key: cord-255137-utg8k7qs
authors: Yinda, Claude Kwe; Vanhulle, Emiel; Conceição-Neto, Nádia; Beller, Leen; Deboutte, Ward; Shi, Chenyan; Ghogomu, Stephen Mbigha; Maes, Piet; Van Ranst, Marc; Matthijnssens, Jelle
title: Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses
date: 2019-01-23
journal: mSphere
DOI: 10.1128/msphere.00585-18
sha: 
doc_id: 255137
cord_uid: utg8k7qs

Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases of diarrhea are likely caused by yet-unidentified viral agents, some of which could be the result of (recent) interspecies transmission from animal reservoirs, like bats. Using viral metagenomics, we screened fecal samples of 221 humans (almost all with gastroenteritis symptoms) between 0 and 89 years of age with different degrees of bat contact. We identified viruses belonging to families that are known to cause gastroenteritis such as Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, and Reoviridae. Interestingly, a mammalian orthoreovirus, picobirnaviruses, a smacovirus, and a pecovirus were also found. Although there was no evidence of interspecies transmission of the most common human gastroenteritis-related viruses (Astroviridae, Caliciviridae, and Reoviridae), the phylogenies of the identified orthoreovirus, picobirnavirus, and smacovirus indicate a genetic relatedness of these viruses identified in stools of humans and those of bats and/or other animals. These findings points out the possibility of interspecies transmission or simply a shared host of these viruses (bacterial, fungal, parasitic, …) present in both animals (bats) and humans. Further screening of bat viruses in humans or vice versa will elucidate the epidemiological potential threats of animal viruses to human health. Furthermore, this study showed a huge diversity of highly divergent novel phages, thereby expanding the existing phageome considerably. IMPORTANCE Despite the availability of diagnostic tools for different enteric viral pathogens, a large fraction of human cases of gastroenteritis remains unexplained. This could be due to pathogens not tested for or novel divergent viruses of potential animal origin. Fecal virome analyses of Cameroonians showed a very diverse group of viruses, some of which are genetically related to those identified in animals. This is the first attempt to describe the gut virome of humans from Cameroon. Therefore, the data represent a baseline for future studies on enteric viral pathogens in this area and contribute to our knowledge of the world’s virome. The studies also highlight the fact that more viruses may be associated with diarrhea than the typical known ones. Hence, it provides meaningful epidemiological information on diarrhea-related viruses in this area.

D iarrhea is the second most common cause of death worldwide and accounts for about 8 to 9% of the 5.9 million yearly deaths in children under the age of 5 (1, 2) . Most of these deaths occur in Southeast Asia and sub-Saharan Africa (3, 4) . The chances of infection with enteric viruses are higher in developing countries than developed countries, probably due to suboptimal sanitation and hygienic conditions and low quality of drinking water, especially in rural areas (5) . In Cameroon, a limited number of studies have investigated the prevalence of enteric pathogens as the cause of gastroenteritis in humans. These studies mainly focused on the epidemiology of a limited number of pathogens such as rotavirus, norovirus, and enteroviruses, revealing significant differences in the prevalence of these viruses in different settings and time periods (4, 6, 7) . In parts of Cameroon, a high prevalence of several enteric viruses such as enterovirus, norovirus, rotavirus, and adenovirus was found in children and adults (8) . Generally in Africa, many episodes of gastroenteritis remain unexplained as no etiological agent is determined (9, 10) . A proportion of the unexplained gastroenteritis cases are likely due to other known viruses, for which no tests were performed. However, a part of these gastroenteritis cases could also be caused by novel viral agents.

Transmission of these enteric viruses is predominantly fecal-oral, and humans are constantly exposed to these viruses through various routes (11) . One of these routes is zoonosis from reservoirs in wild or domestic animals, either by insect vectors or by exposure to animal droppings or tissues. One rich but, until recently, underappreciated reservoir of emergent viruses is bats. Of the ϳ5,500 known terrestrial species of mammals, about 20% are bats (12) . Several viruses pathogenic to humans are believed to have originated in bats over the last several years, including severe acute respiratory syndrome (SARS)-and Middle East respiratory syndrome (MERS)-related coronaviruses, as well as filoviruses, such as Ebola and Marburg viruses, or henipaviruses, such as Nipah and Hendra viruses (13) (14) (15) (16) (17) (18) .

In the Southwest region of Cameroon, bats are hunted and eaten. Such close interactions provide ample opportunity for zoonotic events to occur (19) .

Previously, we identified a plethora of known and novel eukaryotic viruses in Cameroonian fruit bats using a viral metagenomics approach, including viruses known to cause gastroenteritis in humans (sapovirus, sapelovirus, and rotaviruses A and H) and

those not yet associated with gastroenteritis (bastrovirus and picobirna-like viruses) (20) (21) (22) (23) . In the current study, we metagenomically screened 221 human fecal samples collected in the same region (where bats are hunted and eaten), to assess (i) if any viruses of animal origin could be identified and (ii) which known human gastrointestinal viruses were present. These fecal samples were collected from children less than a year old to adults of more than 60 years who had gastroenteritis and/or were in contact with bats. Additionally, since the gut virome typically contains both eukaryotic and prokaryotic viruses (phages), of which the latter usually represents the largest fraction of the gut virome, we also analyzed the phageome of these samples.

Sample characterization. A total of 221 human fecal samples (131 from Kumba and 90 from Lysoka) were collected from two hospitals in the Southwest region of Cameroon, for viral metagenomics screening. From these fecal samples, a total of 63 pools were constituted in categories based on age, bat contact status, and location (see Table S1 in the supplemental material). Illumina sequencing of all the 63 human pools generated in total approximately 708 million raw paired-end (PE) reads (between 4.3 and 53.4 million reads per pool). After trimming, 67% of the reads (471 million) were retained and 86% of these retained trimmed reads (405 million) were annotated using Diamond. Of these, 18% (74 million) could be attributed as viral.

NGS viral read distribution/abundances. In each of the categories of pools, phages make up at least 84% of the total number of viral reads while the maximum proportion of eukaryotic viral reads is 16%. A similar annotation profile was observed for pools of patients in different age groups, different locations, and different bat contact statuses (Fig. S1 ).

Further analysis of eukaryotic viral reads revealed that at least 70% of the reads mapped to viruses of the families Astroviridae, Reoviridae, and Anelloviridae (Fig. 1A) . Other viruses were also present, particularly those that are known to cause gastroenteritis belonging to the families Adenoviridae, Caliciviridae (Sapovirus and Norovirus), and Picornaviridae (of which about 60% were enteroviruses [Fig. 1B and Fig. S2] ). Also, reads from viruses known to cause other human diseases (Parvoviridae) or other animal diseases (Circoviridae) or not associated with any diseases at all (Picobirnaviridae) were present in variable numbers in the different groups ( Fig. 1B to E) . The rest of the viral families were either plant-or insect-associated viruses. Notably, in age groups A to D, the percentage of pools in which Picobirnaviridae viruses were present increased with age with low percentages in age groups A and B (Fig. 1C) . Also, the percentages of pools positive for anelloviruses differed with respect to age, with higher percentages in young children and the elderly. Further, there were no observable trends in the percentage of eukaryotic viral presence with respect to bat contact status or location ( Fig. 1D and E) . Figure 1F shows a heat map of the percentage of pools in which eukaryotic viral families were present in human and bat pools, while Fig. S3 presence in human and bats at the genus level (23) . Astroviridae (Mamastrovirus), Calciviridae (Sapovirus), Picornaviridae (Parechovirus), and Reoviridae (Rotavirus), viral families known to cause gastroenteritis in humans, were identified in both bat and human pools from the same region. Also, mammalian viruses not yet established to cause gastroenteritis (Picobirnaviridae, Circoviridae, and Parvoviridae [Bocaparvovirus]) were also common in both bats and humans from the same regions ( Fig. 1F and Fig. S3 ). Phylogeny of eukaryotic viruses. In this study, we focused on viruses from which near-complete genomes were obtained, particularly those that are known to cause viral gastroenteritis (belonging to the Astroviridae, Caliciviridae [norovirus and sapovirus] , Picornaviridae [enterovirus, parechovirus, cosavirus] , Parvoviridae, Reoviridae, and Adenoviridae [human mastadenovirus]). Furthermore, we also looked at other viruses not fully proven to cause gastroenteritis in humans but which have only sporadically been associated with gastroenteritis, like Picobirnaviridae and small circular singlestranded DNA viruses.

Phylogenetic analysis was done for each of the selected viruses using the protein or nucleotide sequences of suitable conserved regions and representative members of their viral family, genus, or species.

Reoviridae. Reoviridae is a large viral family of segmented dsRNA viruses with a wide host range. They are further divided into two subfamilies and 15 genera. Genomes of viruses belonging to the Reoviridae contain 9 to 12 segments (24) . In total, Reoviridae reads were found in 6 pools, and (nearly) complete genomes of 2 viruses of the family Reoviridae were obtained from pool HP55. Samples in this pool were from two diarrheic children (less than 5 years), originating from Kumba and without contact with bats.

Mammalian orthoreovirus. Mammalian orthoreoviruses (MORVs) contain 10 segments, L1 to L3, M1 to M3, and S1 to S4, coding for 12 to 13 proteins (24, 25) . A MORV strain was identified represented by 16,913 reads (0.4% of all viral reads of the pool). Phylogenetic analysis based on the nucleotide sequences of each of the 10 segments of this MORV ( Fig. 2 and Fig. S4 ) showed topological incongruence with four distinctive patterns. Based on segments L2 and S1, this strain clustered with bat strains WIV3 and WIV5 from China with 86% and 70% nucleotide (nt) identity, respectively ( Fig. 2A and  B ). For the L1 and S2 segments, the human strain clustered with the Ndelle murine strain, also from Cameroon, with 95% and 92% nt identity, respectively (Fig. 2C and D) . On the other hand, segment S3 of the Cameroonian MORV strain clustered with a human strain and a civet MORV strain from China (88% and 89% nt identity, respectively [Fig. 2E] ). The rest of the segments (L3, M1 to M3, and S4) did not cluster together clearly with any of the abovementioned strains (Fig. S4) .

Rotavirus A. Rotavirus A (RVA) contains 11 segments coding for 11 or 12 proteins: VP1 to VP4, VP6, VP7, and NSP1 to NSP6 (26, 27) . We identified a near-complete RVA sequence which made up 99% (4.3 million) of the eukaryotic viral reads of that pool. The NSP3 segment was not identified in the sample. The VP7 gene of this strain was genetically most related to RVA/Human-tc/USA/Wa/1974/G1P1A [8] and RVA/Human-TC/USA/Rotarix/2009/G1P [8] (nt identity of 92 and 97%, respectively) while the VP4 gene was 90% identical to the same strains. The phylogenetic trees of the remaining segments shared the same clustering pattern (Fig. 3A and B and Fig. S5 ). According to the rotavirus classification scheme, this strain is a typical Wa-like G1P [8] named RVA/ Human-wt/CMR/CMRHP55/2014/G1P [8] . CMRHP55 was distantly related to bat RVA strains identified from the same regions (only 69 to 71% nt identity).

Picornaviridae. The Picornaviridae represent a large family of small, cytoplasmic, nonenveloped icosahedral ssRNA viruses consisting of 80 species, grouped into 35 genera. They have a genome of 7.1 to 8.9 kb in size and are most often composed of a single ORF encoding a polyprotein flanked by a 5= and 3= UTR (28) . The members of the family Picornaviridae can cause gastroenteritis, meningitis, encephalitis, paralysis (nonpolio and polio-type), myocarditis, hepatitis, upper respiratory tract infections, and diabetes (29, 30) . Out of the 63 pools, 41 contained Picornaviridae reads, making the Picornaviridae the eukaryotic viral family of which reads could be identified in the highest number of pools.

Enterovirus. The genus Enterovirus (EV) consists of 15 species: Enterovirus A to L and Rhinovirus A to C. EV A, B, C, and D are found in humans; E and F in cattle; G in pigs; H, J, and L in monkeys; K in rodents; and species I in dromedary camels (http://www .picornaviridae.com). In this study, eighteen (nearly) complete genomes of EVs were obtained. The strains were named EV/Human/CMRHPxx/CMR/2014, here referred to as EV-CMRHPxx. All eighteen genomes were found in pools of age groups A and B (Ͻ3 and 3 to 20 years, respectively). Eight of these were identified in age group A, three (EV-CMRHP1, 5A, and 5B) of which were pools consisting of samples of infants who had indirect contact with bats while the rest (EV-CMRHP14, 45, 52A, 52B, and 55) were those that had no contact with bats. The ten other strains were identified in pools belonging to age group B, three of which had direct contact with bats (EV-CMRHP8A, 8B, and 9), 5 indirect contact 4, 35A, 35B, and 39) and two with no contact . Based on the phylogenetic analysis of the VP1 nucleotide sequences, the EVs found in this study were quite divergent from each other, belonging to three different species of Enterovirus, A, B, and C (Fig. 4A ). Most of the strains belonged to the Enterovirus C clade (EV-CMRHP1, 3, 4, 8A, 8B, 9, 14, 18, 35A, 52A, and 55) , while EV-CMRHP35B, 39, and 45 clustered within the Enterovirus B genotype, and EVCMRHP5A, 5B, 52B, and 58 in the genogroup Enterovirus A. Some pools had multiple strains of EV present, and some of these clustered together (CMRHP8A and 8B: vaccine type PV-3), whereas other pools contained distinct EV species (EV-CMRHP35A and 35B; 52A and 52B). The presence of vaccine strains in pool HP8 probably indicates recent vaccination events of the infants in this pool. Apart from EV-CMRHP39 (which clustered with 11C52_CMR), all the EV strains identified here were distantly related to those previously identified in the Far North region of Cameroon (31) . Furthermore, none of the human strains from Cameroon were related to any of the animal EV strains (from chimp or gorilla). A summary of the detailed classification of these EVs using an online typing tool (32) is shown in Table 1 .

Parechovirus. The genus Parechovirus is comprised of two species, Parechovirus A (human parechovirus [HPeV] ) and Parechovirus B (Ljungan virus, isolated from bank voles) (33) . HPeV is subdivided into 19 types (HPeV1 to -19) . HPeV is associated with mild gastrointestinal or respiratory illness; however, severe disease conditions, such as meningitis/encephalitis, acute flaccid paralysis, and neonatal sepsis, may occur (34) (35) (36) . Here, three (nearly) complete HPeVs were identified in pools HP2, HP46, and HP48 with sequence lengths of 7,142 bp, 7,202 bp, and 7 ,219 bp, respectively, collected from children less than 3 years old (age group A). In terms of bat contact status, they were in pools of those either in indirect contact with bats (HP2 and HP48) or without contact (HP46). They were all distantly related to each other, with HPeV-CMRHP46 and HPeV-CMRHP48 having the highest identity (76% and 86% nt and aa identity, respectively). Phylogenetically, HPeVs in HP46 and in HP48 fell into a clade of type 1 HPeVs (Fig. 4B ). The HPeV in HP46 clustered together with HPeV1/Harris strain with 76% nt identity, while CMRHP48 clustered closely with Japanese and Norwegian strains A1086-99 and NO-3694 (84 to 90% nt identity) . Furthermore, HPeV-CMRHP2 clustered distantly with type 16 HPeVs from China and Bangladesh with only 70 to 71% nt identity. Considering the 75% identity demarcation for HPeV types (37, 38) , this strain potentially represents a novel type.

Cosavirus. The genus Cosavirus consists of five species (Cosavirus A, B, and D to F), which have been associated with gastroenteritis in children (39) . Six near-complete [8] strains. Red, Cameroonian human RVA strain identified in this study; blue, Cameroonian bat RVA strains. Trees were constructed human cosavirus (HCoSV) genomes were identified: 1 from children less than 3 years old (HP49), 3 from those between 3 and Ͻ20 years old (HP6A and HP6B, HP57), and 2 from pools of individuals between 20 and Ͻ60 years old (HP44, HP24). Some of these pools had direct or indirect contact with bats (HP6, HP24, and HP44), while others had no contact with bats (HP49 and HP57). Phylogenetic analysis (Fig. 4C ) showed that cosaviruses from HP6B, HP49, and HP57 formed a clade with two other strains from Australia and Nigeria (HCoSV/E1/AUS and HCoSV/NG385/NGA) in species HCoSV E. Meanwhile the strains in HP6A, HP24, and HP44 clustered with HCoSV in species A, D, and B, respectively. Therefore, it seems that humans in Cameroon host a diverse range of cosaviruses.

Cardiovirus. The genus Cardiovirus consists of three species, Cardiovirus A to C. Species B includes Saffold virus (SafV) infecting humans. It has been found in cases with acute flaccid paralysis, respiratory tract infections, and diarrhea in China (40) (41) (42) . Here, we found a near-complete genome of a SafV in one pool (HP35) belonging to the age group between 3 and Ͻ20 years old who had indirect contact with bats. The VP1 Phylogenetic trees were based on the nucleotide sequences of the VP1-P2A region for the species Hepatovirus A and the VP1 region for the rest of the genera. All the trees were constructed using the GTRϩGϩI nucleotide substitution model using RAxML, with the autoMRE flag, which enables a posteriori bootstrapping analysis. Only bootstrap values greater than 70% are shown. Bars indicate nucleotide substitutions per site. Red, novel strains from this study; blue, human Cameroonian enterovirus strains from other studies; green, animal enterovirus strains from Cameroon. segment of the identified SafV was 72 to 74% and 78 to 80% identical (on nt level) to SafV strains in types 5 and 6, respectively. Phylogenetic analysis based on the VP1 region confirmed the clustering of the novel strain between types 5 and 6 with more phylogenetic relatedness to type 6 ( Fig. 4D) . Hence, this novel SafV strain may be a distant member of type 6 or represent a new type.

Hepatovirus A. Hepatitis A virus (HAV), now Hepatovirus A, belongs to the genus Hepatovirus, which consists of nine species (Hepatovirus A to I). The Hepatovirus A species is comprised of a single serotype, HAV, subdivided into human and simian viruses (43) . It causes acute hepatitis throughout the world (44) . There were three (nearly) complete HAV genomes in pools HP2, HP4, and HP6, all of which were pools from those in direct (HP6) or indirect (HP2 and HP4) contact with bats. These strains were either from infants less than 3 years old (HP2) or from children between 3 and Ͻ20 years old (HP4 and HP6). Based on the VP1-P2A region, the nt identity between these strains was 98 to 99%. Strains in HP4 and HP6 were 99% identical to BRAB13, isolated from a patient from the Netherlands in 2001, who was staying in a hippie community with visitors from all over the world and under primitive living conditions (45) . On the other hand, the HAV strain in HP2 was closely related to strain G2B1-VP from France (98% nt identity). Therefore, all strains identified here are genotype IIA (Fig. 4E) , increasing the number of completely sequenced genotype II strains to five (the other two strains are BA/ITA/2012 and CF53/Berne).

Astroviridae. Astroviridae is a family of nonenveloped, spherical viruses with a linear ssRNA(ϩ) genome of 6.8 to 7kb, containing three overlapping ORFs. The family is divided into two genera: genus Mamastrovirus (MAstVs) and genus Avastrovirus (AAstVs). The genera are further divided into 33 and 7 species, respectively (46) . Fourteen out of the sixty-three human pools contained Astroviridae reads, and we were able to obtain eight near-complete genomes of MAstVs (HP2, 3, 6, 34, 35, 43, 45, and 46) . Additionally, these pools were either from children less than 3 years old (HP2, HP45, and HP46), age group 3 to Ͻ20 (HP3, HP6, and HP35), or between 20 and Ͻ60 (HP34 and HP43). Phylogenetic analysis of the RdRp and capsid regions ( Fig. 5A and B) depicted clustering of the novel MAstVs in species 1 (CMRHP2, 3, 34, 35D, 43, and 46) , 6 (CMRHP45), and 9 (CMRHP6). In the MAstVs1 clade, there seems to be topological inconsistency in the different phylogenetic trees. Strain AstV8_Yuc8 (AF260508) clustered with the novel strains CMRHP2, 3, and 35D in the capsid tree, while in the RdRp tree it clustered with the Chinese strain V4-Guangzhou, suggesting a recombination event between these strains in the past. Bat astrovirus identified in Cameroon (23) 

Phylogenetic trees based on the nucleotide sequences of the RdRp (A) and capsid (B) genes of the AstVs identified in this study and representative strains from GenBank. Trees were constructed using the GTRϩGϩI nucleotide substitution model using RAxML, with the autoMRE flag, which enables a (Continued on next page) formed a clade (in the RdRp tree) with other bat astroviruses from Guangxi but was distantly related to the human AstVs from the same region.

Caliciviridae. Caliciviridae are a family of nonenveloped viruses with a linear ss-RNA(ϩ) genome of 7.3 to 8.3 kb, containing two or three ORFs. The family contains five genera (47, 48) . In total, Caliciviridae reads were found in 16 pools belonging to either the Norovirus or Sapovirus genus.

Norovirus. This genus consists of a single species, Norwalk virus (NV), divided into 5 genogroups. Genogroups I, II, and IV infect humans, whereas genogroup III infects bovine species and genogroup V has been isolated from mice (49) . Three nearcomplete NVs were present in the 16 pools that contained Caliciviridae reads (HP1, HP18, and HP59), from people who had indirect (HP1 and HP59) or no (HP18) contact with bats, and from age group A (HP1), B (HP18), or C (HP59). The phylogenetic tree (Fig. 6A) showed that the four NVs belonged to two genogroups: I (NV_CMRHP18, genotype I.3) and II (NV_CMRHP1 and NV_CMRHP59, genotypes II. 12 and II.13, respectively) . The novel strain NV_CMRHP18 was more than 98% similar to strain C13/ 2009CMR_GI.3 (a partial sequence [JF802509]) isolated from the Littoral Region of Cameroon in 2009, whereas strains of genogroup II from the same study (II.4, II.8, II.17) were distantly related to those identified here (II.12 and II.13) (7) . Strains from this previous study were not included in the phylogenetic analysis because only 200 to 300 nt of the capsid region was available in databases. Sapovirus. The genus Sapovirus (SaV) consists of a single species, Sapporo virus. It has been detected in humans, pigs, minks, dogs, sea lions, bats, chimpanzees, rodents, and carnivores (50, 51) . Three near-complete SaV genomes were present in pools HP4 (age group B), HP15 (age group A), and HP22 (age group D) from people who were in indirect contact, were not in contact, and were in direct contact with bats, respectively. Phylogenetic analysis (Fig. 6B) showed that SaV from HP22 could be classified as a GIV genotype, and the SaVs HP4, HP53, HP46, HP56, and HP15 belonged to genotype GII. The phylogenetic tree showed that the bat SaVs found in Cameroon (in blue) (22) clustered together and formed a clade with other bat SaVs from China and Hong Kong but divergent from these human SaVs, indicating no evidence of interspecies transmission of SaVs in this region.

Picobirnaviridae. Picobirnaviruses (PBVs) belong to the family Picobirnaviridae, genus Picobirnavirus, and are small bisegmented dsRNA viruses with a total genome size of about 4 kb. Segment one encodes a polyprotein, containing the capsid protein, and segment two encodes the RdRp. Based on the RdRp gene, PBVs are classified into two genogroups. Although PBV is genetically highly diverse and has been found in stool samples of a broad range of mammals, its true host(s) remain(s) enigmatic. The disease association is unclear, but PBV infection has been associated with gastroenteritis in both animals and humans (52, 53) . Up to 28 out of the 63 pools contained reads annotated as Picobirnaviridae with most of the positive pools from individuals in age groups above 20. We could obtain 37 (near-complete) RdRp sequences of PBVs from these 28 pools. Phylogenetic analysis based on RdRp (Fig. 7) revealed the clustering of the novel strains in four different clades: in genogroup I (26 strains) , in genogroup II (9 strains), and in 2 clades (3 strains) of uncharacterized picobirna-like viruses that use an alternative mitochondrial invertebrate genetic code (Lysoka picobirna-like virus CMRHP9 and CMRHP10B and Kumba picobirna-like virus CMRHP21A). Interestingly, a wolf PBV strain from Portugal (ANS53886) from genogroup I clustered together with human strains from Cameroon with an aa identity of 76% with strains CMRHP26A and CMRHP35. Likewise, in genogroup II, strains CMRHP34A, CMRHP63B, and CMRHP26C clustered closely (75 to 76% aa identity) with a Portuguese feline strain (AGZ93689). Intriguingly, the Cameroonian human picobirna-like viruses CMRHP9 and CMRHP10B were 99% identical to a Cameroonian bat strain picobirna-like virus, P11-300, suggesting a possible interspecies transmission. However, their true host has not yet been determined. It could be that the true hosts of PBVs are found in both humans and bats and that this therefore explains their presence in both.

Small circular, Rep-encoding, ssDNA (CRESS-DNA) genomes. (i) Smacovirus. Smacovirus (SCV) is a relatively recently described virus with a small circular DNA genome with a size of about 2,529 bp. It belongs to the smacovirus group and is an unclassified eukaryotic virus of unknown origin (54) . In this study, we identified two SCV sequences, one complete genome (HuSCV-CMRHP10) and a near-complete genome (HuSCV-CMRHP03). They were identified in pools of patients belonging to age group B, coming from Lysoka and having direct (HP3) or indirect (HP10) contact with bats. These strains shared 99% amino acid identity. Their replicase genes were 94% and 95% identical to chimpanzee (KP233190) and human (HuSCV3, KT600069) strains from the United States, respectively. Based on the capsid region, these novel Cameroonian strains were 98 to 99% identical to the chimp strain and only 85% identical to the human strain HuSCV3. The close genetic relatedness of human strains to a strain found in a chimpanzee sample suggest that these viruses infect a host shared between chimps and humans, and if indeed smacovirus infects mammals, this could be a case of interspecies transmission (55) . Phylogenies of the replicase (Fig. 8A ) and the capsid genes ( Fig. 8B) indeed showed a cluster of these Cameroonian strains with a human Genogroup I and pecovirus (C and D) of the replicase and capsid genes, respectively. The trees were constructed using the LGϩGϩI substitution model using RAxML, with the autoMRE flag, which enables a posteriori bootstrapping analysis. Only bootstrap values greater than 70% are shown. Bars indicate amino acid substitutions per site. Red, Cameroonian human strains; blue, previously known human smacoviruses or pecovirus. and a chimpanzee strain from the United States. However, the topological inconsistency in the replicase and capsid trees may suggest a recombination event between these strains in the (distant) past.

(ii) Pecovirus. Pecoviruses (Peruvian stool-associated circo-like viruses [PeCVs] ) are CRESS-DNA genomes that were first identified in the feces of a patient during an outbreak of acute gastroenteritis in the Netherlands and later in samples of Peruvian children (55, 56) . Subsequently, they were identified in other humans, pigs, a dromedary camel, and a seal (55) (56) (57) (58) . Here we identified a genome sequence (HuPeCV-CMRHP60) of 2,937 bases made up of two ORFs that code for a capsid (372 aa) and a replicase protein (336 aa). Unlike other human PeCVs, the Cameroonian strain shared the same canonical nonamer (NANTATTAC) atop the predicted stem-loop structure with seal, dromedary, and porcine PeCV strains. The Rep showed 31 to 42% aa sequence identity to all other Rep genes, and a Rep-based phylogenetic analysis (Fig. 8C) showed that HuPeCV-CMRHP60 clustered together with pecovirus genomes from a seal and 3 human strains. Based on the cap protein (Fig. 8D) , the Cameroonian strain was only 22 to 42% identical to all other pecoviruses and clustered only distantly from the seal strain, a porcine strain, and the human strains. This demonstrates the existence of a high level of genetic diversity within this group of circular DNA genomes, pointing to the possible existence of multiple species in this clade. Furthermore, we identified 2 incomplete sequences related to sewage-associated circular DNA molecules recovered from a sewage treatment oxidation pond in New Zealand (59), with only 38% aa identity on the Rep protein, further expanding the great diversity of CRESS-DNA genomes in the Cameroonian population.

Bacteriophages. Bacteriophages are viruses that infect and replicate within bacteria. Their presence therefore reflects the gut microbiota of the patients. Because most of the obtained viral reads were classified as bacteriophages, we further investigated the bacteriophage composition of the human samples. With VirSorter (60), a tool developed to identify highly divergent dsDNA phages from metagenomics data, 5,905 of the contigs in our data set were identified as phages. From these, the tool Diamond (61) annotated 2,647 as bacterial, 21 as metazoan, and only 606 (ϳ10%) as viral, while 1,309 contigs remained unannotated. From the contigs annotated as viral by Diamond, most were phages belonging to the Myoviridae (236 contigs), Podoviridae (95 contigs), Siphoviridae (145 contigs), and Microviridae (36 contigs) families. To get insight into the differences in the bacteriophage communities, we compared the VirSorter-identified bacteriophage richness between the different age groups (Fig. S6A) , locations (Fig. S6B, ) and bat contact status (Fig. S6C ), all of which showed no significant differences. To identify the potential bacterial hosts of these phages, we searched for bacterial CRISPR spacer sequences in the phage contigs, to identify its potential host. The search revealed that the most likely hosts of these phages are bacteria of the families Bacteroidaceae, Bifidobacteriaceae, Enterobacteriaceae, Enterococcaceae, Erysipelotrichaceae, Eubacteriaceae, Lactobacillaceae, Odoribacteraceae, Streptococcaceae, and Veillonellaceae (Table S2) .

Network analysis of human and bat phageomes. In order to visualize the genetic relatedness between the human and bat gut phageome, a recently developed bioinformatics tool (vConTACT) was used. It groups phages based on their genome sequences into viral clusters which correlate rather well with viral genera as defined by the International Committee of Taxonomy of Viruses (ICTV) (62) . A total of 30,875 protein clusters were predicted using the prokaryotic and archaeal RefSeq combined with the proteins predicted from the phage contigs identified from the human and bats pools using VirSorter. Using a network analysis approach (Fig. 9) , 792 viral genome clusters were predicted of which 173 contained reference phages together with bat or human phage contigs, whereas the rest contained only bat, only human, or bat-human clusters. Figure 9 shows that both Cameroonian human and bat phage contigs identified in our studies are spread across the known phage sequence space. However, several of the phage contigs constituted completely new clusters (indicated by filled gray ovals), completely unconnected to phages in the reference database. Also, the genetic diversity of several previously known phage subclusters was significantly expanded (as indicated by open ovals) while some clusters (in brown ovals) were made up of only bat and human phages identified in this study.

Recently, we thoroughly investigated the gut virome of fruit bats from Cameroon (20) (21) (22) (23) 63) and showed the presence of many novel and divergent eukaryotic viral families, including viruses known to cause gastroenteritis in humans. The aim of the current study was to investigate the gut virome of humans (n ϭ 221) from Cameroon and to further determine if bat viruses are possible causative agents of gastrointestinal infections in humans.

Twenty-four percent of the 471 million generated trimmed reads were assigned as viral. Most of these reads were bacteriophages, which is in accordance with previous studies (64) . The eukaryotic viral reads include those that belong to viral families that are commonly associated with gastroenteritis in humans (Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, and Reoviridae), viruses that are uncommon causes of gastroenteritis (orthoreovirus), or those that have been identified in humans but not associated with disease (anellovirus, smacovirus, and picrobirna-like viruses). 

VIRSorter_NODE_210_length_3873_cov_4_79189-cat_1

VIRSorter_NODE_388_length_2881_cov_7_17939-cat_1

VIRSorter_NODE_5_length_42493_cov_21_423-circular-cat_1

VIRSorter_NODE_8_length_45832_cov_51_2672-cat_1

VIRSorter_NODE_4_length_43684_cov_82_015-circular-cat_2

VIRSorter_NODE_15_length_28369_cov_37_8786-cat_2

VIRSorter_NODE_16_length_34096_cov_10_5837-cat_1

VIRSorter_NODE_7_length_23030_cov_44_5743-cat_2

VIRSorter_NODE_4_length_46080_cov_143_372-circular-cat_1 VIRSorter_NODE_154_length_5846_cov_32_8156-cat_2

VIRSorter_NODE_2_length_40986_cov_83_5436-cat_2

VIRSorter_NODE_14_length_28627_cov_424_601-cat_2

VIRSorter_NODE_130_length_7398_cov_6_88034-cat_2

VIRSorter_NODE_911_length_1516_cov_2_82279-cat_2

VIRSorter_NODE_60_length_9439_cov_32_4934-cat_1

VIRSorter_NODE_98_length_5449_cov_11_7885-cat_1

VIRSorter_NODE_193_length_2388_cov_2_87797-cat_2

VIRSorter_NODE_25_length_14198_cov_12_3353-cat_2

VIRSorter_NODE_83_length_6779_cov_23_1462-cat_1

VIRSorter_NODE_37_length_8496_cov_10_6883-cat_1

VIRSorter_NODE_97_length_6417_cov_22_439-cat_2

VIRSorter_NODE_20_length_3093_cov_15_1522-cat_1

VIRSorter_NODE_794_length_2121_cov_3_72505-cat_2

VIRSorter_NODE_510_length_2453_cov_9_21212-cat_2

VIRSorter_NODE_11_length_24212_cov_31_2924-cat_1

VIRSorter_NODE_16_length_17400_cov_20_1101-cat_2

VIRSorter_NODE_1_length_45933_cov_26_6238-cat_1

VIRSorter_NODE_4_length_46625_cov_133_007-circular-cat_1

VIRSorter_NODE_52_length_9386_cov_11_0833-cat_2

VIRSorter_NODE_229_length_1757_cov_2_47857-cat_2

VIRSorter_NODE_11_length_20025_cov_19_5373-cat_1

VIRSorter_NODE_22_length_11775_cov_21_2965-cat_1

VIRSorter_NODE_107_length_7429_cov_59_5487-cat_2

VIRSorter_NODE_5_length_61314_cov_65_5801-cat_2

VIRSorter_NODE_8_length_28098_cov_49_3527-cat_2

VIRSorter_NODE_59_length_6288_cov_49_065-cat_1

VIRSorter_NODE_6_length_39977_cov_34_3534-cat_2

VIRSorter_NODE_145_length_6050_cov_14_9503-cat_2

VIRSorter_NODE_3_length_55511_cov_174_071-cat_2

VIRSorter_NODE_512_length_1992_cov_5_2329-cat_1

VIRSorter_NODE_43_length_9047_cov_24_7407-cat_1 VIRSorter_NODE_7_length_27940_cov_25_4928-cat_2

VIRSorter_NODE_30_length_20704_cov_18_18-cat_2

VIRSorter_NODE_284_length_3092_cov_4_56783-cat_2

VIRSorter_NODE_21_length_10227_cov_70_6216_ID_1234280-cat_1

VIRSorter_NODE_244_length_3185_cov_5_53925-cat_1

VIRSorter_NODE_9_length_14015_cov_52_0782-cat_2

VIRSorter_NODE_483_length_3784_cov_3_74777-cat_2

VIRSorter_NODE_163_length_1997_cov_6_07969-cat_1

VIRSorter_NODE_73_length_9441_cov_6_50694-cat_1

VIRSorter_NODE_391_length_2005_cov_13_5311-cat_2

VIRSorter_NODE_48_length_4545_cov_11_4716-cat_2

VIRSorter_NODE_274_length_2499_cov_6_84104-cat_1

VIRSorter_NODE_5_length_45101_cov_33_3939-cat_2

VIRSorter_NODE_84_length_5772_cov_5_66831-cat_1

VIRSorter_NODE_228_length_3330_cov_15_3372-cat_1

VIRSorter_NODE_38_length_6638_cov_33_8407-cat_2

VIRSorter_NODE_110_length_3327_cov_40_0329_ID_1235347-cat_2

VIRSorter_NODE_292_length_3977_cov_5_20205-cat_2

VIRSorter_NODE_73_length_4137_cov_29_2744-cat_2

VIRSorter_NODE_109_length_3682_cov_5_79945-cat_2

VIRSorter_NODE_2060_length_1098_cov_2_56024-cat_2

VIRSorter_NODE_186_length_5287_cov_24_3374-cat_2

VIRSorter_NODE_128_length_4404_cov_8_8202-cat_2

VIRSorter_NODE_8_length_40727_cov_52_8639-circular-cat_1

VIRSorter_NODE_241_length_2048_cov_3_82192-cat_2

VIRSorter_NODE_566_length_1570_cov_4_87877-cat_1

VIRSorter_NODE_236_length_2071_cov_8_333-cat_2

VIRSorter_NODE_21_length_8643_cov_7_23897-cat_1

Halocynthia~phage~JM-2012

Bacillus~phage~NotTheCreek Bacillus~phage~Belinda

Listeria~phage~LP-083-2 VIRSorter_NODE_12_length_23882_cov_20_202-cat_2

Bacillus~phage~W.Ph. Enterococcus~phage~EFLK1

VIRSorter_NODE_421_length_3484_cov_2_88788-cat_2

VIRSorter_NODE_51_length_6073_cov_24_308-cat_2

VIRSorter_NODE_126_length_4338_cov_7_34968-cat_2

VIRSorter_NODE_743_length_2937_cov_5_76678-cat_2

VIRSorter_NODE_572_length_1258_cov_4_2989-cat_2

VIRSorter_NODE_511_length_1714_cov_9_19609-cat_2

VIRSorter_NODE_105_length_2295_cov_5_80162_ID_209_GC022959_GC022959-cat_2 VIRSorter_NODE_351_length_1653_cov_3_89784-cat_2

VIRSorter_NODE_62_length_4317_cov_5_92123_GC022960_GC022960-cat_2

VIRSorter_NODE_70_length_5230_cov_7_68756-cat_1

VIRSorter_NODE_59_length_5445_cov_7_07004-cat_2

VIRSorter_NODE_151_length_2931_cov_21_0263-cat_2

VIRSorter_NODE_87_length_2972_cov_3_15406-cat_2

VIRSorter_NODE_52_length_12117_cov_12_12-cat_2

VIRSorter_NODE_11_length_18974_cov_17_7842-cat_2

VIRSorter_NODE_2774_length_1414_cov_2_55497-cat_2

VIRSorter_NODE_250_length_2007_cov_4_84663-cat_2

VIRSorter_NODE_92_length_4947_cov_8_09199-cat_2

VIRSorter_NODE_1203_length_1540_cov_6_38619-cat_2

VIRSorter_NODE_46_length_7537_cov_11_1706-cat_2

VIRSorter_NODE_2982_length_1113_cov_2_02703-cat_2

VIRSorter_NODE_150_length_2967_cov_3_60415-cat_2

VIRSorter_NODE_856_length_1683_cov_5_93275-cat_2

VIRSorter_NODE_297_length_2600_cov_4_91082-cat_2

VIRSorter_NODE_891_length_1502_cov_2_53754-cat_2

VIRSorter_NODE_234_length_5884_cov_5_88807-cat_2

VIRSorter_NODE_142_length_4144_cov_6_25424-cat_2

VIRSorter_NODE_1046_length_1299_cov_4_62684-cat_2

VIRSorter_NODE_150_length_4016_cov_26_916-cat_1

VIRSorter_NODE_29_length_15514_cov_39_9365-cat_2

VIRSorter_NODE_315_length_2377_cov_6_79043-cat_2

VIRSorter_NODE_53_length_6164_cov_14_1464-cat_2

VIRSorter_NODE_324_length_2523_cov_8_04415-cat_2

VIRSorter_NODE_234_length_3252_cov_10_1729-cat_2

VIRSorter_NODE_14_length_18167_cov_39_9557-cat_2

VIRSorter_NODE_240_length_2054_cov_3_92817-cat_2

VIRSorter_NODE_846_length_2391_cov_4_03933-cat_2

VIRSorter_NODE_476_length_1954_cov_5_94406_GC021836_GC021836-cat_2

VIRSorter_NODE_74_length_3590_cov_49_2966-cat_2

VIRSorter_NODE_568_length_1984_cov_4_76403-cat_2

VIRSorter_NODE_13_length_17922_cov_52_6305-cat_1

VIRSorter_NODE_433_length_2253_cov_3_42233-cat_2 VIRSorter_NODE_335_length_2021_cov_4_10391_GC021842_GC021842-cat_2

VIRSorter_NODE_138_length_3112_cov_4_00791-cat_2

VIRSorter_NODE_1458_length_1041_cov_2_11722_GC021830_GC021830-cat_2

VIRSorter_NODE_42_length_4096_cov_4_64369-cat_1

VIRSorter_NODE_76_length_2941_cov_3_10859_ID_151_GC022959_GC022959-cat_2

VIRSorter_NODE_590_length_1526_cov_7_29262_GC021830_GC021830-cat_2

VIRSorter_NODE_271_length_4659_cov_16_1942-cat_2

VIRSorter_NODE_54_length_4664_cov_9_37127-cat_2

VIRSorter_NODE_407_length_2846_cov_138_023_GC021836_GC021836-cat_1

VIRSorter_NODE_1721_length_1996_cov_5_9359-cat_2

VIRSorter_NODE_428_length_2323_cov_3_73776-cat_2

VIRSorter_NODE_356_length_2384_cov_8_9935-cat_2

VIRSorter_NODE_332_length_2175_cov_10_2507-cat_2

VIRSorter_NODE_1147_length_1321_cov_3_40756-cat_1

VIRSorter_NODE_100_length_4424_cov_7_35335-cat_2

VIRSorter_NODE_1703_length_1463_cov_2_22872-cat_2

VIRSorter_NODE_366_length_3576_cov_8_32009_GC021836_GC021836-cat_2

VIRSorter_NODE_725_length_1855_cov_10_6147-cat_2

VIRSorter_NODE_1238_length_1327_cov_2_0664-cat_2

VIRSorter_NODE_672_length_1295_cov_4_3514-cat_2 VIRSorter_NODE_79_length_6354_cov_62_2409-cat_2

VIRSorter_NODE_78_length_6260_cov_45_9512-cat_2

VIRSorter_NODE_46_length_6519_cov_318_065-circular-cat_2

VIRSorter_NODE_74_length_6662_cov_29_5326-circular-cat_2

VIRSorter_NODE_48_length_6214_cov_694_649-circular-cat_2

VIRSorter_NODE_85_length_6320_cov_501_915-circular-cat_2

VIRSorter_NODE_163_length_3745_cov_46_9332-cat_2

VIRSorter_NODE_116_length_6700_cov_102_421-circular-cat_2

VIRSorter_NODE_127_length_6304_cov_169_211-circular-cat_1

VIRSorter_NODE_20_length_6493_cov_22_3178-circular-cat_1

Microviridae~Bog1249_12

VIRSorter_NODE_30_length_6450_cov_44_4565-circular-cat_1

VIRSorter_NODE_109_length_4750_cov_17_446-cat_1 VIRSorter_NODE_1045_length_1845_cov_5_55713-cat_2

VIRSorter_NODE_108_length_8316_cov_472_248-cat_2

VIRSorter_NODE_64_length_5899_cov_14_19-cat_2

VIRSorter_NODE_487_length_1735_cov_5_00362_GC021842_GC021842-cat_2

Synechococcus~phage~S-CBS1

VIRSorter_NODE_146_length_2708_cov_2_46446_GC021842_GC021842-cat_1

VIRSorter_NODE_52_length_6051_cov_9_17124-cat_2

VIRSorter_NODE_93_length_3875_cov_7_44392-cat_2

VIRSorter_NODE_25_length_9400_cov_16_2758-cat_2

VIRSorter_NODE_113_length_5573_cov_11_161-cat_2

VIRSorter_NODE_367_length_1788_cov_5_45763-cat_1

VIRSorter_NODE_536_length_1612_cov_4_77329-cat_2

VIRSorter_NODE_79_length_6005_cov_26_2043-cat_1

VIRSorter_NODE_48_length_9440_cov_6_63527-cat_1

VIRSorter_NODE_323_length_1422_cov_4_3658-cat_2

VIRSorter_NODE_129_length_3930_cov_23_5902-cat_2

VIRSorter_NODE_560_length_1433_cov_2_40929-cat_2

VIRSorter_NODE_141_length_3439_cov_8_81707-cat_2

VIRSorter_NODE_743_length_1379_cov_4_01382-cat_2

VIRSorter_NODE_976_length_1608_cov_2_55781-cat_2

VIRSorter_NODE_239_length_3424_cov_8_63012-cat_2

VIRSorter_NODE_51_length_4072_cov_6_41852_GC021842_GC021842-cat_2

VIRSorter_NODE_337_length_2689_cov_3_29939-cat_2

VIRSorter_NODE_730_length_1731_cov_6_55562-cat_1

VIRSorter_NODE_659_length_2336_cov_3_83267-cat_2

VIRSorter_NODE_1984_length_1222_cov_4_24629-cat_2

VIRSorter_NODE_883_length_1252_cov_3_38638-cat_2

VIRSorter_NODE_71_length_4503_cov_55_2632_ID_1234741-cat_2

Synechococcus~phage~S-RIP1

VIRSorter_NODE_279_length_5367_cov_4_5949-cat_2

VIRSorter_NODE_86_length_5830_cov_19_66-cat_2

VIRSorter_NODE_31_length_7440_cov_34_4581-cat_2

VIRSorter_NODE_955_length_2525_cov_5_13235-cat_2

VIRSorter_NODE_19_length_25132_cov_20_3998-cat_1

VIRSorter_NODE_2088_length_1191_cov_5_38779-cat_1

VIRSorter_NODE_3496_length_1469_cov_3_86782-cat_2 Riemerella~phage~RAP44

VIRSorter_NODE_185_length_4953_cov_6_15402-cat_1

VIRSorter_NODE_1708_length_1576_cov_4_20547-cat_2

VIRSorter_NODE_44_length_7557_cov_10_863-cat_2

VIRSorter_NODE_233_length_4482_cov_10_1639-cat_2

Pseudomonas~phage~AF VIRSorter_NODE_552_length_2485_cov_4_35756-cat_2

VIRSorter_NODE_192_length_3929_cov_3_8676-cat_1

VIRSorter_NODE_322_length_4472_cov_38_5126_GC021836_GC021836-cat_1

VIRSorter_NODE_538_length_2956_cov_5_02813-cat_1

VIRSorter_NODE_992_length_1573_cov_4_92848-cat_2

VIRSorter_NODE_16_length_23516_cov_138_53-cat_2

VIRSorter_NODE_151_length_1878_cov_116_108_ID_301_GC022959_GC022959-cat_1

VIRSorter_NODE_85_length_8370_cov_15_7844-cat_1

VIRSorter_NODE_15_length_11161_cov_176_621_GC021830_GC021830-cat_1

VIRSorter_NODE_2781_length_1390_cov_3_66794-cat_1

VIRSorter_NODE_1540_length_1662_cov_4_40252-cat_2

VIRSorter_NODE_14_length_17500_cov_14_0744-cat_2

VIRSorter_NODE_300_length_4134_cov_17_8536-cat_2

VIRSorter_NODE_6_length_27203_cov_21_9593-cat_2

Enterobacter~phage~Tyrion VIRSorter_NODE_5_length_48144_cov_42_8117-circular-cat_2

VIRSorter_NODE_10_length_41314_cov_88_2574-circular-cat_2 VIRSorter_NODE_559_length_1988_cov_2_74359-cat_2

VIRSorter_NODE_536_length_1343_cov_4_53318-cat_2

Clostridium~phage~phiCD146 Bordetella~virus~BPP1

VIRSorter_NODE_27_length_13648_cov_10_3894-cat_1

VIRSorter_NODE_16_length_5962_cov_37_6794_ID_31_GC022959_GC022959-cat_2

VIRSorter_NODE_29_length_18268_cov_15_4076-cat_1

VIRSorter_NODE_110_length_5017_cov_16_0623-cat_1

Cyanophage~NATL1A-7

VIRSorter_NODE_51_length_6048_cov_17_5609-cat_1

VIRSorter_NODE_218_length_2204_cov_4_58862-cat_2

VIRSorter_NODE_3_length_38384_cov_31_6491_GC021830_GC021830-cat_2

VIRSorter_NODE_27_length_8525_cov_17_6017-cat_2

VIRSorter_NODE_2_length_41612_cov_24_7299-cat_1

Escherichia~phage~TL-2011b

VIRSorter_NODE_361_length_3416_cov_6_31087-cat_1

VIRSorter_NODE_91_length_5972_cov_36_3963-cat_2

VIRSorter_NODE_376_length_1948_cov_3_65526-cat_2

Synechococcus~phage~S-CBS3

VIRSorter_NODE_48_length_6491_cov_22_8788-cat_2

VIRSorter_NODE_116_length_5103_cov_33_1303-cat_2

VIRSorter_NODE_28_length_11201_cov_16_625-cat_2

Pseudomonas~phage~phiPSA2

VIRSorter_NODE_253_length_2462_cov_8_22893-cat_2

VIRSorter_NODE_810_length_1414_cov_2_10995_GC021842_GC021842-cat_1 VIRSorter_NODE_285_length_4031_cov_5_88012-cat_2

VIRSorter_NODE_245_length_3176_cov_5_55082-cat_2

VIRSorter_NODE_11_length_22035_cov_75_4007-cat_2

Xanthomonas~phage~Xp15

VIRSorter_NODE_399_length_2511_cov_12_2247-cat_2

VIRSorter_NODE_51_length_6198_cov_78_8288_ID_1234693-cat_1

VIRSorter_NODE_1872_length_1092_cov_1_13005-cat_2

VIRSorter_NODE_1511_length_1484_cov_3_12722-cat_2

VIRSorter_NODE_1195_length_1353_cov_8_8895-cat_2

VIRSorter_NODE_69_length_7221_cov_10_606-cat_2

VIRSorter_NODE_555_length_1364_cov_3_66667_GC021836_GC021836-cat_2

VIRSorter_NODE_3_length_41166_cov_1412_67-circular-cat_2

VIRSorter_NODE_23_length_13188_cov_34_6875-cat_1

VIRSorter_NODE_9_length_34390_cov_51_9275-cat_2

VIRSorter_NODE_20_length_21130_cov_32_3079-cat_2

VIRSorter_NODE_10_length_37636_cov_94_1194-cat_2

VIRSorter_NODE_253_length_5676_cov_8_48509-cat_1

VIRSorter_NODE_174_length_3625_cov_24_6435-cat_2

VIRSorter_NODE_63_length_10962_cov_10_2398-cat_1

VIRSorter_NODE_4_length_95574_cov_53_2034-cat_2

VIRSorter_NODE_44_length_12771_cov_25_968-cat_2

VIRSorter_NODE_93_length_5511_cov_39_8675-cat_1

VIRSorter_NODE_1_length_63229_cov_49_3797-cat_2

VIRSorter_NODE_1_length_62610_cov_351_397-cat_2

VIRSorter_NODE_428_length_1474_cov_31_388-cat_2

VIRSorter_NODE_10_length_8122_cov_44_0481_GC021842_GC021842-cat_2

VIRSorter_NODE_84_length_7309_cov_13_3547-cat_2

VIRSorter_NODE_113_length_3110_cov_6_34454-cat_1

VIRSorter_NODE_156_length_3846_cov_90_3208-cat_2

VIRSorter_NODE_3_length_52558_cov_119_096-cat_2

VIRSorter_NODE_58_length_2924_cov_7_11907-cat_1

VIRSorter_NODE_136_length_1738_cov_8_4401-cat_2 VIRSorter_NODE_119_length_3091_cov_3_65196-cat_2

VIRSorter_NODE_71_length_5867_cov_6_41969-cat_2

VIRSorter_NODE_3_length_41933_cov_233_011-cat_2

VIRSorter_NODE_258_length_3503_cov_8_13689-cat_2

VIRSorter_NODE_321_length_1425_cov_3_60831-cat_1

VIRSorter_NODE_3_length_47484_cov_53_1945-cat_2

VIRSorter_NODE_6_length_18914_cov_22_0195-cat_2

VIRSorter_NODE_58_length_6232_cov_20_7313-cat_2 family were identified most frequently (Fig. 1B) . This is partly because it is one of the largest viral families and is made up of at least 29 genera, many of which are transmitted through the fecal-oral or respiratory route (28) . Most of these infections were in pools of individuals less than 20 years of age (Fig. 1C) . This finding is consistent with previous findings from Cameroon, where a high prevalence of EV in children was reported using PCR-based approaches (65) . Furthermore, most of the EVs here were of genotype C, also supporting a recent study that identified a high rate of EV Cs in the northern regions of Cameroon (31) . Therefore, the high prevalence of EV C is probably national. However, the absence of genetic relatedness between the Cameroonian human EV strains and animal strains (from chimp and gorilla [66] ) does not indicate interspecies transmission of EVs from animals. Additionally, we report for the first time (nearly) complete genomes of picornaviruses of the genera Parechovirus, Cardiovirus, Hepatovirus A, and Cosavirus from Cameroonian patients. This broadens the range of picornaviruses found in the Cameroonian population, indicating that picornaviruses might be playing a vital role in gastroenteric viral infection in the Cameroonian population, especially given that most of these were from samples of sick children.

Rotavirus A (RVA), a common viral gastroenteritis-causing agent, was identified only in a limited number of pools. This was previously observed in Cameroon, and possible reasons for the low prevalence could include the acute nature of rotavirus infections or seasonal changes in rotavirus infections (6) . Of note, rotavirus vaccination was introduced in Cameroon in April 2014, coinciding with the period of sample collection of this study (February to September 2014); however, the vaccination campaign had not started in the sampling locations within this period, and therefore, the result represents a prevaccination rotavirus prevalence status. The identified rotavirus strain showed 3% nt differences with the vaccine strain, further suggesting that this was a wild-type RVA strain, rather than a vaccine-derived strain.

Uncommon human gastroenteric virus: mammalian orthoreovirus (MORV). This first MORV strain from Cameroon showed topological incongruence in its phylogeny, thereby pointing to possible reassortment events in the past. The phylogenetic clustering of some segments to strains from animals (rodents and bats) could be an indication of a zoonotic event or could also be due to the absence of related strains in databases from an unknown host. Given that this strain was from a pool of samples from two children suffering from severe diarrhea, it is not unlikely that this strain might have contributed to the disease. Therefore, MORV might be playing a greater role in diarrheal diseases in this region than was previously known. Hence, extensive epidemiological studies in different regions and in different hosts are required to fully delineate the prevalence, genomics, and interspecies transmissibility of MORV.

Viruses not (yet) associated with gastroenteritis: Picobirnaviridae, smacovirus, and Anelloviridae. Apart from the above-mentioned gastroenteritis-related viruses, several other viruses with unelucidated gastroenteric roles were also identified in this study. First, we observed fewer reads of picobirnaviruses (PBVs) in pools from children than in adults. Previous studies also detected a relatively low percentage of children with PBVs (67, 68) . This therefore adds up to the notion that PBVs are likely to be absent in infants and young children and only start to increase with age and potentially a changing diet, though this needs to be further proven (69, 70) . Interestingly, the genetic relatedness of a human picobirna-like virus with one that was found in a bat pool from the same region suggests an interspecies transmission. However, these picobirna-like sequences are translated using an alternative mitochondrial codon, indicating that their hosts may not be mammals. A principal component analysis of the codon usage bias of different known mitochondrial genome sequences, mitoviruses, and PBVs seems to suggest that they may have the same lifestyle as mitoviruses known to infect fungal mitochondria (71) . However, the recent identification of a bacterial ribosomal binding site in PBV genomes suggests prokaryotes as a potential host (72) . Given that the mitochondria have descended from ancient eubacterial endosymbionts (73) , this may explain the clustering of these PBVs with mitoviruses. Therefore, the question about the true host of PBVs remains controversial.

Second, for the first time, two strains of African smacovirus (SCV) were identified in Cameroonian samples. Their genetic relatedness to a chimpanzee strain (isolated from a captive chimp in a zoo in San Francisco) and a strain from a child from the United States (54, 55) indicates either an interspecies transmission event or the presence of a shared viral host in both humans and chimps. Although the role of smacovirus in gastroenteritis has not been elucidated, their presence in cases of unexplained diarrhea in French patients seems to indicate a potential role in gastroenteritis (54) ; hence, these could be instances of interspecies transmissions.

The percentages of pools positive for anelloviruses were higher in age categories of children and the old and lower for the middle-aged groups. Given the well-established notion that infants and the elderly have reduced immunity (74, 75) , this could be in line with previous studies that suggest a link between the burden of anelloviruses and host immune competence (76) (77) (78) . Despite their ubiquity, Anelloviridae have an undefined implication in hosts' health and are thought to be probably asymptomatic (harmless) or even beneficial. However, they have been associated with hepatitis, pulmonary diseases, hematologic disorders, myopathy, and lupus, but it is not clear if their presence is the cause or the result of disease progression (79) (80) (81) (82) .

Human viruses and interspecies transmission from bats. In bats from the same area, we were able to identify gastroenteritis-related and nonrelated viruses. Here, the corresponding viruses identified from the families Astroviridae (astrovirus), Caliciviridae (sapovirus), and Reoviridae (RVA) are genetically diverse from those identified in bats from the same region, indicating no evidence of recent interspecies transmissions between bats and humans (63) . However, genetic relatedness of human MORV to animal strains showed the possibility of zoonosis between humans and not only bats but animals in general. Additionally, the presence of some Cameroonian strains of SCV and PBV in bats or other animals would indicate interspecies transmissions if their infectivity in these animals is fully elucidated.

Human and bat phageome. In this study, we detected a huge phage community with a great diversity beyond the range of known bacteriophages in reference databases, potentially representing the gut microbiome diversity in the patients (83, 84) . Overall, this further supports the idea that the full phageome richness is still to be completely elucidated (85) . Furthermore, network analysis indicates the presence of completely novel phage groups and that phage genera in the gut microbiota might be shared between humans and bats.

Conclusion. Several diverse viruses were discovered in the gut virome of Cameroonians. Some of these were already known to be the causative agent of gastroenteritis, whereas others are likely to be the cause of gastroenteric problems in the patients. Further screening of patients for these viruses will be needed to establish their prevalence in the population, allowing for more appropriate measures and treatment and prevention of viral gastroenteritis. Also, to be able to completely elucidate the role of the novel viruses like pecovirus and smacovirus, more studies are required. Further attention should also be given to newly identified viruses (for example, MORV) and their potential as emerging pathogens in the human population.

Ethical authorization. Ethical authorization for the use of human samples was obtained from the Cameroon National Ethics Committee, Yaoundé. All human experiments were performed in accordance with the Ministry's National Ethics Committee guidelines.

Sample collection and preparation. Human fecal samples were collected between February and September 2014, after informed consent was obtained from patients in two different hospitals (Lysoka Health District and Kumba District Hospital of the Southwest region of Cameroon). This region was chosen because here bats are hunted, sold, and eaten. Diarrheic patients and/or people who came into contact with bats directly (by eating, hunting, or handling) or indirectly (if a family member was directly exposed to bats) were eligible for sampling. A total of 221 samples were collected from subjects between age 0 and Ͻ3 years (age group A, 80 samples), 3 and Ͻ20 (age group B, 63 samples), 20 and Ͻ60 (age group C, 65 samples), and 60 and older (age group D, 13 samples). All the samples were from people who had symptoms of gastroenteritis, except 2 from age group C who had contact with bats. Samples were then placed into labeled tubes containing universal transport medium (UTM), placed on dry ice, and stored at Ϫ20°C, until being shipped to the Laboratory of Viral Metagenomics, Leuven, Belgium. The samples were stored at Ϫ80°C until used (63) .

Fecal samples were first diluted using UTM, and equal volumes of the dilutions were pooled based on the location, age, and bat contact status (direct, indirect, or none). Each pool contained two to five samples, and for the different age groups (A to D) we had 22, 17, 20, and 4 pools, respectively . The pools were then treated according to the NetoVIR protocol (86) . Briefly, the pools (10% [wt/vol] fecal suspensions) were homogenized for 1 min at 3,000 rpm with a Minilys homogenizer (Bertin Technologies) and filtered using an 0.8-m PES filter (Sartorius). The filtrate was then treated with a cocktail of Benzonase (Novagen) and micrococcal nuclease (New England Biolabs) at 37°C for 2 h to digest free-floating nucleic acids. Total nucleic acids (both RNA and DNA) were extracted using the QIAamp viral RNA minikit (Qiagen) according to the manufacturer's instructions but without addition of carrier RNA to the lysis buffer. First-and second-strand synthesis and random PCR amplification for 17 cycles were performed using a slightly modified whole-transcriptome amplification (WTA2) kit procedure (Sigma-Aldrich). WTA2 products were purified with MSB Spin PCRapace spin columns (Stratec), and the libraries were prepared for Illumina sequencing using a slightly modified version of the Nextera XT library preparation kit (Illumina), which is described in detail in reference 86. Samples were pooled in an attempt to obtain an average of approximately 10 million paired-end reads per pool. Sequencing was performed on a NextSeq 500 high-output platform (Illumina) for 300 cycles (2 ϫ 150-bp paired ends).

Genomic and phylogenetic analysis. NGS reads were analyzed as described in the work of Yinda et al. (20, 63) . Briefly, raw reads were trimmed using Trimmomatic (parameters: HEADCROP: and FastUniq to remove identical reads. The de novo assembly or reads and annotation of reads were performed using SPAdes (with the meta flag) and Diamond (with the sensitive option using the GenBank nonredundant database), respectively (61, 87, 88) . Open reading frames (ORFs) of contigs of interest were identified and further analyzed for conserved motifs in the amino acid sequences using NCBI's conserved domain database (CDD) (89) . Nucleotide and amino acid alignments of viral sequences were done with MUSCLE implemented in MEGA7 (90) or MAFFT (91) . Substitution models were determined using ModelGenerator (92) , and phylogenetic trees were constructed using RAxML (93) , with the autoMRE flag, which enables a posteriori bootstrapping analysis. All trees were visualized in FigTree (http://tree.bio.ed.ac.uk/software/figtree/) and midpoint rooted for purposes of clarity.

Phageome analysis. Contig annotation with DIAMOND is dependent on the accuracy of the database used, and in most databases, phages are poorly annotated. However, VirSorter uses a manually curated database of virus reference genomes augmented with metagenomic viral sequences sampled from freshwater, seawater, and human gut, lung, and saliva. Hence, for further identification of bacteriophages, scaffolds Ͼ1 kb were classified using VirSorter (decontamination mode [60] ). Only scaffolds assigned to categories 1 and 2 were considered bacteriophage contigs and were filtered for redundancy at 95% nucleotide identity over 70% of the length using Cluster Genomes (94) . Then, trimmed reads from each pool were mapped using Bowtie 2 (95) to the bacteriophage contigs, and the generated BAM files were filtered to remove reads that aligned at Ͻ95% identity using BamM (http://ecogenomics.github .io/BamM/). Abundance tables were obtained and normalized for total number of reads of each sample. For the richness comparison, Mann-Whitney tests were used, and for the clustering, an Adonis test was performed. All downstream analyses were done in R (96) using the vegan package (97) . Furthermore, to identify the potential corresponding bacterial host, a database of these contigs was made to which a nucleotide BLASTN search (100% identity without gaps) was performed using a fasta file of CRISPR sequences (98) as query. These sequences correspond to different bacterial hosts, and their presence in the phage genome highlight the potential host of the phage.

To see if the phage community of these humans is related to those of the bats from the same locality, a visualization of the network of both human and bat phageomes was performed using vConTACT (62) . Initially, proteins were predicted using Prodigal (99) , and combined with the Viral RefSeq of archaeal and prokaryotic predicted proteins. A database was generated from the contigs of bat pools, human pools, and viral RefSeq proteins, and BLASTp was performed against the combined proteins. The output of blast was used to run vConTACT, and the output network was visualized in Cytoscape (100).

Data availability. All sequences were deposited in GenBank under the following accession numbers: MH608285 to MH608287 and MH933752 to MH933860 (details in Table S3 ). Raw reads were submitted to the NCBI's Short Read Archive (SRA) under the project ID PRJNA491626.

Supplemental material for this article may be found at https://doi.org/10.1128/ mSphere.00585-18. 

EF051629_HPeV-1/BNI-788St/DEU/xx

JN867764/HCoSV/A13-NP6/NPL

GU985458_Mink_AstV-SMS AY720892_HumanAstV5-Goiania/GO/12/94/Brazil

FJ890351_Sea_lionAstV1 Human-AstV_CMRHP35D

HQ889774_PigeonANV-SH10 Human-AstV_CMRHP6

Z25771_HumanAstV-Newcastle Human-AstV_CMRHP46

Human-AstV_CMRHP3 FJ973620_HumanAstV-VA1

ITA FJ402983_HumanAstV-MLB1-WD0016

JX857869_HumanAstV-VA4/human/Nepal/s5363

HQ916317_BovineAstV/B76-2/HK

FJ890352_Sea_lionAstV2 Z25771_HumanAstV-Newcastle HQ916313_BovineAstV/B18/HK

HQ916317_BovineAstV/B76-2/HK

Human-AstroV_CMRHP35D Human-AstroV_CMRHP46

AY038599.2_CaliciVirus/Human/NLV

U07611.2_CaliciVirus/Human/NLV

FJ498786_Pig/F19-10/CAN/2007/GVIII

KJ858687_Chimp/IJC09

GU230162_Pig/F8

Kumba_picobirna-like virus_CMRHP21A

AHX00960_Human_picobirnavirus ANS53886_Picobirnavirus_wolf

BAJ53289_Human_picobirnavirus SHWC01c3537_Shahe_picobirna-like_virus_2

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G31_RVA/Bat-wt/CMR/BatLi08/2014/G31P [42] G30_RVA/Bat-wt/CMR/BatLi10/2014/G30P [42] G3_RVA/Bat-wt/CHN/MYAS33/2013_G3P [10] G25_RVA/Bat-wt/KEN/KE4852/07/2007/G25P [6] G21_RVA/Cow-wt/JPN/Azuk-1/2006/G21P [29] G13_RVA/Horse-tc/GBR/L338/1991/G13P [18] G3_RVA/Human-tc/JPN/AU-1/1982/G3P [39] G15_RVA/Cow-tc/IND/Hg18/1995/G15P [21] G30_RVA/Bat-wt/CMR/BatLi09/2014/G30P [42] G22_RVA/Turkey-tc/DEU/03V0002E10/2003/G22P [35] G8_RVA/Human-tc/IND/69M/1980/G8P [4] 10G18_RVA/Pigeon-tc/JPN/PO-13/1983/G18P [17] G20_RVA/Human-wt/ECU/Ecu534/2006/G20P [28] G26_RVA/Pig-wt/JPN/TJ4-1/2010/G26P [x] G14_RVA/Horse-tc/USA/FI23/1981/G14P [12] G1_RVA/Human-wt/CMR/CMRHP55/2014/G1P [8] G7_RVA/Turkey-tc/IRL/Ty-3/1979/G7P [17] G3_RVA/Bat-tc/MSLH14/2012/G3P [3] G6_Cow G25_RVA/Bat-wt/CMR/BatLy03/2014/G25P [43] G19_RVA/Chicken-tc/GBR/Ch-1/197x/G19P [17] G1_RVA/Human-tc/USA/Wa/1974/G1P[1]A8 G10_RVA/Human-tc/GBR/A64/1987/G10P [14] G9_RVA/Human-tc/USA/WI61/1983/G9P[1]A8 G30_RVA/Bat-wt/CMR/BatLy17/2014/G30P [47] G27_RVA/SugarGlider-tc/JPN/SG385/2012/G27P [36] G24_RVA/Cow-tc/JPN/Dai-10/2007/G24P [33] G11_RVA/Pig-tc/MEX/YM/1983/G11P[9]7 G16_RVA/Mouse-tc/USA/EW/XXXX/G16P [16] ACKNOWLEDGMENTS C.K.Y. was supported by the Interfaculty Council for Development Cooperation (IRO) from the KU Leuven. N.C.-N. and L.B. were supported by the Flanders Innovation & Entrepreneurship (VLAIO). This work was supported by KU Leuven grant EJX-C9928-StG/15/020BF. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.C The authors declare no competing financial interests.