Genetic landscape and macro-evolution of co-circulating Coxsackieviruses A and Vaccine-derived Polioviruses in the Democratic Republic of Congo, 2008-2013

Abstract

Enteroviruses (EVs) are among the most common viruses infecting humans worldwide but only a few Non-Polio Enterovirus (NPEV) isolates have been characterized in the Democratic Republic of Congo (DR Congo). Moreover, circulating vaccine-derived polioviruses (PVs) [cVDPVs] isolated during multiple outbreaks in DR Congo from 2004 to 2018 have been characterized so far only by the sequences of their VP1 capsid coding gene. This study was carried to i) investigate the circulation and genetic diversity of NPEV and polio vaccine isolates recovered from healthy children and Acute Flaccid Paralysis (AFP) patients, ii) evaluate the occurrence of genetic recombination among EVs belonging to the Enterovirus C species (including PVs) and iii) identify the virological factors favoring multiple emergences of cVDPVs in DR Congo. The biological material considered in this study included i) a collection of 91 Sabin-like PVs, 54 cVDPVs and 150 NPEVs isolated from AFP patients between 2008 and 2012 in DR Congo and iii) a collection of 330 stool specimens collected from healthy children in 2013 in the Kasai Oriental and Maniema provinces of DR Congo. Studied virus isolates were sequenced in four distinct sub-genomic regions 5’-UTR, VP1, 2C ATPase and 3D pol . Resulting sequences were compared through comparative phylogenetic analyses. Virus isolation showed that 19.1% (63/330) healthy children were infected by EVs including 17.9% (59/330) of NPEVs and 1.2% (4/330) of type 3 Sabin-like PVs. Only one EV-C type, EV-C99 was identified among the NPEV collection from AFP patients whereas 27.5% of the 69 NPEV isolates typed in healthy children belonged to the EV-C species: CV-A13 (13/69), A20 (5/69) and A17 (1/69). Interestingly, 50 of the 54 cVDPVs featured recombinant genomes containing exogenous sequences in at least one of the targeted non-structural regions of their genomes: 5’UTR, 2C ATPase and 3D pol . Some of these non-vaccine sequences of the recombinant cVDPVs were strikingly related to homologous sequences from co-circulating CV-A17 and A20 in the 2C ATPase region as well as to those from co-circulating CV-A13, A17 and A20 in the 3D pol region. This study provided the first evidence uncovering CV-A20 strains as major recombination partners of PVs. High quality AFP surveillance, sensitive environmental surveillance and efficient vaccination activities remain essential to ensure timely detection and efficient response to recombinant cVDPVs outbreaks in DR Congo. Such needs are valid for any epidemiological setting where high frequency and genetic diversity of Coxsackieviruses A13, A17 and A20 provide a conducive viral ecosystem for the emergence of virulent recombinant cVDPVs.

Enteroviruses from Humans and Great Apes in the Republic of Congo: Recombination within Enterovirus C Serotypes

“…Although discordant in terms of prevalence, these results are concordant with previous studies reporting the circulation of a wide range of enteroviruses in both humans and great ape populations from different African countries and elsewhere [ 16 , 19 , 20 , 22 , 40 , 41 , 42 , 43 ]. Interestingly, the strains and amplified genome fragments from all territories and from humans and NHPs are almost identical.…”

“…In contrast, no recombination events were observed with the genome sequences of strains CV-A13 (DQ995644) and PV3 (KY941933). Based on data from the cVDPV literature in outbreak regions, such as Cambodia, Madagascar, Democratic Congo and Nigeria, CV-A, including CV-A13, CV-A17, CV-A20 and CV-A11, have been reported as partners most frequently involved in recombination with PV strains [ 14 , 16 , 41 , 46 , 49 , 51 ]. In addition to infecting humans and being enteroviruses of human origin, CV-A has also been found in NHPs.…”

“…Indeed, it is well-known that genetic recombination contributes to genetic variation and evolution of enteroviruses, thus promoting the emergence and spread of new strains [ 10 , 11 , 12 ]. For example, the majority of circulating vaccine-derived poliovirus strains have been shown to be recombinant, consisting of either wild poliovirus strains with vaccine strains or poliovirus strains with non-polio enterovirus strains, particularly group C enteroviruses, including coxsackievirus A [ 13 , 14 , 15 , 16 ].…”

Genetic and phenotypic characterization of recently discovered enterovirus D type 111

“…Furthermore, none of the most common EV types circulating among humans in Central Africa (CV-A13, EV-C99, CV-A20, CV-A24, CV-Bs or echoviruses of diverse types [11, 14, 51]) was detected in the panels of NHP stools in which EV-D111 and EV-D120 were found. Yet, NHPs are susceptible to many types of human EVs, as observed in several occasions [45, 46, 52–55].…”

Molecular Epidemiological, Serological, and Pathogenic Analysis of EV-B75 Associated With Acute Flaccid Paralysis Cases in Tibet, China

“…To date, there are 112 gene sequences in the GenBank database, associated with various clinical manifestations including AFP ( Oberste et al, 2004 ; Bingjun et al, 2008 ; Rao et al, 2012 ; Laxmivandana et al, 2013 ; Sadeuh-Mba et al, 2013 ; Tao et al, 2014a ; Fernandez-Garcia et al, 2017 ; Maan et al, 2019 ; Sadeuh-Mba et al, 2019 ) (47 isolates worldwide), aseptic meningitis ( Avellon et al, 2006 ) (8 isolates in Spain, 2005), encephalitis ( Lewthwaite et al, 2010 ; Kumar et al, 2012 ) (13 isolates in India, 2006–2010), diarrhea ( Rao et al, 2013 ; Patil et al, 2015 ) (7 isolates in India, 2005–2011), respiratory diseases ( Opanda et al, 2016 ; Hellferscee et al, 2017 ) (5 isolates in total), and others ( Oberste et al, 2004 ) ( Figure 1 ). With the addition of the seven Tibetan EV-B75 isolates from this study, no significant or typical temporal and spatial aggregation of EV-B75 was observed worldwide.…”