Acute gastroenteritis (AGE) remains a major public health concern and is one of the leading causes of pediatric hospitalization. In low- and middle-income countries, morbidity and mortality rates remain high [1][2]. Rotaviruses are the principal etiological agents of infantile gastroenteritis. Antigenic diversity within the viral outer capsid proteins VP7 and VP4, as well as genetic variability of their encoding genes, has led to a classification into G and P genotypes [3]. At least 32 G genotypes and 47 P genotypes have been described, producing numerous G/P combinations [3]. Molecular epidemiology studies have significantly advanced Rotavirus vaccine development. In November 2014, the Senegalese Ministry of Health and Social Action, with Gavi support, introduced the two-dose monovalent live-attenuated human Rotavirus vaccine RV1 (RIX4414 strain, G1P[8] specificity; Rotarix, GlaxoSmithKline Biologicals) into the national Expanded Program on Immunization (EPI). RV1 is administered at 6 and 10 weeks of age. Although genotypes G1 to G4 are globally prevalent, emergent genotypes such as G9 and G12 currently not included in vaccines are being increasingly reported worldwide [4][5]. The emergence of novel genotypes highlights the need for ongoing Rotavirus surveillance both before and after vaccine introduction. The primary objective of this study was to monitor the molecular evolution of circulating rotavirus strains in children under 5 years of age in Senegal, comparing the periods before and after implementation of the national Rotavirus vaccination program.

During the pre-vaccine period (2010-2014), a total of 683 stool specimens were collected, of which 333 tested positive for Rotavirus, corresponding to a positivity rate of 48.76%. This rate declined to 15.29% in the post-vaccine period (2015-2020), when 89 of 582 samples were positive. The p value indicates a statistically significant difference (p < 0.05) (Table 1).

Table 1.Distribution of rotavirus cases according to vaccination periods.

A total of 313 Rotavirus-positive stools underwent genotyping: 235 from the pre-vaccine period and 78 from the post-vaccine period.

Pre-vaccine genotypes

VP7 genotypes

Among the 235 strains, 177 (75.31%) were successfully typed for VP7. The VP7 genotyping revealed five different G genotypes: G1, G2, G8, G9, and G12, with G1 and G12 predominating (Table 2).

Table 2.Distribution of rotavirus genotypes during the pre-vaccine period (2011-2014).

VP4 genotypes

Two P genotypes were identified P[6]andP[8] with P[8] predominating at approximately 57.87% (Table 2).

VP7/VP4 combinations

Simultaneous typing of VP7 and VP4 was achieved for 170 samples (72.34%), revealing distinct G/P associations (Table 2). The most frequent combination was G12P[8](28.81%), followed by G1P[6](21.46%), G9P[8](15.81%), and G1P[8](14.68%).

Post-vaccine genotypes

VP7 genotypes

Four VP7 genotypes were detected: G1, G2, G3, G9, and G12 with G3 being the most common, followed by G1 (Table 3).

Table 3.Distribution of Rotavirus genotypes during the post-vaccine period (2015-2020).

VP4 genotypes

VP4 genotyping identified three primary genotypes: P[4],P[6], andP[8], along with mixed types P[8]P[6] and P[4]P[6]. P[8] remained the dominant VP4 genotype (Table 3).

VP7/VP4 combinations

Concurrent VP7/VP4 genotyping was achieved for 66 strains (84.61%). The most frequent G/P association was G3P[8](18.18%), followed by G1P[8](12.12%) (Table 3).

Acute gastroenteritis remains one of the leading causes of morbidity and mortality among children under five years of age in developing countries, with Rotavirus as the most common infectious etiology. Laboratory-diagnosed Rotavirus AGE, particularly among younger children, substantially declined following Rotavirus vaccine introduction in Senegal. Rotavirus vaccine was introduced in November 2014, and rapidly reached 89% two-dose coverage by the end of 2015, and 96% by 2020 [14]. Infants were the first to benefit from vaccine. Our findings reveal a substantial decline in the number of circulating Rotavirus strains in the country after vaccine introduction. Genotyping at the Rotavirus Reference Laboratory (collaborating laboratory of the World Health Organization) was carried out according to the available budget. That’s why all positive Rotavirus were not genotyped.

Among the G genotypes identified, G1 was most frequent during the pre-vaccine period of our study, followed by G12 and G9, whereas after vaccination G3 became predominant, followed by G12, G1, and untyped genotypes. The genotyping protocol used makes it possible to detect more than 95% of the main genotypes responsible for human Rotavirus infections. So the untyped strains will not have an impact on the distribution of genotypes, especially during the pre-vaccination period. These results confirm that the globally common strains (G1, G2, G3, G4, and G9) are not detected in the same proportions in Senegal compared with developed countries [15]-[17] and even some other African nations. For example, in Zimbabwe the predominant strains were G9 (34%), G2 (26%), G1 (13%), G8 (5%), and G12 (4%) [4]; similarly, in Thailand G1 accounted for 50%, G2 for 26.9%, G3 for 10.1%, and G9 for 4.3% [18].

Since vaccine introduction, genotype G3 has dominated in Senegal, similar to findings in Malaysia [19], whereas G12 predominates in Ivory Coast [20]. Although G3 was never a predominant genotype in Senegal studies. The dominant genotypes in Zimbabwe (G9, G2) differ from those in Senegal [4]. Our results show that P[8] and P[6] genotypes were the most common both before and after vaccination, mirroring the relatively stable P-type distribution observed in Zimbabwe, despite a marked quantitative decline [4].

Before vaccination, the predominant strains in our study were G12P[8] (28.81%), G1P[6] (21.46%), G9P[8] (15.81%), and G1P[8] (14.68%). Globally, prior to vaccine introduction, five G/P genotype combinations were most often associated with rotavirus diarrhea: G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8][17][21][22]. Other studies have shown that globally rare strains were more frequently detected in Africa (27%), Asia (14%), and South America (11%) compared with North America (5%) and Europe (4%) [23][24]. Among these African strains, some (G12P[8], G3P[6], G1P[6], and G9P[6]) were present and predominant in Senegal before vaccination [24].

However, after introduction of the G1P[8] Rotarix vaccine, G12P[8] was replaced by G3P[8] (18.18%), followed by G1P[8] (12.12%), G3P[6] (9.09%), and G1P[6] (9.09%) in our study. This aligns with the work of Bilbera and al., who reported that the most important circulating genotypes during the post-vaccination period included G2P[4] and five other G/P combinations (G1P[8], G3P[8], G9P[8], G4P[8], G12P[8]) [25]. These findings highlight the strong effectiveness of the vaccine against genotypes such as G12P[8] and G1P[6].

Although G3P[8] has been detected in several countries, the detection rate varies. Few G3P[8] strains have been detected in Germany, Hungary, Japan and the USA. In Australia and Spain, the detection rate was moderate, between 14.4 and 37.4%. G3P[8] was predominant in Brazil, Indonesia and Thailand during the 2016-2017 seasons [19]. This emergence of G3P[8] could be due to a high coverage rate of the Rotarix vaccine. In Australia, the dominance G3P[8] is attributed to high Rotarix vaccine coverage-related vaccine-induced selective pressure. The dominance of G3P[8] in Thailand and Hungary is also attributed to vaccine-induced selective pressure, although Rotarix is only available on the private market and has lower national coverage in these two countries. Furthermore, the G3P[8] dominance in Spain is also attributed to vaccine-induced selective pressure, although RotaTeq has been primarily used there [19].

Notably, 90% of circulating strains worldwide share epitopes on VP4 and 30% on VP7, which enables cross-recognition by neutralizing antibodies [26]. The Rotarix® vaccine (GSK) contains an attenuated strain belonging to the same G1P[8] group as the Wa strain, conferring protection against both homotypic and heterotypic strains [22]. Regardless of the changes in genotype distributions, the overall prevalence of rotavirus has decreased substantially in all countries following rotavirus vaccine introduction [27].

Because of its segmented genome, the virus can undergo point mutations, gene rearrangements, or gene reassortment, generating extensive genetic diversity. Mixed-genotype infections may also allow reassortment of RNA segments. Numerous reports have described natural reassortment events between animal and human rotavirus strains [28].

Unusual genotype combinations were observed during the study period. From 2010 to 2014, the dominant G and P genotypes were G1, G12,P[8]andP[6], whereas between 2015 and 2020 the predominant types shifted to G3, G12,P[8]andP[6].

Before vaccine introduction, the leading genotype associations were G12P[8], G1P[6], G9P[8], and G1P[8]. After vaccine rollout, G3P[8] became the most prevalent combination, followed by G1P[8], G1P[6], and G3P[6].

The emergence of the G3 genotype could pose a challenge to vaccine effectiveness. Enhanced surveillance of these newly circulating genotypes is therefore essential to ensure early detection and to guide vaccine policy and effectiveness assessments.