank accession number is shown before each strain name

Fig. 4

Phylogenetic tree based on the VP7 gene of G3 strains. The human rotavirus strain Wa (genotype G1) was used as an outgroup. Numbers at nodes represent the bootstrap value, and values higher than 70% are shown. The scale bar shows the genetic distance, expressed as nucleotide substitutions per site. The strains identified in this study belong to lineages I and III (indicated by a filled circle). The GenBank accession number is shown before each strain name

Fig. 5

Phylogenetic tree based on the VP7 gene of G9 strains. The human rotavirus strain DS-1 (genotype G2) was used as an outgroup. Numbers at nodes represent the bootstrap value, and values higher than 70% are shown. The scale bar shows the genetic distance, expressed as nucleotide substitutions per site. Strains from the present study (indicated by a filled circle) belong to lineage VI. The GenBank accession number is shown before each strain name

Fig. 6

Phylogenetic tree based on the VP4 gene of P[8] strains. The human rotavirus strain 366 (genotype P[4]) was used as an outgroup. Numbers at nodes represent the bootstrap value, and values higher than 70% are shown. The scale bar shows the genetic distance expressed as nucleotide substitutions per site. All strains from the present study (indicated by a filled circle) belong to lineage III (sublineages III.1 and III.4). The GenBank accession number is shown before each strain name

Fig. 7

Amino acid sequence alignment of the VP7 proteins of the vaccine strains Rotavac and RotaSiil with Sabahan G9 strains reported in this study. Antigenic epitopes are indicated above the residue numbers. Residues that differed from Rotavac are highlighted in green. Residues that differed from RotaSiil are highlighted in blue. Residues that differed from both Rotovac and RotaSiil are highlighted in yellow. Amino acid substitutions that have been shown to be associated with escape from neutralization by monoclonal antibodies are indicated by an asterisk (*)

Fig. 8

Rotavirus G and P genotypes found in a previous study by Amit et al., 2021 [9] (a) and in the current study (b). In both studies, G3P[8] was the predominant genotype. The present study shows the emergence of G9 strains replacing the G12 strain that was in circulation previously