By Kelly A. Reynolds, MSPH, PhD
A new virus has been isolated from environmental waters and sewage and associated with acute diarrheal disease on every continent. Clusters of cases in newborn babies and infections in children suggest the virus targets the immunocompromised. More information is needed relative to the waterborne route, occurrence, public health threat and treatment of these novel organisms.
Despite the widespread prevalence of diarrhea, identification of the causative agents in gastrointestinal disease is not accomplished for up to half of all cases. New tools of genetic analysis are helping to reduce the gap in characterizing etiological agents of disease, aiding in the discovery of new organisms with potential links to adverse health effects.
In 2009, researchers were working to identify causative agents of diarrheal disease in 141 pediatric stool samples from children in northern California. After all tests were negative for common diarrheal agents, researchers discovered and genetically sequenced a previously unidentified organism. Results indicated this new virus had a high percentage of genetic relatedness to Aichi virus, another recently identified member of the Picornaviridae family that is part of the genus Kobuvirus. This virus was definitely different than Aichi and worthy of a new genus. The genus was subsequently named Klassevirus (for Kobu-Like viruses Associated with Stool and Sewage).
Around this same time period, genetic sequencing identified similar viruses that shared approximately 90 percent of the same genomic nucleotide identity with klasseviruses. These were called Salivirus (from Stool Aichi-LIke virus). The genome of this new virus also shared a high percentage of similarity with the Picornaviridae family but was clearly distinct from other well-known family members, including rhinovirus, poliovirus and enteroviruses. Currently, in the genus Salivirus, there is only one species and two serotypes of the virus: salivirus A1 and A2. The second type of salivirus was first identified from wastewater in Thailand around 2012.1
Prevalence in feces and the environment
Picornaviruses cause illnesses ranging from mild (i.e., the common cold and diarrhea) to serious or fatal (i.e., paralysis, meningitis and respiratory failure). Scientists are still evaluating whether or not saliviruses cause human disease. While the virus has been isolated from both humans and chimpanzees and up to nearly nine percent of feces from ill humans, larger studies are needed to definitively determine clear disease outcomes following exposure.2
Numerous small-scale studies have found saliviruses and klasseviruses in feces of ill individuals around the globe. A study of 216 fecal samples from children with diarrhea in China resulted in an isolation rate of four percent (9/216) whereas a survey of stool from 96 healthy children resulted in zero positives.3
From 2015-2016, researchers in Thailand surveyed children hospitalized in Chang Mai with acute gastroenteritis (i.e., diarrhea) using molecular screening of fecal samples. Salivirus was detected in a small percentage of samples (one out of 229 or 0.44 percent). While the number may seem low, this was the first report of the virus infecting young children in the Southeast Asian country.1
Perhaps one of the largest epidemiological studies of the suspected pathogen were conducted in India.4 A total of 468 fecal samples were collected along with clinical and demographic details. Six (1.2 percent) were positive for salivirus and from pediatric patients with diarrheal illness. This study took the extra step of extensively surveying the stool for other enteric viruses including rotavirus, norovirus, astrovirus, sapovirus, adenovirus, human parechovirus, aichivirus, enterovirus, bocavirus and common bacterial agents of diarrheal illness, including pathogenic E. coli, Salmonella, Shigella and Vibrio. No other agents were found.
Like other human enteroviruses, salivirus appears to be waterborne. It is frequently isolated from rivers and found to be ubiquitous in sewage. One survey of Arizona wastewaters detected the virus in 15 percent (7/47) of samples collected monthly over a one-year time frame. Concentrations averaged 105 in influent and 104 in effluent.5 A previous study of wastewater in Japan found a 93 percent (13/14) positive rate in raw sewage and 29 percent (4/14) in treated wastewater supplies.6 Consistent with other picornaviruses, salivirus characteristics suggest a fecal-oral route of transmission.
Suspected outbreaks and severe illness
One of the earliest suspected outbreaks of salivirus occurred in a cluster of newborn babies at a neonatal hospital in Hungary in 2013. Concentrations in stools were greater than a billion viruses per gram. All of the infants were under the age of five days and presented with symptoms of diarrhea. Additionally, 40 percent showed symptoms of fever, vomiting and loss of appetite.7
In the India cohort mentioned earlier, symptoms ranged from mild to severe and included diarrhea in all six patients, fever in five and vomiting in one. The population was young (mean age of 8.5 months) and although all recovered fully, their illness was severe enough to require an average four-day stay in the hospital and intravenous treatment in two patients.
In 2018, the CDC reported an outbreak of another picornavirus, enterovirus A71, in the state of Colorado. This outbreak was linked to severe neurologic disease in more than 44 children.8 Symptoms in 14 additional cases included acute flaccid myelitis as evidenced by a sudden onset of muscle weakness in the arms or legs. (Symptoms are reminiscent of polio infections from the early 20th century another enterovirus disease.) A similar health effect was seen in Nigerian and Tunisian children suffering non-polio acute flaccid paralysis (AFP), where salivirus was found in the stool samples of ill children but not in healthy controls.
Another case of severe illness related to salivirus is notable. In this single case, human salivirus/klassevirus was isolated from respiratory secretions—a site not previously identified to harbor the viruses. While the child was co-infected with adenovirus, the infection was surprisingly severe, resulting in death. Such a severe outcome lead researchers to question if the co-infection with salivirus prompted the increasingly negative effect.9
In the most recent (2013-2014) surveillance of waterborne disease outbreaks associated with drinking water in the United States, none were definitively characterized as salivirus. Five percent of reported outbreaks, however, representing two out of 42 events, were reported as unknown etiology. Viruses, such as the salivirus, are not routinely targeted for testing and thus may be missed in cases where no pathogen is identified.
Evidence continues to grow relative to the widespread occurrence and potentially pathogenic nature of saliviruses. Any new emergence of a pathogen is a concern as it reminds us of the evolutionary nature of microbes and how quickly their genomes can adapt to exhibit increasing virulence factors.
Although more monitoring of salivirus disease associations will continue, other studies are needed to evaluate water treatment efficacy for these new organisms. Some Picornaviridae survive wastewater treatment processes. How salivirus prevalence, survivability and treatment resistance relates to public health risk is still a question.
(1) Kumthip K, Khamrin P, Yodmeeklin A, Maneekarn N. Salivirus infection in children with diarrhea, Thailand. Arch Virol. 2017;162(9):2839-2841. doi:10.1007/s00705-017-3435-9
(2) Reuter G, Pankovics P, Boros Á. Saliviruses-the first knowledge about a newly discovered human picornavirus. Rev Med Virol. 2017;27(1):e1904. doi:10.1002/rmv.1904
(3) Shan T, Wang C, Cui L, et al. Picornavirus Salivirus/Klassevirus in Children with Diarrhea, China. Emerg Infect Dis. 2010;16(8):1303-1305. doi:10.3201/eid1608.100087
(4) Itta KC, Patil T, Kalal S, Ghargi KV, Roy S. Salivirus in children with diarrhoea, western India-Clinical Key. Int J Infect Dis. 2016;52:14-15.
(5) Kitajima M, Iker BC, Rachmadi AT, Haramoto E, Gerba CP. Quantification and Genetic Analysis of Salivirus/Klassevirus in Wastewater in Arizona, USA. Food Environ Virol. 2014;6(3):213-216. doi:10.1007/s12560-014-9148-2
(6) Haramoto E, Otagiri M. Prevalence and Genetic Diversity of Klassevirus in Wastewater in Japan. Food Environ Virol. 2013;5(1):46-51. doi:10.1007/s12560-012-9098-5
(7) Boros Á, Raáb M, Károly É, et al. A cluster of salivirus A1 (Picornaviridae) infections in newborn babies with acute gastroenteritis in a neonatal hospital unit in Hungary. Arch Virol. 2016;161(6):1671-1677. doi:10.1007/s00705-016-2824-9
(8) Colorado Department of Publich Health and Environment. Enterovirus. Accessed January 15, 2019.
(9) Pei N, Zhang J, Ma J, et al. First report of human salivirus/klassevirus in respiratory specimens of a child with fatal adenovirus infection. Virus Genes. 2016;52(5):620-624. doi:10.1007/s11262-016-1361-7
About the author
Dr. Kelly A. Reynolds is a University of Arizona Professor at the College of Public Health; Chair of Community, Environment and Policy; Program Director of Environmental Health Sciences and prior, Director of Environment, Exposure Science and Risk Assessment Center (ESRAC). She holds a Master of Science Degree in public health (MSPH) from the University of South Florida and a doctorate in microbiology from the University of Arizona. Reynolds is WC&P’s Public Health Editor and a former member of the Technical Review Committee. She can be reached via email at firstname.lastname@example.org