Emerging and re-emerging viruses in Malaysia,
Kok Keng Teea,b,*, Yutaka Takebeb, Adeeba Kamarulzamana
aDepartment of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
bLaboratory of Molecular Virology and Epidemiology, AIDS Research Center,
National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
Received 5 December 2007; received in revised form 27 August 2008; accepted 11 September 2008
Corresponding Editor: Jane Zuckerman, London, UK
Malaysia (28300N, 1128300E) is located in the heart of South-
east Asia with a population of approximately 27 million as of
2007. It is made up of Peninsular Malaysia and the Malaysian
Borneo, which are separated by the South China Sea, divided
into a federation of 13 states and three federal territories
including the Kuala Lumpur Federal Territory. Themajority of
the population is concentrated in Peninsular Malaysia with
area of the country. The local climate is tropical and char-
acterized by annual monsoons from October to January.
Progressive development over the last 50 years since
independence in 1957 has meant that infectious diseases
have gradually ceased to be the leading cause of death, with
chronic diseases such as cardiovascular disease, cancer,
chronic respiratory diseases, and diabetes mellitus becoming
International Journal of Infectious Diseases (2009) 13, 307—318
Highly pathogenic avian
emerged in Malaysia. Several of these viruses have resulted in significant morbidity and mortality
to those affected and they have imposed a tremendous public health and economic burden on the
state. Amongst the most devastating was the outbreak of Nipah virus encephalitis in 1998, which
resulted in 109 deaths. The culling of more than a million pigs, identified as the amplifying host,
ultimately brought the outbreak under control. A year prior to this, and subsequently again in
2000 and 2003, large outbreaks of hand-foot-and-mouth disease due to enterovirus 71, with rare
cases of fatal neurological complications, were reported in young children. Three other new
viruses —Tioman virus (1999), Pulauvirus (1999), and Melaka virus(2006) — whoseorigins haveall
been linked to bats, have been added to the growing list of novel viruses being discovered in
Malaysia. The highly pathogenic H5N1 avian influenza has also been detected in Malaysia with
outbreaks in poultry in 2004, 2006, and 2007. Fortunately, no human infections were reported.
Finally, the HIV/AIDS epidemic has seen the emergence of an HIV-1 recombinant form
(CRF33_01B) in HIV-infected individuals from various risk groups, with evidence of ongoing
and rapid expansion.
# 2008 International Society forInfectious Diseases. Published by ElsevierLtd. All rights reserved.
Over the past decade, a number of unique zoonotic and non-zoonotic viruses have
* Corresponding author. Tel.: +81 3 5285 1111;
fax: +81 3 5285 1258..
E-mail address: email@example.com (K.K. Tee).
1201-9712/$36.00 # 2008 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.
more commonplace amongst the increasingly more affluent
Malaysians. However over the last decade attention has once
again been drawn to infectious diseases, with the emergence
of new infections and the re-emergence of diseases pre-
viously well-controlled in the Asian region in general, and
in Malaysia in particular.1,2In Southeast Asia alone, the
discovery of new human viruses that cause large and devas-
tating epidemics, such as the severe acute respiratory syn-
drome (SARS) coronavirus and the highly pathogenic avian
influenza(HPAI)H5N1 virus,havebeen reported.Unlikesome
countries in the region, Malaysia was spared from the out-
break of SARS coronavirus and has yet to identify the HPAI
H5N1 infection in humans that adversely affected neighbor-
ing countries (although frequent outbreaks in poultry have
been reported). Nevertheless, in the last decade, Malaysia
has been battling different challenges caused by various
known or novel zoonotic and non-zoonotic viruses identified
for the first time in the country.
In this article we provide historical, epidemiological,
clinical, and scientific insights into the emerging, re-emer-
ging, and recombinant viruses identified in Malaysia
between 1997 and 2007 (Figure 1). Although the discovery
of novel viruses on some occasions may be explained partly
as being an artifact of increased surveillance and reporting
efforts in the country — the best example being the inves-
tigation of Nipah virus, which led to the incidental discov-
ery of other novel zoonotic viruses — recent studies, taking
into account various socio-economic, environmental, and
ecological factors associated with the emergence of infec-
tious diseases,3—6show that lower-latitude developing
countries including Malaysia are particularly at risk of
emerging infectious disease events due primarily to zoono-
tic pathogens of wildlife origin and vector-borne patho-
gens.2Here, we discuss probable events that have been
implicated in the appearance of these viruses, with the aim
of strengthening the existing preventive measures and
strategies for managing potentially new and unfamiliar
diseases in the future.
Human enterovirus 71 (EV-71) and 11 other group A coxsack-
ieviruses (CV-A) are members of the human enterovirus A
(HEV-A) species from the Enterovirus genus of the Picorna-
viridae family. Enteroviruses are distributed worldwide and
can be transmitted effectively through the fecal—oral route
and to a lesser extent, by respiratory transmission. The great
majority of enterovirus infections are asymptomatic, but
some can lead to serious illnesses particularly in infants
and the immunocompromised. Hand-foot-and-mouth disease
(HFMD) in children is usually caused by enteroviruses such as
CV-A10, CV-A16, and EV-71.
An epidemic of HFMD was first reported in Sibu, Sarawak
(Malaysian Borneo) in April 1997,7—10followed by smaller
outbreaks inPeninsular Malaysia
(Figure 1).7,8,11More than 2600 children were infected. Most
presented with a febrile illness and characteristic lesions on
the palms, soles, and oral mucosa, but a small proportion,
mainly children <6 years of age, presented with severe
neurological complications such as aseptic meningitis, polio-
myelitis-like acute flaccid paralysis, or fatal encephalomye-
litis. Cardiopulmonary symptoms
pulmonary edema with secondary myocardial dysfunction
leading to rapid cardio-respiratory decompensation were
also reported. Twenty-nine children eventually succumbed
to the disease in Sarawak10and 12 in Peninsular Malaysia.11
in thesame year
such as neurogenic
viruses and their year(s) of emergence at various locations in Malaysia are shown. Viral outbreaks in Singapore during the same period
are also indicated. HPAI H5N1, highly pathogenic avian influenza subtype H5N1; NiV, Nipah virus; CHIKV, chikungunya virus; EV-71,
enterovirus 71; HIV-1 CRF33_01B, HIV type 1 circulating recombinant form (CRF33_01B); MelV, Melaka virus; TiV, Tioman virus; PulV,
Pulau virus; SARS-CoV, severe acute respiratory syndrome coronavirus.
Zoonotic, non-zoonotic, and vector-borne viruses emerged in Malaysia between 1997 and 2007. The abbreviations for the
308 K.K. Tee et al.
EV-71 was isolated fromneuronal or non-neuronal samples
from most of the infected children, including those who
succumbed to the infection,7—9,11suggesting its role as the
etiologic agent. Different lineages of EV-71 subgenotypes C1
and C2 and two previously undefined subgenotypes B3 and B4
were identified in these outbreaks, with novel subgenotype
B3 being the most prevalent strain in Sarawak in 1997,
particularly among patients with the milder form of
HFMD.7,12—14Further outbreaks occurred in 2000 and 2003
in Sarawak where newly identified subgenotypes B4 and B5
were predominant.12,15,16Interestingly, phylogenetic and
recombination analyses revealed that some EV-71 strains
isolated in the 1997 outbreak were intertypic recombinant
involving EV-71 subgenotype B3, CV-A16, and various HEV-A
species.17,18These recombinant strains were isolated from
uncomplicated HFMD cases and were thought to have
reduced viral fitness and adaptation to host immunity com-
pared to the parental strains. The pathogenic potential and
clinical attributes of these recombinants, however, are not
Subsequent to the first outbreaks in Malaysia, several
large EV-71-associated HFMD outbreaks were also reported
across the Asia Pacific region: in Taiwan in 1998;19in Western
Australia in 1999;20in Singapore,21,22Japan,23Korea,12and
Despite the occurrence of numerous HFMD and EV-71 out-
breaks worldwide since 1969, no outbreaks involving fatal
cases of brainstem encephalitis and neurogenic pulmonary
edema have been reported,27except for those in Malaysia,
Taiwan (which claimed 78 lives19), and recently in Vietnam
and China. This shows that over the past decades EV-71 may
have evolved to become more pathogenic than its ancestral
other infectious agents in the pathogenesis of the disease
cannot be ruled out. This includes the description of acute
flaccid paralysis caused by adenoviruses9,28and echovirus 7-
Furthermore, a prospective study conducted during the
2000 and 2003 HFMD outbreaks in Sarawak showed that co-
infection with another enterovirus or adenovirus among
children with EV-71 was common.16
Diverse EV-71 subgenotypes determined from different
genomic regions indicate that multiple EV-71 lineages have
been circulating in the Asia Pacific region since 1997, with
each subgenotype causing distinct outbreaks of varying clin-
ical manifestations and neurovirulence. Driven by such com-
plexity, it has not been possible to identify a single
neurovirulent genotype nor its pathogenic mechanisms asso-
ciated with the severe neurological outcomes — although
recent studies have suggested that subgenotype B516and
particular subgenotypes from the genogroup C14,30are linked
with neurological complications. Continued molecular epi-
demiological surveillance is essential to delineate the tem-
poral trends of EV-71 transmission, the neuropathogenic
potential of its subgenotypes, and to plan for effective
clinical interventions plus preventive measures.12,15
during these outbreaks.
In September 1998, an outbreak of respiratory illness and
encephalitis with low morbidity and mortality rates occurred
respiratory and encephalitis syndrome) in the Kinta district of
Ipoh, Perak state in Peninsular Malaysia.31Later in the month,
a group of workers linked with pig farming presented with
fatality rate.32—34The disease affecting humans was initially
diagnosed as Japanese encephalitis (JE), which is endemic in
the outbreak based on preventive measures against JE in the
Kinta district and also throughout the country. The infected
eventually transported to pig farms and abattoirs in other
states in Malaysia, and also to neighboring Singapore.
Peninsular Malaysia.34Approximately 70% of the infected
patients were of Chinese ethnicity and were directly involved
in pig farming activities (as pig farmers and workers). Those
the onset of illness, suggesting direct viral transmission from
pigs to humans with a short incubation period. These patients
presented with an acute illness with fever, headache, dizzi-
ness, vomiting, and reduced levels of consciousness, before
rapidly progressing to severe encephalitis that was associated
with a high mortality rate.36,37Up to 25% of cases had con-
comitant respiratory syndromes.34,38A similar outbreak was
then reported in Singapore among abattoir workers who had
handled infected pigs imported from Malaysia.39
Inearly March 1999,anovelparamyxovirus responsible for
the outbreak was isolated from the cerebrospinal fluid of an
encephalitic patient from Sungai Nipah village, and was later
named the Nipah virus (NiV).34,40The discovery of NiV played
a critical role and was an important turning point in control-
ling the outbreak. Strong evidence showed that transmission
of NiV to humans was through close contact with infected
pigs,41,42and affected those directly involved in pig farming
activities such as assisting in pig breeding and birthing of
piglets, those administering injections or medications to
pigs, and those handling dead pigs. This led to an immediate
halt in direct handling and transportation of pigs within the
country and subsequently the culling of over a million pigs.40
Human-to-human transmission of NiV was also described
among healthcare workers,43although this was uncommon.44
The overall case fatality rate for the outbreak reported by
the Ministry of Health was 38.5%; 109 fatalities from 283
cases of viral encephalitis.45
Genetic characterization revealed that NiV is closely
related to the Hendra virus (HeV), a paramyxovirus species
causing severe respiratory disease in horses and humans in
Queensland, Australia, which first emerged in 1994.46The
full-length genome sequences of NiV and HeV are approxi-
mately 18 kb,47significantly longer than the average size of
15.5 kb of other viral genomes from the Paramyxovirinae
subfamily. NiVand HeValso share similar genomic organiza-
tion, both having increased nucleotide length of the 30non-
coding region in most of the genes. Taking together the
close phylogenetic relationship of NiV and HeV40,48plus its
distinct divergence and little immunological cross-reactiv-
ity with other established genera within the Paramyxovir-
idae, the two geographically remote viruses were classified
as belonging to a new genus — Henipavirus49,50(Figure 2).
Emerging and re-emerging viruses in Malaysia 309
This unique relationship between NiV and HeV played an
important role in identifying the natural reservoir for NiV in
Malaysia. Based on findings that fruit bat species of the
genus Pteropus are natural hosts of HeV,51,52extensive
serological surveillance within and outside the outbreak
epicenters was conducted involving various species of wild
fruit bats plus other wildlife and domestic animals. Neu-
tralizing antibodies against NiV were detected among the
variable flying foxes (previously known as the Island flying
foxes; Pteropus hypomelanus), Malayan flying foxes (Pter-
opus vampyrus), and other species of the order Chiroptera,
suggesting widespread infection of NiV in the bat popula-
tion in Peninsular Malaysia.53,54A novel method of collect-
ing free-living fruit bat urine samples using plastic sheets
was then adopted, and eventually NiV was isolated from
urine samples and swabs from fruits partially eaten by the
variable flying foxes,55corroborating the serological evi-
dence that fruit bats are the natural hosts of NiV.56Follow-
ing this feat, serological and/or genetic evidence of NiV
circulating among the expansive species of flying foxes was
also reported in Thailand,57Indonesia,58Cambodia,59,60
Bangladesh,61,62and India63indicating wide dissemination
of NiV across Southeast and South Asia, especially in coun-
tries where populations of the Pteropus species are over-
lapping. Recent studies have also shown NiV circulating in
Madagascar located in the southeastern part of Africa64and
Ghana in West Africa.65
The discovery of NiV as the causative agent of severe
febrile encephalitis in humans and the identification of
pteropid fruit bats as the natural hosts has helped regional
as well as international scientific communities to be better
prepared with management strategies for similar emerging
zoonotic diseases, as witnessed in the recent NiV-associated
encephalitis outbreaks in Bangladesh.61,62,66,67During the
Bangladesh outbreaks between 2001 and 2005, the transmis-
sion pattern of NiV, however, seemed different from that in
Malaysia because there wasnoinvolvement ofpigs,andmany
of the patients who presented largely with neurological
symptoms were young males who may have had direct con-
tact with fruits eaten by bats or had consumed contaminated
date palm sap.68In addition, NiV spread occurred over a wide
area in the country complicated by cases of human-to-human
transmission.69In some areas, the case fatality rate was as
high as 75%.66In India, a similar viral encephalitis outbreak
was also reported in 2001 in the city of Siliguri, West Bengal
not far from Bangladesh.70Anthropogenic factors such as
unrestrained deforestation and human population expansion
in Bangladesh and India could possibly have been linked to
these outbreaks. The high virulence of NiV and HeV and the
wide range of susceptible hosts plus the absence of thera-
peutic and prophylactic interventions have led to the classi-
fication of these viruses as Biosafety Level 4 pathogens.71
The pursuit of the natural host of NiV led to the unexpected
discovery of another novel zoonotic virus in 1999. On an
island about 25 km off the eastern coast of Peninsular Malay-
sia, a new virus of the Paramyxoviridae family called the
Tioman virus (TiV) was identified.72,73TiV was isolated from
pooled urine samples of free-living variable flying foxes (P.
hypomelanus) roosting on tree branches along the coastal
region of the island. TiV displayed characteristic microscopic
features similar to those of other viruses in the Paramyxovir-
idae family: spherical, pleiomorphic, and enveloped viral
particles with glycoprotein
revealed cross-reactivity with the Menangle virus (MenV),
another newly described Paramyxoviridae member that
caused infections among pigs and humans in New South
Wales, Australia in 1997.74Similar to NiV, evidence of TiV
circulating among bats in wide geographical proximity has
the nucleocapsid (N) gene between the two viruses (Figure 2).
The N protein shows significant sequence homologies with
other Rubulavirus members, including the mumps virus
(approximately 50%). Human disease caused by TiV has not
been documented thus far, although possible human infec-
tions, asdeterminedbythepresence ofantibodiesagainstTiV
among the island inhabitants, have been observed.75Animal
experiments have demonstrated that TiV is neurotropic caus-
ing necrosis in the cerebrum and hypothalamus in intracere-
in pigs, mainly by affecting the lymphoid tissues.77
The first sporadic outbreak of chikungunya virus (CHIKV)
infection occurred between late 1998 and early 1999 in Port
Klang, Kuala Lumpur.78Fifty-one patients living in low-cost
acid sequence of the complete N gene of select Paramyxovirinae
subfamily members. Nipah virus and Tioman virus, two newly
emergent paramyxoviruses in Malaysia, are clustered within the
Henipavirus and Rubulavirus genus, respectively. Rubulavirus
genus: MuV, mumps virus; MenV, Menangle virus; TiV, Tioman
virus; MaV, Mapuera virus; SV5, simian parainfluenza virus 5;
SV41, simian parainfluenza virus 41; hPIV2, human parainfluenza
virus 2; hPIV4a, human parainfluenza virus 4a; hPIV4b, human
parainfluenza virus 4b. Respirovirus genus: SeV, Sendai virus;
hPIV3, human parainfluenza virus 3. Henipavirus genus: NiV,
virus; CDV, canine distemper virus. Avulavirus genus: NDV, New-
castle disease virus. Unclassified viruses: SalV, Salem virus;
TPMV, Tupaia paramyxovirus.
Phylogenetic reconstruction of the deduced amino
310 K.K. Tee et al.
and squatter estates presented with fever, polyarthritis of
the small joints of the hands and feet, transient maculopap-
ular rashes, myalgia, and arthralgia. The clinical symptoms
resembled those of the more ubiquitous classical dengue
since dengue virus is endemic in the country.79
Chikungunya virus (chikungunya, from the root verb kun-
gunyala that means ‘to dry up or become contorted’ in
Makonde language in Tanzania80) is related to group A arbo-
viruses. CHIKV is an Alphavirus from the Togaviridae family
that shares the same vectors responsible for spreading den-
gue virus, namely Aedes aegypti and, to a lesser extent,
Aedes albopictus, which are the common peridomestic mos-
quito species in the Southeast Asia region. Studies conducted
populations in Malaysia, indicating the presence of CHIKV
infection.81,82However, until recently, outbreaks causing
human diseases have not been reported.
Seven years after its first appearance, new CHIKV infec-
tions re-emerged in Bagan Panchor (about 50 km from Ipoh),
Perak between March and April 2006.83,84More than 200
villagers in a fishing community were infected with CHIKV
strains derived from a common ancestral lineage from the
1998/99 outbreak, but this recent outbreak had a notably
higher number and rate of infections. This outbreak coin-
cided with the largest ever CHIKV epidemics affecting the
Indian Ocean territories between 2005 and 2006, where in
Reunion alone more than 266 000 people, about a third of the
total population, were infected. In India, an estimated 1.4
million human cases were reported during 2006. In these
outbreaks, a substantial proportion of patients also showed
unusual clinical manifestations, including severe neurologi-
cal symptoms and fulminant hepatitis.85,86Although unclear,
plausible explanations for the re-emergence of CHIKV in this
region include tourism and migration labor (Malaysia is
greatly dependent on migrant workers from neighboring
countries where CHIKV is endemic78), viral mutation, and
CHIKV introduction into a naı ¨ve population.87Phylogenetic
evidence has shown that the contemporary Malaysian strains
isolated in 2006 were, however, distinct from the epidemic
strains reported in the Indian subcontinent (2005—2006),
suggesting that CHIKV is indeed endemic in Malaysia.83Since
the concurrent re-emergence of CHIKV in the Indian Ocean
region and Malaysia seem to be unrelated, it is possible that
other factors could have played an important role in driving
these outbreaks. Climate anomalies, for instance, may have
favored the mosquito vectors and consequently facilitated
CHIKV emergence in these areas.88,89
Pulau virus and Melaka virus
During the search for NiV in fruit bats on Tioman Island in
1999, another novel virus, initially thought to be a bat
paramyxovirus, was identified. While serological tests
excluded the presence of a paramyxovirus, further electron
microscopic, serologic, and phylogenetic investigations
established the fusogenic agent as a reovirus.90Designated
as Pulau virus (PulV) (pulau denotes ‘island’ in the Malay
language), PulV is a dsRNA virus displaying the typical ultra-
structural morphology of a reovirus. PulV formed large syn-
cytium in Vero cells and showed serologic reactivity against
Nelson Bay virus (NBV), another known bat Orthoreovirus
isolated from the Australian flying foxes (Pteropus alecto).91
To date, PulV has not been associated with any human
diseases, and very little is known about the host range,
pathogenesis, and epidemiology of this newly recognized
More recently in 2006, another novel Orthoreovirus
named Melaka virus (MelV) associated with acute respiratory
an adult male who developed a high fever and acute respira-
tory symptoms. Icosahedral viruses similar to those of the
Orthoreovirus genus were noted on microscopic examination
of mammalian cell lines infected with MelV, and serological
studies of the patient serum showed neutralization activity
against PulV. Nucleotide analysis of the small (S) segments
revealed a close genetic relationship ofMelV to PulVand NBV,
and clustering within the Orthoreovirus genus subgroup III of
the Reoviridae family. In the meantime, two adolescent
children of the index patient also developed fever (without
respiratory symptoms) approximately 6 days after the onset
of his illness. Interestingly, epidemiological investigations of
the index case revealed that about one week before he
developed the illness, he had a bizarre exposure to a bat
antibodies against MelV were detected from the family
members including his wife who was asymptomatic. Although
direct evidence of bat-to-human transmission ofMelV has not
been documented, the role of the bat as a possible reservoir
ofMelVhas notbeen ruled out.MelVis believed tobe thefirst
Orthoreovirus associated with acute respiratory disease in
HIV type 1 (clade CRF33_01B)
Since the first cases of AIDS reported in 1986,93the rise in
HIV/AIDS in Malaysia has continued unabated. As of Decem-
ber 2007, a total of 80 938 HIV type 1 (HIV-1) infections have
been identified, while 10 334 people have died of AIDS-
related illnesses nationwide. Of these, 72% were injecting
drug users (IDUs), followed by 16% transmission via hetero-
sexual route (Figure 3a). It has been suggested that the early
epidemic was a spillover from Thailand, located at Malaysia’s
northern border. Malaysia is currently defined as a country
with a ‘concentrated’ HIV-1 epidemic, based on relatively
low rates of infection in the general population as measured
by a prevalence of less than 0.1% among women attending
government antenatal clinics, and seemingly isolated high
prevalence rates among high-risk groups such as IDUs and
female sex workers. In 2003 it wasreported that Malaysia had
the fifth fastest growing HIV infection rate in the Asia Pacific
region, with the infection rate doubling every three years
HIV-1 exhibits tremendous genetic diversity that is driven
by high rates of mutation and recombination, coupled with
high viral turnover and the persistent nature of infection.94—
97By these mechanisms, HIV-1 group M, which is largely
responsible for the global pandemic, diversified into 11 sub-
types and subsubtypes (A1, A2, B, C, D, F1, F2, G, H, J, and K)
and various types of recombinants.98,99HIV-1 recombinants
with epidemic spread are known as circulating recombinant
Asia: CRF01_AE, CRF15_01B, and CRF34_01B in Thailand and
CRF07_BC and CRF08_BC in China. In addition to CRFs,
Emerging and re-emerging viruses in Malaysia311
various types of unique recombinant forms (URFs) that are
detected in a single individual or a single epidemiologically-
linked cluster have been identified in the region, where
multiple lineages of HIV-1 strains co-circulate in the same
Theevolutionof the HIV-1epidemicinMalaysia produceda
in 2003.100Phylogenetic analyses of the HIV-1 protease and
reverse transcriptase genes found 19% CRF01_AE/B intersub-
type recombinants (a recombinant involving CRF01_AE and
in Kuala Lumpur, all having a recombination profile different
from other previously described CRFs. Designated as HIV-1
(Figure 3b), this novel CRF was disseminating at a significant
proportion among various high-risk populations, especially
among the IDUs. Wide distribution of CRF33_01B involving
all major ethnic and risk groups has provided evidence that
groups has occurred in Malaysia.101,102
in molecular epidemiological features of HIV-1 epidemics
between Thailand and Malaysia.101In the early phase of the
Thai epidemic, two HIV-1 strains, CRF01_AE and subtype B,
populations. CRF01_AE was distributed among persons at risk
of sexual exposure, while subtype B was distributed mainly
Thailand presented opportunities for inter-clade recombina-
the generation of various forms of CRF01_AE/B recombi-
nants.105—107A similar molecular epidemiological trend has
been observed in Malaysia. Studies conducted in 1992—1997
showed that CRF01_AE and subtype B were prevalent among
81% of heterosexuals and 55—92% of IDUs, respectively.108—110
of non-recombinant pure subtypes and the establishment of
CRF33_01B as the emerging epidemic strain in Malaysia.101
cular epidemiological surveillance has shown that CRF33_01B
YJ, personal communication). Such genetic complexity and
dynamicity of HIV-1 provides opportunities for new recombi-
nants to develop and spread within Malaysia and also in the
region, thus presenting new challenges to disease diagnosis
and treatment, particularly in the development of antivirals
and vaccine candidates.
Highly pathogenic avian influenza (H5N1)
The highly pathogenic avian influenza (HPAI) H5N1 virus that
originated in southern China in the mid-1990s,112was respon-
Malaysia (1986—2007). Inset: Distribution of HIV-1 infections in different risk categories. Abbreviations: IDU, injecting drug user;
Hetero, heterosexual; Homo/Bi, male homo-/bisexual; MCT, mother-to-child transmission. (b) Structural representation of the novel
HIV-1 CRF33_01B identified in Malaysia. Full-length genetic sequence revealed short subtype B fragments are recombined into the gag
and pol gene in the backbone of CRF01_AE. The recombinant structures of all HIV-1 CRFs are available at the HIV Sequence Database,
Los Alamos National Library.98
(a) Cumulative numbers of HIV-1 infections, AIDS cases, and AIDS-related deaths reported by the Ministry of Health in
312 K.K. Tee et al.
sible for large disease outbreaks in poultry in China and other
countries in the region in 2003—2004. Affected countries
faced severe economic loss due to mortality in poultry and
the loss of domestic and international trade of poultry and its
products. Widespread circulation among avian populations
and the significant number of human infections and deaths
caused by HPAI H5N1 (as of June 19, 2008, 385 human cases
including 243 deaths have been reported; www.who.int/csr/
disease/avian_influenza/country/en) have raised concern
over the plausible genetic mutation event (genetic reassort-
ment) that could lead to the generation of an influenza strain
with enhanced transmissibility among humans, possibly trig-
gering a pandemic.113
In Malaysia, the first ever outbreak of HPAI caused by
subtype H5N1 was reported in August 2004 in a village in
the state of Kelantan located approximately 22 km from
the Thai border in northeastern Peninsular Malaysia.114,115
The virus, discovered in fighting cocks smuggled from a
neighboring country, was transmitted mainly among the
local village chickens. Molecular analysis showed that the
H5N1 strain was highly homologous to the H5N1 strains
previously isolated from Thailand and Vietnam. A few
weeks following the first outbreak, eight other outbreaks
were reported, largely affecting poultry in villages located
around the index case. In these outbreaks, no human cases
or deaths were reported and the disease was brought under
control by depopulation and quarantine/clinical surveil-
lance of poultry and birds within a 1-km and 10-km radius
of the index case, respectively, coupled with restrictions
on the movement of birds and their products to other
In February 2006, fresh outbreaks of HPAI H5N1 emerged
over a wider geographical area involving villages in Kuala
Lumpur and the states of Perak and Pulau Pinang along the
more industrialized western coast of Peninsular Malay-
sia.115Phylogenetic analysis of the H5 and PB2 genes
revealed that the H5N1 strain isolated from infected vil-
lage chickens, ducks, and quails was different from that of
the 2004 outbreak and was highly similar to the H5N1
isolates from Indonesia and China, suggesting different
H5N1 lineages were introduced into the country, possibly
by the poultry trade rather than through migratory
birds.116Although these outbreaks were brought under
control through effective disease control and preventive
efforts, including the culling of about 60 000 birds, a
similar outbreak re-occurred in another village in Selangor
state not far from Kuala Lumpur in June 2007.115Through
effective control measures, the
resolved several months later.
In Malaysia, cock fighting is a popular albeit illegal activity
among village folks. Fighting cocks smuggled from neighbor-
ing countries (i.e., Thailand and Indonesia) have been impli-
cated in the introduction and spread of HPAI H5N1 in
Peninsular Malaysia. Such public health threats — that
increase the risk of infection in humans — could be avoided
by implementing a stricter ban by the authorities on cock
fighting and smuggling activities in the country. In addition,
continued surveillance of avian populations including domes-
tic ducks (thought to be the potential reservoir and source of
H5N1 persistence117) is important to counter possible re-
occurrence or re-introduction of HPAI H5N1, a phenomenon
that is not uncommon in the Southeast Asia region.118
2007 outbreak was
Over the last eleven years, between 1997 and 2007, Malaysia
has witnessed the unprecedented appearance of eight novel
viruses that have never been documented in the country
NiV, CHIKV, and HIV-1 recombinant, have caused serious
human infections and/or deaths of varying magnitudes and
are of epidemiological importance, whereas others have yet
to be known to cause widespread human diseases (e.g., MelV
and HPAI H5N1) or cross into a wider range of susceptible
hosts (e.g., TiVand PulV). Factors leading to this emergence
are not entirely understood but various features associated
with such a trend — including socio-economic, environmen-
tal, and ecological factors3—6— have been hypothesized.
Unlike enterovirus infections that usually occur in densely
populated areas, where hygiene levels are poor and food or
it of the environment, viral hosts/vectors, or humans, have
in Malaysia. For instance, early studies implicated the effects
of the El Nin ˜o/Southern Oscillation (ENSO) phenomenon in
1997/98 in the emergence of NiV.119Directly preceding these
outbreaks, Malaysia experienced a severe drought resulting
from the El Nin ˜o conditions (the largest and warmest to
sive slash-and-burn deforestation activities in Indonesia. This
series of environmental and human events may have affected
the natural habitat of the pteropid bats, forcing their migra-
tion and subsequent encroachment into fruit orchards sur-
rounding the pig-farming area, resulting in the unanticipated
ENSO and showed evidence that NiV is frequently present in
fruit bats in Malaysia, and that its spillover — from bats to pigs
and subsequent transmission to human — was largely a chance
encroachment and agricultural expansion by humans, con-
founded by the temporal and spatial dynamicity of both the
virus and hosts, and the hosts (pigs) immunity against NiV
infection.119—121In fact, similar anthropogenic drivers have
been linked to outbreaks in Malaysia, Bangladesh, and India,
raising concerns that these countries, which are currently
experiencing promising economic growth, are still at risk of
cultural intensification activities not be closely regulated.
Overlapping the NiV epidemic was the first sporadic out-
break of Aedes mosquito-borne CHIKV infections in Kuala
Lumpur in 1998. The arbovirus then re-emerged seven years
later in northern Malaysia, coinciding with the drought-asso-
ciated CHIKV outbreaks affecting countries cresting the
Indian Ocean,88by far the largest CHIKVepidemic on record.
The cause of the disease outbreaks remains multifactorial.
Previous lessons have suggested that increased tourism, viral
adaptation, and host immunity,87plus importation of migrant
workersfromcountries whereCHIKVis endemic,78mayplaya
the effect of a warmer climate has also been reported.88As a
whole, such a climate abnormality of prolonged drier-than-
average conditions may be critical in introducing new viruses
Emerging and re-emerging viruses in Malaysia313
Emerging and re-emerging viruses in Malaysia, 1997—2007.
Virus FamilyGenus PropertiesYear of
Locations in MalaysiaRemarks
Enterovirus 71 PicornaviridaeEnterovirus+ssRNA,
Fatal cases of brainstem encephalitis reported
Novel subgenotypes B3, B4, and B5 emerged
Recombinant involving coxsackievirus and
other human enteroviruses identified
Sporadic outbreak causing febrile illness
Endemic virus re-emerged 7 years later
Aedes aegypti as vector
Novel bat paramyxovirus, closely related
to Hendra virus
Febrile illness and encephalitis with high
Acquired via close contact with infected pigs
Novel bat paramyxovirus, closely related to
Human infections and diseases in experimentally
infected animals have been reported
Novel bat Orthoreovirus
No human/animal disease reported
Novel recombinant descended from subtypes
B and CRF01_AE
Widespread among all major risk groups
Outbreaks confined to poultry and have been
linked to fighting cocks smuggled from
60 000 birds culled to control outbreak
1998 Port Klang,
Bagan Panchor, Perak2006
Nipah virus ParamyxoviridaeHenipavirus
1998 Ipoh, Perak; Seremban,
1999 Tioman Island
1999 Tioman Island
HIV type 1 (clade
RetroviridaeLentivirus 2003 Kuala Lumpur
avian influenza H5N1
Orthomyxoviridae Influenzavirus A
?ssRNA, enveloped2004 Kelantan
2006 Kuala Lumpur; Perak;
2006 Melaka virus ReoviridaeOrthoreovirus dsRNA,
Novel bat Orthoreovirus associated with
acute respiratory disease in the human
K.K. Tee et al.
into the country, although more research is certainly needed
to validate this relationship.122
The discovery of bat-associated NiV (a Henipavirus), TiV
(Rubulavirus), and PulV and MelV (both within the Orthor-
eovirus genus) has highlighted the significant role that bats
play as important reservoir hosts of emerging viruses.123,124
Although yet to cause severe, widespread human outbreaks,
medical and research institutions should adopt a proactive
approach in understanding and managing the potential
threats posed by these viruses. This includes conducting
large-scale surveillance to determine the prevalence, both
in bats and humans of these viruses (as in Bangladesh, for
example, during the recent NiV outbreaks62,68,69), establish-
ing diagnostic systems in public health laboratories that
include the diagnosis of these viruses, and reviewing the
traditional/medicinal practice of drinking fresh bat blood or
eating improperly cooked bat products among certain rural
HIV is among the most genetically diverse human patho-
gens. In addition, co-circulation of two or more HIV-1 sub-
types in any population can lead to co-infection in
strains,106,107,126as occurred with clade CRF33_01B in
Malaysia, a fact that further increases the genetic plasticity
of HIV-1. The possible phenotypic advantage inherited from
recombination among different HIV-1 clades remains uncer-
tain. However, it has been reported that HIV recombinants
strains,127,128as reflected by the high prevalence of such
recombinants in particular populations with risk practices.
Further genetic diversification of HIV-1, which will add
further to the problems in the development of antivirals
and vaccines, could be reduced by limiting the incidence of
infections among the high-risk groups and among those who
are already infected.
As Malaysia progresses towards becoming a developed
country in the new millennium, a number of zoonotic,
non-zoonotic, and vector-borne viruses have been reported
for the first time in the country. Although a decade has past,
the potential health threats faced by the population are far
from over. In fact, the momentum with which these diseases
are spreading has intensified over time, as seen by the
exponential increase in the annual HIV/AIDS incidence in
Malaysia and elsewhere in the world, the temporal persis-
tence of EV-71 infections, the sporadic expansion of CHIKV
worldwide, the broad regional distribution and aggressive
NiVoutbreaks in Bangladesh and India, and the re-occurrence
of highly pathogenic H5N1 avian influenza in poultry and
humans. Taken together, indispensable lessons learnt from
the past plus current understanding of the probable circum-
stances leading to disease emergence suggest calls for better
preparedness to deal with impending infectious disease risks.
We would like to acknowledge Kaw Bing Chua, Sai Kit Lam,
and colleagues for their inspiring work which led to the
discovery and identification of many of the viruses reviewed
in this article. We also thank Timothy D. Mastro for critical
reading of the article and the anonymous reviewers for
constructive comments and suggestions.
A.K. and Y.T. received financial support from the Ministry
of Science, Technology and Innovation, Malaysia (eScience-
Fund 02-01-03-SF0379) and the Ministry of Health, Labour
and Welfare, Japan (H18-AIDS-General-016), respectively.
Conflict of interest: No conflict of interest to declare.
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