Presence of Human Enteric Viruses in the Stools of Healthy Malawian 6-Month-Old Infants

Rodríguez-Díaz, Jesús*,†; Mira-Pascual, Laia*,†; Collado, Maria Carmen*,†; Endo, Akihito*; Hyöty, Heikki; Mangani, Charles§; Maleta, Kenneth§; Ashorn, Per||; Salminen, Seppo*

Journal of Pediatric Gastroenterology & Nutrition:
doi: 10.1097/MPG.0000000000000215
Original Articles: Gastroenterology

ABSTRACT: The acquisition of intestinal microbiota is essential for infants who are also in close contact with intestinal viruses. We assayed the presence of human enteric viruses in the faeces of 44 healthy breast-fed 6-month-old infants from rural Malawi. Half of the infants tested harboured enteroviruses, although the infants had no gastric symptoms, suggesting a viral community mainly composed of human asymptomatic enteroviruses.

Author Information

*Functional Foods Forum, University of Turku, Turku, Finland

Department of Biotechnology, Institute of Agrochemistry and Food Technology—Spanish National Research Council (IATA-CSIC), Valencia, Spain

School of Medicine, University of Tampere, Tampere, Finland

§Department of Community Health, College of Medicine, University, Blantyre, Malawi

||Department of International Health, School of Medicine, University of Tampere, Tampere, Finland.

Address correspondence and reprint requests to Akihito Endo, PhD, Functional Foods Forum, University of Turku, Itäinen Pitkäkatu 4A, FI-20014 Turku, Finland (e-mail:

Received 11 October, 2013

Accepted 11 October, 2013

Drs Rodríguez-Díaz and Mira-Pascual contributed equally to the article.

This work was funded by the Academy of Finland.

J.R.D. was the recipient of a JAE-DOC contract from CSIC/FSE. J.R.D., L.M., and M.C.C. were supported by Fun-C-Food CSD2007-00063 from the Consolider-Ingenio program from the Spanish Ministry of Science and Innovation. The other authors report no conflicts of interest.

Article Outline

Intestinal viruses are known to produce viral gastroenteritis, human rotaviruses and human noroviruses being the 2 major threats to the health of infants (1). Most of the studies to date have focused on elucidating whether the gut microbiota or supplementation of gut microbiota with probiotics can help fight pathogenic intestinal viruses, mostly rotavirus (2). Two independent reports have shown that the gut microbiota may not protect against pathogen intestinal viruses. Kane et al (3) used the mouse mammary tumour virus to show that the gut microbiota plays an essential role in the evasion of mouse mammary tumour virus to the immune system. In the second study, Kuss et al (4), using a poliovirus model, showed that intestinal microbiota promote enteric virus replication and systemic pathogenesis in mice. A few studies have, however, examined the total human viral populations in healthy infants (5,6). In the present study, we assayed the presence of intestinal viruses in the faeces of 6-month-old breast-fed infants from Malawi, to shed some light on the viral microbiota.

The study population comprised 44 healthy 6-month-old infants, who were enrolled in an epidemiological clinical trial assessing the effect of selected dietary interventions on early childhood growth (registration no.: NCT00524446), which has been described elsewhere (7). The trial adhered to the principles of the Declaration of Helsinki and regulatory guidelines in Malawi. Written informed consent was obtained from all of the participant mothers and the trial protocol was reviewed and approved by the College of Medicine's research and ethics committee (University of Malawi) and the ethical committee of the Pirkanmaa Hospital District, Finland.

The stool samples were collected at enrollment into the clinical trial, which started when infants were 6 months old and before the participants had started receiving any nutritional interventions. The infants were recruited in 2 close locations: Lungwena Health Centre (n = 38) and the Malindi Hospital catchment area (n = 6). The clinical characteristics and patterns of dietary intakes of the infants at enrollment are shown in Table 1.

Viral RNA and DNA were extracted from stools using the NucleoSpin RNA-DNA virus KIT (Macherey-Nagel, Bethlehem, PA). Stool suspensions (10%) were centrifuged, and the supernatants were processed as indicated by the manufacturer. RNA and DNA were finally eluted in 50 μL of RNAse-DNAse–free H2O and stored at −80°C until use. RNA was retrotranscribed using the Maxima First-Strand cDNA Synthesis Kit (Fermentas GmbH, St Leon-Rot, Germany) as per the manufacturer's instruction.

The detection and characterization of viruses were performed using a combination of several molecular techniques. Polymerase chain reaction (PCR) was used for adenovirus, whereas reverse transcription-PCR (RT-PCR) was used for detection of enterovirus, rotavirus, norovirus, and astrovirus (8,9).

Positive PCR amplifications were sequenced to confirm the results, sequence analyses were carried out with DNAMAN (version 4.0) for Windows (Lynnon BioSoft, Pointe-Claire, Canada), and sequence similarities were analysed with the BLAST program ( (10).

Complementary DNA was subjected to quantitative PCR (qPCR), with the primer pair EV1 and EV2. qPCR was performed using a LightCycler (version 2.0) system (Roche, Indianapolis, IN) and LC Fast Start DNA Master SYBR green I (Roche). The reaction mixture (10 μL) contained 5 μL of 2 times master mix, 0.5 μL of each primer (10 μmol/L), and 1 μL of cDNA. Reaction mixtures without a template were run as controls. The cycling conditions were as follows: 95°C for 10 minutes, followed by 45 cycles of 3 steps consisting of denaturation at 95°C for 10 seconds, primer annealing at 60°C for 20 seconds, and primer extension at 72°C for 20 seconds. Absolute quantification was performed after comparing the crossing points of each sample with a regression curve constructed with known amounts of control DNA. For statistical analysis, SPSS 17.0 software (SPSS Inc, Chicago, IL) was used. The χ2 test was used to establish differences in the virus prevalence between the studied groups. Comparisons among data of >2 groups of infants were done by applying the Kruskal-Wallis test. A P < 0.05 was considered statistically significant. The possible correlation between variables was studied by applying the Spearman rank correlation coefficient, and significance was established at 0.5%.

Half of the samples were positive for human enteroviruses (HuEV, 22/44, 50%) as demonstrated by nested PCR (Table 2). Gastroenteritis and diarrhoea episodes were not found at sampling time points in any of the infants harbouring enteroviruses, suggesting the “asymptomatic” presence of the enterovirus. This finding confirms the higher presence of enteroviruses in healthy infants as described in Western countries previously, but with a lower number of infants studied (5,6,11). All of the positive samples were successfully sequenced, and the sequences possessed >90% identities with known HuEV strains after BLAST analysis of the sequences (Table 2). Three of the samples (sample IDs 7, 113, and 117) were positive for strains that are included in the oral poliovirus vaccine. These positives are probably the result of recent vaccinations (12,13). Most of the positive samples could be quantified by qPCR, giving a result of 105 to 106 viral copies per gram of stool. Some positive samples gave a signal that was below the quantification limit (Table 2); this can be explained by the fact that nested PCR is usually more sensitive than direct PCR used for the quantification purposes. The statistical analyses (Table 3) showed that there were no seasonal differences in the prevalence, amounts, and genogroups of the detected enteroviruses. Infants who consumed animal milk (cows or goats) had higher tendency to harbour enteroviruses (P = 0.061).

One sample was found to be positive for rotavirus (accession no. AB807827). The sequencing of the VP7 gene amplification product showed that this sample belongs to the G1 genotype. The infant had diarrhoea at the time of sampling, and diarrhoea and fever lasted 7 and 12 days, respectively. These would be because of the rotavirus infection.

We have used a classical molecular approach to look for the most common and widespread human intestinal viruses that include adenovirus, rotavirus, norovirus, astrovirus, and entorovirus. We chose this option because metagenomic approaches were not suitable for detecting human enteric viruses: the vast majority of viruses found with these approaches in the human gut are bacteriophages and pathogenic plant viruses with a poor representation of human viruses (14,15). Hence, we can state that asymptomatic enteroviruses can be seen in healthy infants in rural Malawi.

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1. Buesa J, Rodríguez-Díaz J. Goyal S. Molecular virology of enteric viruses (with emphasis on caliciviruses). Viruses in Foods. New York:Springer; 2006. 43–100.
2. Rodríguez-Díaz J, Monedero V. Watson R, Preedy V. Probiotics against digestive tract viral infections. Bioactive Food as Dietary Interventions for Liver and Gastrointestinal Disease. San Diego:Academic Press; 2013. 271–284.
3. Kane M, Case LK, Kopaskie K, et al. Successful transmission of a retrovirus depends on the commensal microbiota. Science 2011; 334:245–249.
4. Kuss SK, Best GT, Etheredge CA, et al. Intestinal microbiota promote enteric virus replication and systemic pathogenesis. Science 2011; 334:249–252.
5. Kapusinszky B, Minor P, Delwart E. Nearly constant shedding of diverse enteric viruses by two healthy infants. J Clin Microbiol 2012; 50:3427–3434.
6. Simonen-Tikka ML, Klemola P, Suomenrinne S, et al. Virus infections among young children—the first year of the INDIS study. J Med Virol 2013; 85:1678–1684.
7. Grzeskowiak L, Collado MC, Mangani C, et al. Distinct gut microbiota in southeastern African and northern European infants. J Pediatr Gastroenterol Nutr 2012; 54:812–816.
8. Iturriza-Gomara M, Megson B, Gray J. Molecular detection and characterization of human enteroviruses directly from clinical samples using RT-PCR and DNA sequencing. J Med Virol 2006; 78:243–253.
9. Rodriguez-Diaz J, Querales L, Caraballo L, et al. Detection and characterization of waterborne gastroenteritis viruses in urban sewage and sewage-polluted river waters in Caracas, Venezuela. Appl Environ Microbiol 2009; 75:387–394.
10. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol 1990; 215:403–410.
11. Witso E, Palacios G, Cinek O, et al. High prevalence of human enterovirus a infections in natural circulation of human enteroviruses. J Clin Microbiol 2006; 44:4095–4100.
12. Fine PE, Carneiro IA. Transmissibility and persistence of oral polio vaccine viruses: implications for the global poliomyelitis eradication initiative. Am J Epidemiol 1999; 150:1001–1021.
13. Minor PD. The polio-eradication programme and issues of the end game. J Gen Virol 2012; 93 (pt 3):457–474.
14. Zhang T, Breitbart M, Lee WH, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 2006; 4:e3.
15. Reyes A, Haynes M, Hanson N, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010; 466:334–338.

enteric viruses; enterovirus; healthy infants

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