Quantiﬁcation and Genotyping of Aichi Virus 1 in Water Samples
in the Kathmandu Valley, Nepal
Received: 24 December 2016 / Accepted: 2 February 2017 / Published online: 9 February 2017
Ó Springer Science+Business Media New York 2017
Abstract Aichi virus 1 genomes were detected by quan-
titative PCR in groundwater from shallow dug (10/22) and
tube wells (1/15), river water (14/14), and sewage (1/1),
with the maximum concentration of 4.0 9 10
Nucleotide sequencing analysis demonstrated the preva-
lence of genotype B in the virus positive samples.
Keywords Aichi virus 1 Á Groundwater Á Kathmandu
Valley Á Picornaviridae
Aichi virus 1 (AiV-1) is a single-stranded, positive-sense
RNA virus that belongs to the genus Kobuvirus in the
family Picornaviridae (Reuter et al. 2011). AiV-1 is con-
sidered as a potential causative agent of viral gastroenteritis
in humans, primarily transmitted through contaminated
food and water (Reuter et al. 2011).
Recent environmental studies have demonstrated a high
prevalence of AiV-1 in various types of water samples,
such as raw and treated sewage, reclaimed water, and river
water (Kitajima and Gerba 2015). Quantitative PCR
(qPCR) was employed in some of these studies, obtaining
quantitative data on the prevalence of AiV-1 in water,
whereas nucleotide sequencing analysis combined with
conventional PCR was used to determine the distribution of
AiV-1 genotypes (Kitajima and Gerba 2015). Considering
that a limited number of studies have been conducted so far
on the AiV-1 detection in water and most of them were
conducted in developed countries, it is highly recom-
mended to study the prevalence of AiV-1 in water samples
in developing countries.
The Kathmandu Valley, the capital city area of Nepal, is
well recognized as an area where waterborne diseases are
one of the most serious public health concerns, partially
because of low coverages of proper drinking water and
wastewater treatment systems. People in the valley mainly
depend on groundwater for their domestic water use. Since
contamination of groundwater by waterborne pathogens
could pose a health risk to humans, their prevalence in
water needs to be surveyed prior to the risk estimation.
However, a limited number of studies in Nepal have been
reported on the prevalence of waterborne pathogens, such
as pathogenic bacteria (Inoue et al. 2014; Tanaka et al.
2012), protozoa (Haramoto et al. 2011; Ono et al. 2001,
Shrestha et al. 2015, 2016), and viruses (Haramoto et al.
2011), in water samples.
This study aimed to determine the prevalence of AiV-1
genomes in various types of water samples, including
groundwater, in the Kathmandu Valley. The ﬁrst water
sampling was conducted in the wet season (August–
September) of 2009 (Haramoto et al. 2011), followed by
additional sampling campaigns in both wet (August 2010)
and dry seasons (May 2011). During the sampling periods,
a total of 53 water samples were collected from nine
shallow dug wells (n = 22), six shallow tube wells
(n = 15), eight sites along the Bagmati River and its
tributaries (n = 14), a tap in a house supplied with tanker
water (n = 1), and a sewage pipe (n = 1).
Nucleotide Sequence Accession Numbers The nucleotide
sequences determined in this study have been deposited in the
GenBank database under accession numbers LC200515–LC200529.
& Eiji Haramoto
Interdisciplinary Center for River Basin Environment,
Graduate Faculty of Interdisciplinary Research, University of
Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511,
Division of Environmental Engineering, Faculty of
Engineering, Hokkaido University, North 13 West 8, Kita-ku,
Sapporo, Hokkaido 060-8628, Japan
Food Environ Virol (2017) 9:350–353