Molecular Epidemiology of Enteric Calici Viruses


Enteric caliciviruses (norovirus – NoV and sapovirus – SaV), are responsible for most food-borne gastroenteritis outbreaks worldwide. Human norovirus (NoV), is the leading cause of foodborne illness in the US, accounting for 58% of all case. In the U.S., human NoVs are listed as Category B biodefense pathogens by NIH, and are on the EPA “candidate contaminant list” for the regulation of drinking water. NoVs are highly contagious and the infectious dose is low, with an estimated medium infectious dose of 18 viral particles. The virus is shed at very high titers during peak shedding, with a load of approximately 10-11 log10 genomic copies per gram/ml in stool samples. About 20% of NoV-infected individuals do not show clinical signs, and asymptomatic individuals, such as food handlers, can be important sources of infection. Besides the fecal-oral transmission route, Human NoVs display high antigenic and genetic diversity, with over 25 genotypes within at least three genogroups (GI, II, IV).

The role of NoV as a causative agent of gastroenteritis in Africa is not well studied. However, outbreaks and sporadic cases of NoV associated gastroenteritis have been reported from some African countries. No published data is available about the epidemiology of NoV infection in Ethiopia. SaVs are important enteric pathogens that can cause diarrhea in humans and animals. SaV infects both children and adults and have been found to cause outbreaks of gastroenteritis in day-care centres, healthcare facilities and elementary schools. SaV also causes sporadic cases of acute gastroenteritis requiring hospitalization as well as symptomatic and asymptomatic infections not requiring hospitalisation. Human SaVs but not animal SaVs have also been reported in some African countries. So far no data is available about the detection of SaV in Ethiopia from humans or animals.

The major objectives of this project are:
a) Detection and characterization of human and animal NoVs and SaVs from human and animal (domestic and wild ruminants or pigs) fecal specimens from gastroenteritis outbreaks or sporadic cases in Ethiopia adjacent or nearby monitoring sites for water viral contamination, from drinking water and water sources for irrigation, and from unprocessed leafy greens (lettuce) using the water irrigation sources. We estimated that >40 calicivirus samples will be from Ethiopia.

b) Dr. Saif’s lab has historical human and animal NoV and SaV strains whose complete genomes have not been characterized. For comparison of strains from developing and developed countries, 36 such US samples will be sequenced at JCVI. Complete genome sequencing of both US and Ethiopian samples will improve our understanding of recombination frequency among caliciviruses.

The proposed study will add new knowledge to enteric calicivirus databases regarding potential virus transmission routes and strain diversity, which could be critical for the design of preventive strategies, the development of better diagnostics and future vaccine design. New strains may grow in cell culture and/or in animal models, providing research tools for pathogenesis and immunological studies.

The initial white paper submitted can be downloaded here. Since white papers are not always approved exactly as submitted, this document may not exactly describe the final form of the project. Please contact if you have any questions.

All Publications that use data generated and/or are supported by the Sequencing Center at JCVI should acknowledge the sponsor as: This project has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under contract numbers N01-AI30071 and/or HHSN272200900007C.

Investigators and Collaborators

Suman Das, PhD

Assistant Professor, J.Craig Venter Institute