Identification and molecular characterization of the first complete genome sequence of Human Parechovirus type 15

Abstract

Using a metagenomics approach, we have determined the first full-length genome sequence of a human parechovirus type 15 (HPeV15) strain, isolated from a child with acute flaccid paralysis and co-infected with EV-A71. HPeV15 is a rarely reported type. To date, no full-length genome sequence of HPeV15 is available in the GenBank database, where only limited VP1 sequences of this virus are available. Pairwise comparisons of the complete VP1 nucleotide and deduced amino acid sequences revealed that the study strain belongs to type 15 as it displayed 79.6% nucleotide and 93.4% amino acid identity with the HPeV15 prototype strain. Comparative analysis of available genomic regions and phylogenetic analysis using the P2 and P3 coding regions revealed low nucleotide identity to HPeV reference genomes. Phylogenetic and similarity plot analyses showed that genomic recombination events might have occurred in the UTRs and nonstructural region during HPeV15 evolution. The study strain has high similarity features with different variants of HPeV3 suggesting intertypic recombination. Our data contributes to the scarce data available on HPeVs in Africa and provides valuable information for future studies that aim to understand the evolutionary history, molecular epidemiology or biological and pathogenic properties of HPeV15. Human parechoviruses (HPeVs) are non-enveloped viruses that belong to one of the four species of genus Parechovirus within the Picornaviridae family. HPeV positive-sense single-stranded RNA genome is about 7300 bases in length, flanked by 5′ and 3′ untranslated regions (UTRs). The genome encodes a polyprotein which is cleaved by the viral protease (3 C) to produce the mature structural (VP0, VP3 and VP1) and nonstructural (2A-C, 3A-D) proteins 1. HPeVs can be transmitted through the fecal-oral and respiratory routes 1,2. HPeV infections are common throughout the world and most often cause asymptomatic or mild gastrointestinal or respiratory symptoms 1,2. However, syndromes such as encephalitis, aseptic meningitis, acute flaccid paralysis (AFP), sepsis and myocarditis have been increasingly recognized in primary HPeV infection in neonates and infants 2. After EVs, HPeVs are considered the second most common cause of central nervous system (CNS) viral infections 2. However, HPeV infections are currently underdiagnosed given that routine diagnostic assays are generally lacking in clinical settings 1,3. Following HPeV intestinal replication, infectious viruses are shed in feces where viruses can be detected by PCR and virus isolation 3. However, HPeVs are known for poor adaptation to cell cultivation systems and not all types replicate in cell lines routinely used for enterovirus (EV) detection 4,5. Because specific types could be missed or underdiagnosed using viral isolation, molecular identification methods are highly recommended for the routine detection of HPeVs in clinical samples 3,4. To date, 19 different HPeV types (HPeV1 to 19) have been described based on sequence similarity within their VP1 capsid pro...

Detection and genetic diversity of parechoviruses in children with acute flaccid paralysis in Cameroon

“…Overall, 11% (22/200) of the samples tested were positive for HPeV RNA ( Table 1 ). The most affected age group was 2 to < 5 years, thus suggesting that children and infants may be at higher risk of HPeV infection [ 27 , 28 , 43 ]. Age data were missing for 54 AFP cases and were therefore excluded from the analysis of the association between age and HPeV detection.…”

Genetic diversity and recombination event in bovine parechovirus infecting Japanese cattle

“…In the present study, a putative recombination breakpoint was found in the non-structural coding region 2B. In human parechoviruses, several recombination events have been reported in multiple regions, including the non-structural region; however, hot spots of recombination breakpoint have not been reported [17][18][19][20][21][22][23][24][25]. GC content is related to genomic stability and protection of recombination [26,27].…”

Human parechovirus are emerging pathogens with broad spectrum of clinical syndromes in adults

“…Similar PeV‐1, 3, and 4 are the most prevalent in Asia, with higher diversity from China, India, and Pakistan 27,59‐66 . In Africa, there is a high prevalence of PeV‐A1, 2, and 3, with evidence suggesting the circulation of many genotypes in the region 10,16,25,31,67‐69 …”

“…27,[59][60][61][62][63][64][65][66] In Africa, there is a high prevalence of PeV-A1, 2, and 3, with evidence suggesting the circulation of many genotypes in the region. 10,16,25,31,[67][68][69] Moreover, most of what is known about HPeVs comes from pediatric infections. The first report of HPeV infection in adults was in 1986, during an outbreak of AFP in Jamaica that claimed the lives of two women aged 26 and 27 years, linked to PeV-A1 (formerly Echovirus 22).…”