Contents lists available at ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid Research paper Typing of Human Cosaviruses by sequencing of full VP1: Update on global genetic diversity and identification of possible new genotypes circulating in Tunisia, North Africa Dorra Rezig a, ⁎ , Asma Lamari a,b , Henda Touzi a , Zina Meddeb a , Henda Triki a a University of Tunis El Manar, Pasteur Institute of Tunis, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles, 13 Place Pasteur, 1002- Le Belvédère BP74, Tunis, Tunisia b University of Tunis El Manar, Faculty of Sciences, BP94 Cité Rommana, 1068 Tunis, Tunisia ARTICLE INFO Keywords: Picornaviridae Human Cosaviruses Sequencing full VP1 Genetic diversity New genotypes ABSTRACT Human Cosaviruses (HCoSVs) are relatively newly characterized picornaviruses; they have been described in non- polio acute flaccid paralysis, diarrheal patients, and healthy individuals. Previous studies showed HCoSV cir- culation in Tunisia and only six genotypes circulating in the country were reported. In the present study, we sequenced 27 complete VP1 genomic region from HCoSV isolates in human feces from healthy individuals and patients with acute flaccid paralysis in Tunisia. Most of the Tunisian sequences belong to species A (78%, 21 out of 27). Three sequences belong to species B, two to species E and one sequence to species D. The Tunisian sequences belonged to genotype A6, A7, A8, A10, A1, A17 and E2. Based on genetic distance criteria for as- signing genotypes corresponding to neutralization serotypes in enteroviruses we also identified 4 new HCoSV genotypes named A25, B2, B3 and D6. Our study updates the genetic classification of HCoSVs, proposes new genotypes within species A, B and D and contributes to a better knowledge of the HCoSV circulation throughout the world. 1. Introduction The Picornaviridae family has expanded considerably thanks mainly to metagenomic analyzes from various human, animal and environ- mental samples (Tapparel et al., 2013). Human Cosaviruses (HCoSVs) are relatively newly characterized picornaviruses; they have been dis- covered in 2008. These viruses were detected in human fecal specimens of patients presenting non-polio acute flaccid paralysis (AFP), acute diarrhea or acute gastroenteritis and healthy individuals in different countries: United States, Italy, China, Australia, Afghanistan, Pakistan, Nigeria, Thailand, India, Bolivia, Japan, Burkina Faso, Tunisia and Brazil (Blinkova et al., 2009; Campanini et al., 2013; Dai et al., 2010; Holtz et al., 2008; Kapoor et al., 2008; Kapusinszky et al., 2012; Khamrin et al., 2012; Maan et al., 2013; Menage et al., 2017; Nix et al., 2013; Okitsu et al., 2014; Phan et al., 2012; Rezig et al., 2015; Stocker et al., 2012; Yang et al., 2016; Yu et al., 2017). In addition, three re- ports on infection with HCoSVs in immunocompromised patients were published. A first study reported a 43-year-old woman from northern Italy who was receiving prolonged immunosuppressive therapy following bilateral lung transplantation (Campanini et al., 2013). The second study conducted in HIV-1 immunocompromised patients, in Amsterdam (The Netherlands) showed excretion of HCoSVs associated with diarrhea (Oude Munnink et al., 2014) and we recently reported HCoSV infection in a Tunisian patient with Major Histocompatibility Complex class II (MHC class II) combined immunodeficiency (Lamari et al., 2019). Despite their association with various clinical presenta- tions, their implication as the causative agents of these diseases is still to be confirmed. HCoSVs were also reported in the environment mainly sewage and river water samples (Bibby and Peccia, 2013; Blinkova et al., 2009; Bonanno Ferraro et al., 2018; Guerrero-Latorre et al., 2018; Haramoto and Otagiri, 2014; Kitajima et al., 2015; Prevost et al., 2015; Thongprachum et al., 2018) and in animals like in piglets (Goecke et al., 2017; Okitsu et al., 2016). Classically, HCoSVs are screened by mole- cular techniques, especially nested reverse transcription PCR (RT-PCR) with primers targeting the 5′ non coding region (5′NC). In a previous study, we reported replication of HCoSVs in primary cell cultures of human embryonic lung MRC5 with a cytopathic effect observed 24–48 h after inoculation (Rezig et al., 2014). Genetic identification https://doi.org/10.1016/j.meegid.2019.104115 Received 23 September 2019; Received in revised form 6 November 2019; Accepted 8 November 2019 ⁎ Corresponding author at: Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles, Pasteur Institute of Tunis, University of Tunis El Manar, 13 Place Pasteur, 1002- Le Belvédère BP74, Tunis, Tunisia. E-mail address: dorra.rezig@issbat.utm.tn (D. Rezig). Infection, Genetics and Evolution 78 (2020) 104115 Available online 09 November 2019 1567-1348/ © 2019 Elsevier B.V. All rights reserved. T