Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico

Abstract

Hepatitis E virus (HEV) is an emerging public health problem with an estimated 20 million infections each year. In Mexico, Orthohepevirus A, genotype 2, has been reported in humans, but genotype 3 has only been reported in swine (zoonotic). No diagnostic tests are publicly available in Mexico, and only partial sequences have been reported from swine samples. Hence, research is necessary to determine circulating strains, understand the features and dynamics of infection on pig farms, determine how to implement surveillance programs, and to assess public health risks. In this study, a next-generation sequencing (NGS) approach was applied to obtain a complete genome of swine HEV. Liver, feces, and bile samples were taken at slaughterhouses and a farm in Mexico. RT-PCR was used to determine positive samples and confirmed by Sanger sequencing. Of the 64 slaughterhouse samples, one bile sample was positive (B1r) (1.56%). Of 21 sample pools from farm animals, 14 were positive (66.66%), representing all stages of production. A complete sequence strain MXCDg3_B1c|_2016 was obtained from the bile of a domestic swine in the fattening stage. In addition, two partial sequences—MXCDg3_H2cons|_2016 (1473 nt) and MXCDg3_C3Acons|_2016 (4777 nt)—were obtained from sampled farm animals. Comparison with all reported genome HEV sequences showed similarity to genotype 3 subgenotype a (G3a), which has been previously reported in acute cases of human hepatitis in the US, Colombia, China, and Japan.

Tracing the History of Hepatitis E Virus Infection in Mexico: From the Enigmatic Genotype 2 to the Current Disease Situation

“…The finding of three genotypes in Mexico places the country as unique in Latin America, where HEV-Gt1 and -Gt3 have been found in humans and HEV-Gt3 in swine (Figure 2). swine was confirmed over the complete genome sequencing of one sample and two partial genomes [89]. In association with serological evaluation, these studies confirmed the endemicity of HEV in animals intended for human consumption, emphasizing the need for adequate food safety and surveillance systems.…”

“…Molecular detection of HEV-RNA in clinical and epidemiological contexts pursues two main goals: diagnosis of active infections and genome sequencing for genotyping. In Mexico, only scientific studies have been published addressing molecular HEV detection, and for most Latin American countries, short partial sequences of the HEV genome are commonly reported (Supplementary Table S1) [25,[27][28][29]40,89,.…”

“…The author obtained a partial genome corresponding to ORF-2 from nine liver samples; consecutive sequencing analysis showed that the genome corresponded to HEV-Gt3 [ 88 ]. This molecular epidemiological description of the circulation of HEV-Gt3 in farm pigs from Mexico was complemented by a study carried out in samples from the center of Mexico where the circulation of HEV-Gt3 on swine was confirmed over the complete genome sequencing of one sample and two partial genomes [ 89 ]. In association with serological evaluation, these studies confirmed the endemicity of HEV in animals intended for human consumption, emphasizing the need for adequate food safety and surveillance systems.…”

“…Molecular detection of HEV-RNA in clinical and epidemiological contexts pursues two main goals: diagnosis of active infections and genome sequencing for genotyping. In Mexico, only scientific studies have been published addressing molecular HEV detection, and for most Latin American countries, short partial sequences of the HEV genome are commonly reported ( Supplementary Table S1 ) [ 25 , 27 , 28 , 29 , 40 , 89 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 , 122 , 123 , 124 , 125 , 126 , 127 , 128 , 129 , 130 , 131 , 132 , 133 , 134 , 135 , 136 , 137 …”