Rabies is a fatal zoonotic disease caused by rabies virus (RABV) and remains a public health problem in Malaysia. Malaysia was declared rabies-free in 2012, however rabies outbreaks occurred at few states in Peninsular Malaysia three years later; and for the first time, in Sarawak (East Malaysia) in 2017 which has caused more than 20 human deaths. This study describes the phylogenetic analysis of the complete nucleoprotein (N) gene of RABV from animal samples in Malaysia from year 2015 to 2018. The N gene of 17 RABVs from Perlis, Kedah and Sarawak were amplified and sequenced. The nucleotide and deduced amino acid similarities of N gene analysis indicated that there is high similarity among the local RABVs. Phylogenetic analysis of the N gene revealed that all Malaysia RABVs belonged to the Asian clade. Among these, RABVs from Peninsular Malaysia were clustered together with RABVs from Thailand, Vietnam and other Southeast Asia countries except Indonesia. However, RABVs from Sarawak were grouped together with Indonesian strains from Kalimantan. Our study provides baseline genetic information of the potential origins of the circulating RABVs in Malaysia. This crucial information helped the authority in policies making and strategies to be taken in outbreak control. Continuous surveillance program to monitor the disease trend, strict border control, vaccination of dog and cat population and public awareness are important steps to control the spread of the RABV.

African swine fever (ASF) is a transboundary haemorrhagic viral disease that affected domestic and wild pigs of all ages. The disease is caused by African swine fever virus (ASFV) and was introduced to China in 2018 before spreading rapidly to neighbouring Asian countries. As such, putting countries free from ASF like Malaysia at risk. ASF is highly lethal with no vaccine or treatment available. In February 2021, we confirmed backyard pigs from various locations in Sabah were infected with ASF using real time polymerase chain reaction (realtime PCR). Further characterization of the Sabah ASFVs indicated that they were of p72 genotype II with intergenic region (IGR) variant II that displayed an addition tandem repeat sequence (TRS) insertion, similar to ASFV from Indonesia, Vietnam and China. These results indicate and support the transboundary expansion of a homogenotypic ASFV (p72 genotype II and IGR variant II) in the Europe and Asia-Pacific, emphasizing the need for a holistic international collaboration in control and preventing further spreading of the current ASF pandemic. Importantly, our results informed the first detection and characterization of ASF, a disease previously not detected in Malaysia. This information is crucial for further mitigation and preventive measures.

Avian Infectious Bronchitis (IB) is a highly contagious disease which can cause huge economic losses to the poultry industry. Forty five IB viruses (IBV) were isolated from poultry in Malaysia during 2014-2016. Phylogenetic analysis of the spike glycoprotein 1 (S1) gene revealed that all isolates were clustered into five distinct groups. The predominant type of IBV isolated was QX strains (47%), second was 4/91 type (27%), followed by Malaysian strain MH5365/95 (13%), Massachusetts type (11%) and finally Taiwanese strains (2%). Four types of S1 protein cleavage recognition motifs were found among the isolates which includes HRRRR, RRSRR, RRFRR and RRVRR. To our knowledge, this is the first report describing the motif RRVRR and are unique to Malaysian strains. Six IBVs were grouped in Malaysian MH5365/95 strains. Among these, one isolate was different from others where it only shared 82% identity with MH5365/95 and to others. It formed its own branch in the Malaysian cluster suggesting it may be a variant unique to Malaysia. Alignment analysis of the S1 amino acid sequences indicated that point mutations, insertions and deletions contribute to the divergence of IB variants. This study indicated at least five groups of IBV are circulating in Malaysia with most of the isolates belonged to QX strains. As new IBV variants continue to emerge, further study need to be carried out to determine whether the current available vaccine is able to give protection against the circulating virus.