Advances in Microbiology, 2013, 3, 442-449 Published Online September 2013 (
Methods for Detection of Viruses in
Water and Wastewater
Alicja Hryniszyn1, Magdalena Skonieczna2, Jarosław Wiszniowski1
1Environmental Biotechnology Department, Silesian University of Technology, Gliwice, Poland
2Biosystems Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
Received July 3, 2013; revised August 3, 2013; accepted August 13, 2013
Copyright © 2013 Alicja Hryniszyn et al. This is an open access article distributed under the Creative Commons Attribution License,
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Viruses present in water might be harmful for human health and life. Nowadays over 100 pathogenic human virus spe-
cies occur in water polluted with sewage. Chlorination, which is the most popular disinfection method is not able to
remove easily viruses from treated water. Due to this, it’s necessary to detect viruses in water before treatment in order
to determine disinfectant dose and to ensure the sanitary safety level of treated water. The aim of this article is to review
viruses detection methods as well as the problems related to implementation of those methods in analysis of water and
wastewater samples.
Keywords: Viruses; Analytical Problems; Environmental Samples; Detection Methods
1. Introduction
Nowadays water is used for consuming, irrigation or rec-
reation. Water quality, independently of its use is very
important for human health both in developed countries
and developing countries. World Health Organization
(WHO) guidelines involving quality of drinking water
emphasizes the need of clean, void of viruses and para-
sites water, which is supplied to consumers. Polish legis-
lation does not take into consideration detection of viruses
in drinking water and sewage which are used in irriga-
tion, and recreation reservoirs. Most common human dis-
eases include acute inflammation of intestines and stom-
ach. Among main viruses, which are responsible for dis-
eases of the digestive system are rotaviruses (20% to 30%
cases), adenoviruses (5% cases), human caliciviruses
(5% to 10% cases) and astroviruses (5% cases) [1]. Some
of diseases caused by enteroviruses might cause death.
For example, among Hepatitis E Virus infected women’s
mortality rate is 20% [2]. Other diseases can lead to se-
rious complications such as inflammation of the heart
muscle, inflammation of meninges, inflammation of brain,
respiratory disorder and acute liver failure [2-4]. Basic
source of enteroviruses is feces from infected people
(viruses are excreted in big amounts, account from 105 to
1011 virus particles per gram of stool). Excreta gets to
sewage, solid waste or they can create with rainfall water
or meltwater surface outflow. Viruses can infiltrate from
surface outflow to surface water. Enteroviruses get to
human organism as a result of infected crustaceans con-
sumption, infected crop and contaminated drinking water
consumption, polluted air inhalation (aerosoles) or bath-
ing in contaminated water reservoirs. The most effective
virus removal method from water or wastewater is
ozonation. Application of concentration of residual ozone
amount to 0.51 mg/l and contact time amount 2 minutes
(in temperature 20˚C, with pH 7.2) enables Polio 1 virus
inactivation [5]. Nevertheless, the most popular disinfec-
tion method is water chlorination. The fact that water or
sewage chlorination enables bacteria removal is not
equivalent with the fact that it can eliminate viruses. For
example, in order to poliovirus total inactivation in mu-
nicipal wastewater, the concentration of residual chlorine
should be 9.0 mg/l (contact time should be 30 minutes)
but for proper sewage disinfection in case of bacteria
Salmonella lower concentration of residual chlorine is
required (from 1.0 to 2.0 mg/l) [6].
Therefore, in order to ensure drinking water/waste-
water sanitary safety, appropriate disinfectant dose and
contact time selection in treated medium, are very im-
portant analytical techniques and methods, which enable
detection of viruses. Detection of viruses in sewage and
drinking water requests detection methods which are:
sensitive, resistant for false-positive results and enabling
full automation. Moreover applied methods should be
opyright © 2013 SciRes. AiM
fast and inexpensive. Method, which fulfils all needed re-
quirements, as yet was not worked out.
2. Virus Detection Methods in Water
Virus detection methods are applied for many years in
medical diagnosis. Some of these methods were modified
in order to be utilized in analysis of environmental sam-
ples. For analysis of environmental samples were adapted
following methods: Polymerase Chain-Reaction (PCR)
[7-12], Nucleic Acid Sequence—Based Amplification
(NASBA) [13-15], microarray technique [16,17], Atomic
Force Microscope (AFM) [16], fluorescent microscopy
[18-23], electron microscopy [18,23-26], application of
biosensors [27,28], Enzyme Linked Immunosorbent As-
say (ELISA) [29-32] and flow cytometry [33-36]. Some
of these methods were modified by: 1) concentration
(ELISA tests, PCR and NASBA reactions, microarrays
application) [7,17,29], 2) different methods combining
(PCR reaction combines with plaque forming tests, ato-
mic force microscopy combines with protein microarray
technology) [37-39], 3) change of filter pore size (epif-
luorescence microscopy) [23], 4) dilution of sample (flow
cytometry) [16].
Application of Chosen Methods for Virus
Detection in Water Environment
As mentioned before, for viruses detection in water en-
vironment combined methods can be used. For example,
PCR reaction can be combined with plaque forming tests.
Polymerase chain reaction is used to amplification of
specific deoxyribonucleic acid (DNA) sequence. In this
reaction double stranded DNA, which is called template
DNA is amplified. During several years PCR technique,
due to its high specificity, was adopted to detection of
enteroviruses and Hepatitis A virus (HAV) in environ-
ment [40-43]. However, this technique has got a lot of
disadvantages. The main of them is low sensitivity. Al-
though PCR reaction is very sensitive (it enables detec-
tion of a single virus), it still does not fulfill standards
which are determined for virus detection. Even if viruses
which are present in water are concentrated, volume of
environmental sample is still too large for PCR reaction.
Secondly, it does not enable univocal determination if
detected virus is infectious or even not if result is posi-
tive. Moreover, PCR reaction enables only detection of
one type of virus at one time and in water exist many
types of them [7].
Viruses are capable to forming plaques on bacterial
lawn or cell layers and cause their morphological alterna-
tions which can be observed by light microscope [44,45].
Nevertheless, the plaque forming test is time consuming
and poor in specificity [7]. PCR reaction combined with
plaque forming tests was developed to simultaneous de-
tection of Poliovirus, Coxsackie virus, Echovirus and
Hepatitis A virus in water [7]. Water samples were in-
oculated with mixture containing Poliovirus type, strain
Lsc, CoxB3 or Echovirus. Contrary to PCR reaction used
in medical diagnosis both samples, inoculated and uni-
noculated, were concentrated by electropositive filter.
Afterwards, recovery of viruses was determined and
short-term culture was set. Thereafter ribonucleic acid
(RNA) was extracted and purified. Viral nucleic acid was
detected by multiplex-PCR and than identified by semi-
nested PCR [7]. Semi-nested PCR is a kind of nested
PCR. Nested PCR, consist of carrying out PCR reaction,
then repetition of PCR with second pair of starters, which
are located closer to center of amplified DNA fragment.
When in repetition of PCR reaction only one starter
which was used before is changed, then this method is
called semi-nested PCR [46].
For detection of viruses in water environment also
Nucleic Acid Sequence Based Amplification (NASBA)
is used. NASBA technique is used for RNA detection. It
abuses three enzymes: T7 RNA polymerase, reverse tran-
scriptase and RNase H which enable amplification of one
stranded template RNA. NASBA was implicated to de-
terminate concentration of viruses in wastewater from
wastewater treatment in Saint-Nicolas in Canada. Sam-
ples were collected from: raw waste water, waste water
after aerobic digestion with activated sludge and waste
water treated by UV. The samples were concentrated be-
fore analysis (precipitation of viruses from solution with
the aid of 8% polyethylenoglycol 600 and centrifugation)
[15]. In order to estimate influence of matrix before vi-
ruses detection waste water samples were analyzed for
total bacteria and fecal coliforms. Afterwards, samples
were inoculated with HAV (106 PFU/ml). Then each 5 µl
of sample were heated to 100˚C (lysis of viral cells) and
were analyzed by NASBA. Analysis of amplification
product was subjected to dot-blot hybridization [15]. Al-
though significantly bacterial contamination of raw waste
water (2 × 105 fecal coliforms/ml) results of analysis
showed strong specific to HAV signal. This indicates that
presence of bacteria do not influence on results of analy-
sis. Detection limit of this method for Hepatitis A Virus
is 4 × 102 PFU/ml. On the other hand, bacterial presence
in the sample might negatively influence on results of
enzymatic test ELISA. In enzyme-linked immunosorbent
assay is a test where ligand binds covalently to peroxi-
dase. During the test ligand binds with antibody of inter-
est. Unbound ligand is washed out and bound ligand in
examined by addition of substrate, which are converted
into colored products, as a result of enzyme activity [47].
Very important agent, which influences on sensitivity of
ELISA tests is antibody affinity to antigen of interest.
However, use of high affinity antibodies could be ineffi-
Copyright © 2013 SciRes. AiM
cient if recognizable epitopes are hidden in protein
structure, or if they do not have proper to recognize its
conformation [48]. Main advantage of ELISA compared
with other methods is its cost-effectiveness and the fact
that it is relatively simple [49]. ELISA was used for de-
tection of rotavirus antigen in water samples (two sam-
ples of tap water, 4 samples of drinking water and 26
samples of water for domestic use) [29]. Firstly tem-
perature and pH of samples were measured. Then sam-
ples were transported in containers with ice to laboratory.
There residual free chlorine was neutralized by addition
of sodium thiosulfate solution. The sample were adjusted
to pH 3.5 (1 N HCl and 0.0015 N AlCl3) and gently
mixed at room temperature. The samples were filtered
with aid of negatively charged filter. Filter was washed
by 0.14 NaCl, pH 3.5 in order to remove excess of Al3+
ions. Then the viruses were eluted with aid of 2.9%
tryptose phosphate broth (TPB), containing 6% glycine,
pH 9.0, neutralized by 4 N HCl and stored at 4˚C. There-
after elute was centrifugated. To samples was added mix-
ture of streptomycin and penicillin (to reduce bacterial
influence), Hanks salt solution and broth. The samples
were adjusted to pH 7.4 by 4 N HCl, vigorously mixed
and stored at 80˚C. Prepared samples were subjected to
ELISA, where 96 well plates were coated by specific
polyclonal antibodies. Sampled water was put to wells
and was incubated with horseradish peroxidase conju-
gated to specific polyclonal antibody (1 h). The wells
were washed five times with Tris-buffered solution. Then
buffer containing tetramethylbenzidine (TMB) and hy-
drogen peroxide were added. Content of wells was mixed
and samples were incubated for 10 minutes, at room
temperature. At the end sulfuric acid was added to wells
and absorbance of product was measured. In the same
experiment 5 liters of tap water was inoculated with bo-
vine rotavirus (5.7 × 104 IFU), concentrated and sub-
jected to ELISA. In experiment was also used standard
addition method. In this method two analysis were set
simultaneously—analysis of sample of interest and ana-
lysis of the same sample with addition of definite amount
of standard, which is also determined substance [29].
Promising method which may be used in the near future
is device which is called laboratory-on-a chip (LOC). It
is a kind of biosensor. Biosensors are devices, which can
responds to certain properties of analyte and convert
these responses into detectable signal, the most common
kind of signal is electrical [50]. LOC technology does not
require manual samples preparation and measurements
using sample signal detection (optical or electrochemical)
do not require special laboratory environmental (outdoor
analysis are enable). Moreover, lab-on-chip enables bio-
chemical reactions (immunological reactions, enzymatic
reactions and DNA determination). Chip is constructed
with elements as: wells, channels, electrodes and filters
[51]. Wells are storages of buffer, samples and waste. On
it samples are directly proceed, PCR reaction is set and
DNA of interest is detected. Wells and reaction chambers
are connected by micro-channels. In turn, micropumps,
microvalves and heaters are used to preparation of sam-
ple and/or separation of reagents, agitation, incubation
and separation of different biochemical reactions and
physical processes [27]. Lab-on-chip technology is fast
and sensitive to detect microbiological pathogens in en-
vironmental samples. There are several approaches to use
it in environmental microbiology. The simplest approach
is placing on miniature chip a termocycler. Chip com-
bines cell capturing with lyses, amplification of biologi-
cal material (PCR), detection of pathogens in real time
and analysis of data [27]. Comparison of described me-
thods is presented in Table 1.
Implementation of virus detection methods, for virus
detection in water environment aside from economical
agents, can come to grip with several impediments which
include: considerable dilution of sample, influence of
environmental matrix on analysis results and mutagenic
variability of viruses. In water contaminated with faeces
viruses are present in relatively small amounts (20 vi-
ruses in 100 ml of ground water) [55]. Therefore often
concentration of samples before exact determination of
viruses content is needed. To this end there were worked
out series of methods which include: concentration by
absorption—elution technique, with the aid of negatively
charged filter (this is a method which is used in enzy-
matic test ELISA) [29], application of positively charged
filter (in case of methods based on molecular biology) [7],
precipitation of viruses from solution with the aid of 8%
polyethylenoglycol 600 and centrifugation (in case of
Nucleic Acid Sequence—Based Amplification—NASBA)
[15]. In analyzed environmental samples (water) apart
from viruses, there are also other substances (suspensions,
humic acids, detritus or other microorganisms e.g. bacte-
ria). Humic acids are important factors which inhibits
PCR reaction. Although the PCR reaction is very sensi-
tive (it enables detection of single virus), by the reason of
inhibitors presence its sensitivity does not fulfill re-
quirements which are define for detection of viruses
which are present in water [37]. Suspension and detritus
presence impedes counting of viruses with the aid of
methods based on direct observation, such as transmis-
sion electron microscopy [23,56]. On the other hand
bacterial presence in the sample might negatively influ-
ence on results of enzymatic test ELISA. In this case, in
order to reduce bacterial influence on results of determi-
nation inhibitors of growth and cell division should be
added during water samples preparation [29].
Another impediment during virus detection in envi-
ronmental samples is mutagenic variability. By reason of
igh mutation rate (for instance, mutation rate of rotavi- h
Copyright © 2013 SciRes. AiM
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Table 1. Advantages and disadvantages of chosen virus detection methods for environmental sample application.
Virus detection
method Advantages Disadvantages
It enables fast viruses detection (virus detection with aid
of lab-on-chip methods lasts 7 do 16 minutes) [27].
It enables cheap analysis (25$ for analysis) [50].
Size of biosensors enables easy transport [51].
Reduction of sample volume and volume of reagents [27].
Possibility of intermolecular observations in real time [27].
High sensitivity of method (limit of detection of viruses in
water sample in method lab-on-chip is 102 - 104 [27].
Methods are is still in research phase.
It is cost-effective [49]. Concentration of sample is necessary [29].
It is susceptible to influence of bacteria which might be in sample [29].
It is relatively simple [49]. It can be inefficient if recognizable epitopes are
hidden in protein structure [48].
Specificity [7].
PCR does not enable detection of several types of viruses in
the same time (it is possible to detect various types of viruses with
aid of multiplex-PCR but this technique requires more primers.
Application of many primers mutually interfere each other which
may make it difficult to detect viruses) [52].
Inhibition of reaction due to humic acids [37].
Low sensitivity [7].
Concentration of sample is necessary [7].
Short detection time [7].
Can be use only for organisms, which are already known [53].
Time-consuming [7].
High analysis cost (one analysis costs 400 $) [50].
forming test
It enables to distinguish between pathogenic
and nonpathogenic viruses [37].
Difficulties associated with plaque observation [44].
High sensitivity [37].
It shortens detection time [37].
It enables removal of PCR inhibitors [37].
It enables to distinguish between pathogenic
and nonpathogenic viruses [37].
forming test
with PCR
High limit of detection (0.425 PFU/ml
for 8.5 × 106of poliovirus 1 Lsc [54].
Limit of detection is only 4 × 102 PFU/ml(for Hepatitis A Virus) [15].
Concentration of sample is necessary [15]. NASBA It is resistant to influence of matrix [15].
Can be use only for organisms, which are already known [53].
ruses is from 0.31 × 105 to 2.97 × 105 nt (nucleotides)/
cycle [57], nucleotide sequences in nucleic acids change
very fast. It prevents design of starters and probes, which
are used in detection of viruses by molecular techniques:
PCR reaction, NASBA techniques and microarrays. There-
fore these techniques can be used only for organisms,
which are already known, but they do not take into con-
sideration appearing of new viruses, which are result of
mutagenic, recombinatic variability or getting new genes
So far, there were used traditional indirect methods for
detection of viruses—plaque forming test. Main disad-
vantages of plaque forming test are: time consumption
(from 3 to 14 days) [58], high analysis cost (one analysis
costs 400 $) [50] and difficulties associated with plaque
observation (arisen plaques can be hooded by bacterial
colony) [27]. Solution for above mentioned problems
might be application of two techniques: biosensors or
method based on connection between: plaque forming
tests and PCR reaction.
Application of biosensors enables detection of viruses
during 7 to 16 minutes [27]. In addition this technique is
very sensitive (limit of detection of this method is 102 to
104 cells/ml) and enables observation of intermolecular
interactions in real time [27,59]. Moreover analysis of
environmental samples with the aid of biosensors are
relatively cheap (25 $ for water sample per analysis) [50].
However among advantages of second method, men-
tioned above, is high sensitivity (for example in semi-
nested PCR sensitivity for Poliovirus is 2.4 PFU/ml),
possibility of distinguishing between pathogenic and
non-pathogenic viruses [37], and ability to remove in-
hibitors of PCR reaction (e.g. humic acids), which are
present in primary matrix of sample. Both of mentioned
methods can shorten time of virus detection in water
Plaque froming tests connected with PCR reaction en-
able detection of viruses present in water in time of 2 to 4
days [37]. In this method detection time is shorter than
detection time in traditional plaque forming test, within
shorter incubation period. Techniques based on biosen-
sors in terms of time saving are much better [27].
3. Summary and Discussion
Considering that, monitoring of viruses present in treated
and untreated water is necessary (guidelines of World
Health Organization (WHO), associated with quality of
drinking water), analysis of water samples is needful.
After review, is considered that traditional methods of
viruses detection, such as plaque forming tests, mainly
due to individual cost of analysis, are not popular in
monitoring of water environment [50]. Also immunolo-
gical tests and techniques, based on direct observation of
viruses, become less applicable than techniques based on
molecular biology. Techniques based on direct observa-
tion of viruses did not enable detection of viruses, which
are present in environment in concentrations above
106/ml (samples are concentrated, what results in high
concentration of contaminants on microscope measured
grid surface). An example is transmission electron mi-
croscopy [23,56]. In addition, phenomenon of autofluo-
rescence, which occurs in epifluorescence microscopy,
does not make method based on direct observation of
viruses attractive. However, enzymatic tests, such ELISA,
are fallible, if recognizable epitopes are hidden in protein
structure, or if they do not have proper to recognize its
Nowadays, techniques based on molecular biology are
modified by connecting plaque forming tests with PCR,
or are replace by biosensors. This eventuate from high
mutagenic variability, which makes starters and probes
designing difficult and complexity of matrix, in which
may occur substances inhibiting PCR reactions and
4. Conclusions
Discussed techniques, for viruses detection, are used on a
large scale in medical diagnosis, but are less popular in
environmental analysis of water and sewage samples.
The reason of this fact is that during detection of viruses
it occurs numerous impediments, which include: high
dilution of samples, significant matrix influence on re-
sults/reliability of analysis and mutagenic variability of
viruses. After review, it can be claimed that most appli-
cable techniques can be: connection of cell cultures (pla-
que forming tests) with molecular biology techniques
(PCR) and biosensors. However the most optimal solu-
tion seems to be biosensors application due to time sav-
ing and unit prize of analysis. Nowadays they are appli-
cative on small-scale as systems which are used to run
PCR reaction on material from environmental samples,
because they are still in research phases [27].
Both in Poland and highly developed countries’ law,
the main emphasis is putting on health safety of drinking
water in terms of content of pathogenic bacteria and
parasites. Formal constraints involving monitoring of
viruses do not exist. We should pay attention to the fact
that applied disinfectant is not always able to deactivate
enteroviruses present in treated water. Researches have
shown that in the United States of America every year
the treatment of diseases caused by enteroviruses costs 5
to 6 milliard dollars [50]. Implementation of methods
which enables monitoring of viruses present in water and
food beyond fairly economical issues (charges for treat-
ment) has arguably its social overtone.
To date, no guidelines/standard methods, which enable
monitoring of viruses presence in environmental samples
have been worked out.
5. Acknowledgements
This work was supported by grant BKM/514/RAU-1/
2013 t. 26 from Silesian University of Technology in
Gliwice, Poland.
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