Genetic characterization of rabies virus isolates in Korea

Mass vaccination has led to the elimination of rabies since 2014 in South Korea

PURPOSE

Rabies is one of the most fatal diseases, but it is 100% preventable in animals by vaccination. In this study, we present the epidemiological features of, and national preventive measures against, rabies in Korea.

MATERIALS AND METHODS

Data related to rabies and the population density of raccoon dogs in Korea were collected from the Animal and Plant Quarantine Agency, the Korean Centers for Disease Control and Prevention, and the National Institute of Environmental Research. Rabies diagnosis was confirmed with a fluorescent antibody test using brain samples of animals in accordance with the procedures described by the World Organization for Animal Health. Serological assays for dogs and cattle were conducted using the fluorescent antibody virus neutralization test.

RESULTS

From 1993 to 2016, a total of seven human rabies cases and 437 animal rabies cases in five different species were reported. An increase in the distribution of bait vaccine seemed to be related to a dramatic decrease in rabies prevalence in endemic rabies regions. Two Korean provinces and the capital city, Seoul, were involved in rabies outbreaks. Korean rabies strains are most closely related to the eastern Chinese strain belonging to the Arctic-like lineage. The yearly seropositive rates ranged from 50.4% to 81.2% in dogs and from 25% to 60.5% in cattle residing in endemic rabies regions.

CONCLUSION

This study indicates that national preventive measures, including mass vaccination and distribution of bait vaccines, have contributed to a substantial decrease in the number of rabies cases in Korea.

Spatio-temporal Analysis of the Genetic Diversity of Arctic Rabies Viruses and Their Reservoir Hosts in Greenland

There has been limited knowledge on spatio-temporal epidemiology of zoonotic arctic fox rabies among countries bordering the Arctic, in particular Greenland. Previous molecular epidemiological studies have suggested the occurrence of one particular arctic rabies virus (RABV) lineage (arctic-3), but have been limited by a low number of available samples preventing in-depth high resolution phylogenetic analysis of RABVs at that time. However, an improved knowledge of the evolution, at a molecular level, of the circulating RABVs and a better understanding of the historical perspective of the disease in Greenland is necessary for better direct control measures on the island. These issues have been addressed by investigating the spatio-temporal genetic diversity of arctic RABVs and their reservoir host, the arctic fox, in Greenland using both full and partial genome sequences. Using a unique set of 79 arctic RABV full genome sequences from Greenland, Canada, USA (Alaska) and Russia obtained between 1977 and 2014, a description of the historic context in relation to the genetic diversity of currently circulating RABV in Greenland and neighboring Canadian Northern territories has been provided. The phylogenetic analysis confirmed delineation into four major arctic RABV lineages (arctic 1–4) with viruses from Greenland exclusively grouping into the circumpolar arctic-3 lineage. High resolution analysis enabled distinction of seven geographically distinct subclades (3.I – 3.VII) with two subclades containing viruses from both Greenland and Canada. By combining analysis of full length RABV genome sequences and host derived sequences encoding mitochondrial proteins obtained simultaneously from brain tissues of 49 arctic foxes, the interaction of viruses and their hosts was explored in detail. Such an approach can serve as a blueprint for analysis of infectious disease dynamics and virus-host interdependencies. The results showed a fine-scale spatial population structure in Greenland arctic foxes based on mitochondrial sequences, but provided no evidence for independent isolated evolutionary development of RABV in different arctic fox lineages. These data are invaluable to support future initiatives for arctic fox rabies control and elimination in Greenland.

Next to dog-mediated rabies, wildlife rabies continues to pose a public health problem, particularly in the northern hemisphere. Control of this zoonosis at the animal source has been proven the most efficient route to reduction of human rabies burden. Successful elimination of red fox-mediated rabies in Western Europe and parts of North America has demonstrated the viability of wildlife rabies control strategies. In some regions, the epidemiology of wildlife rabies is well understood; this is not the case for arctic rabies, particularly in Greenland. Previous molecular epidemiological studies demonstrated the occurrence of one particular arctic rabies virus (RABV) lineage (arctic-3) but were limited by low sample numbers and limited sequence length so as to preclude generation of high resolution phylogenetic analysis. Here, a unique set comprised of 79 complete genome sequences of RABVs from Greenland, Canada, USA (Alaska) and Russia collected over the past four decades was analysed. The use of next generation sequencing (NGS) allowed simultaneous determination of host derived sequences encoding mitochondrial proteins from the same brain tissue of 49 arctic foxes. These sequence data combined with geographical and temporal information permit the study of the genetic diversity and evolution of circulating RABVs in Greenland against the background of reservoir host genetics. The results reveal the existence of a single arctic RABV lineage (arctic-3) in Greenland, which has evolved into multiple distinct variants. These analyses provide an improved knowledge of the evolution of the circulating viruses at the molecular level and a better understanding of the historical perspective of the disease in Greenland compared to other parts of the Arctic. This knowledge will support policy on rabies control in mammalian wildlife reservoirs.

Recent emergence and spread of an Arctic-related phylogenetic lineage of rabies virus in Nepal

Rabies is a zoonotic disease that is endemic in many parts of the developing world, especially in Africa and Asia. However its epidemiology remains largely unappreciated in much of these regions, such as in Nepal, where limited information is available about the spatiotemporal dynamics of the main etiological agent, the rabies virus (RABV). In this study, we describe for the first time the phylogenetic diversity and evolution of RABV circulating in Nepal, as well as their geographical relationships within the broader region. A total of 24 new isolates obtained from Nepal and collected from 2003 to 2011 were full-length sequenced for both the nucleoprotein and the glycoprotein genes, and analysed using neighbour-joining and maximum-likelihood phylogenetic methods with representative viruses from all over the world, including new related RABV strains from neighbouring or more distant countries (Afghanistan, Greenland, Iran, Russia and USA). Despite Nepal's limited land surface and its particular geographical position within the Indian subcontinent, our study revealed the presence of a surprising wide genetic diversity of RABV, with the co-existence of three different phylogenetic groups: an Indian subcontinent clade and two different Arctic-like sub-clades within the Arctic-related clade. This observation suggests at least two independent episodes of rabies introduction from neighbouring countries. In addition, specific phylogenetic and temporal evolution analysis of viruses within the Arctic-related clade has identified a new recently emerged RABV lineage we named as the Arctic-like 3 (AL-3) sub-clade that is already widely spread in Nepal.

Rabies is endemic in most Asian countries and represents a serious public health issue, with an estimated 31,000 people dying each year of this disease. The majority of human cases are transmitted by domestic dogs, which act as the principal reservoir host and vector. However, molecular epidemiology and evolutionary dynamics of the main etiological agent, the rabies virus (RABV), remains largely unappreciated in some regions such as in Nepal. Based on a subset of 24 new Nepalese isolates collected from 2003 to 2011 and representative RABV strains at a global scale, phylogenetic analysis based on the complete nucleoprotein and glycoprotein genes sequences revealed the presence of a surprising wide genetic diversity of RABV circulating in this country. The presence of three different co-existing phylogenetic groups was identified: an Indian subcontinent clade and two different Arctic-like sub-clades within the Arctic-related clade, namely Arctic-like (AL)-1, lineage a (AL-1a), and AL-3. Among these clusters, the AL-3 sub-clade appears as the major Nepalese phylogroup which emerged relatively recently in this country, within the last 30 years. These data has raised some concerns about the exchange of RABV between different countries, and provided key elements for implementation of effective control measures of rabies in Nepal.

Molecular characterization of KGH, the first human isolate of rabies virus in Korea

The complete genome sequence of the KGH strain of the first human rabies virus, which was isolated from a skin biopsy of a patient with rabies, whose symptoms developed due to bites from a raccoon dog in 2001. The size of the KGH strain genome was determined to be 11,928 nucleotides (nt) with a leader sequence of 58 nt, nucleoprotein gene of 1,353 nt, phosphoprotein gene of 894 nt, matrix protein gene of 609 nt, glycoprotein gene of 1,575 nt, RNA-dependent RNA polymerase gene of 6,384 nt, and trailer region of 69 nt. Sequence similarity was compared with 39 fully sequenced rabies virus genomes currently available, and the result showed 70.6-91.6 % at the nucleotide level, and 82.8-97.9 % at the amino acid level. The deduced amino acids in the viral protein were compared with those of other rabies viruses, and various functional regions were investigated. As a result, we found that the KGH strain only had a unique amino acid substitution that was identified to be associated either with host immune response and pathogenicity in the N protein, or with a related region regulating STAT1 in the P protein, and related to pathogenicity in G protein. Based on phylogenetic analyses using the complete genome of 39 rabies viruses, the KGH strain was determined to be closely related with the NNV-RAB-H strain and transplant rabies virus serotype 1, which are Indian isolates, and was confirmed to belong to the Arctic-like 2 clade. The KGH strain was most closely related to the SKRRD0204HC and SKRRD0205HC strain when compared with Korean animal isolates, which was separated around the same time and place, and belonged to the Gangwon III subgroup.

Comparison of four diagnostic methods for detecting rabies viruses circulating in Korea

It is essential to rapidly and precisely diagnose rabies. In this study, we evaluated four diagnostic methods, indirect fluorescent antibody test (FAT), virus isolation (VI), reverse transcriptase polymerase chain reaction (RT-PCR), and rapid immunodiagnostic assay (RIDA), to detect rabies in animal brain homogenates. Out of the 110 animal brain samples tested, 20 (18.2%) were positive for rabies according to the FAT. Compared to the FAT, the sensitivities of VI, RT-PCR, and RIDA were 100, 100, and 95%, respectively. The specificities of VI, RT-PCR and RIDA were found to be 100, 100, and 98.9%, respectively. Rabies viruses circulating in Korea were isolated and propagated in murine neuroblastoma (NG108-15) cells with titers ranging from 10^1.5 to 10^4.5 TCID₅₀/mL. Although the RIDA findings did not completely coincide with results obtained from FAT, VI, and RT-PCR, RIDA appears to be a fast and reliable assay that can be used to analyze brain samples. In summary, the results from our study showed that VI, RT-PCR, and RIDA can be used as supplementary diagnostic tools for detecting rabies viruses in both laboratory and field settings.

Molecular characterization of Korean rabies virus isolates

The nucleoprotein (N) and glycoprotein (G) of 11 Korean rabies virus (RABV) isolates collected from animals diagnosed with rabies between 2008 and 2009 were subjected to molecular and phylogenetic analyses. Six isolates originated from domestic animals (cattle and dogs) and five were obtained from wild free-ranging raccoon dogs. The similarities in the nucleotide sequences of the N gene among all Korean isolates ranged from 98.1 to 99.8%, while those of the G gene ranged from 97.9 to 99.3%. Based on the nucleotide analysis of the N and G genes, the Korean RABV isolates were confirmed as genotype I of Lyssavirus and classified into four distinct subgroups with high similarity. Phylogenetic analysis showed that the Korean isolates were most closely related to the non-Korean NeiMeng1025B and 857r strains, which were isolated from rabid raccoon dogs in Eastern China and Russia, respectively. These findings suggest that the Korean RABV isolates originated from a rabid raccoon dog in Northeastern Asia. Genetic analysis of the Korean RABV isolates revealed no substitutions at several antigenic sites, indicating that the isolates circulating in Korea may be pathogenic in several hosts.

Molecular epidemiology of rabies virus circulating in South Korea, 1998-2010

We analyzed the nucleotide sequences of the G-L (glycoprotein-large protein) intergenic non-coding region of 33 strains of the rabies virus (RABV) isolated in South Korea in 1998-2010 and compared the sequences with those of previously reported non-Korean strains. The similarities of the nucleotide sequences of the G-L region among all Korean RABV isolates ranged from 97.1 to 100%. Based on the phylogenetic analysis of the G-L region, the Korean RABV isolates were classified into three distinct subgroups with high similarity and were most closely related to the non-Korean NeiMeng1025C isolate, which was isolated from a rabid raccoon dog in eastern China, suggesting that the Korean RABV isolates originate from a rabid raccoon dog in northeastern Asia. Our results indicated that G-L region, as a useful phylogenetic indicator, is equivalent to the nucleoprotein (N) or glycoprotein (G) gene for study of RABV molecular epidemiology and that the Korean RABV isolates showing a few substitutions in the G-L region are continuously circulating in South Korea.

Genetic evidence for domestic raccoon dog rabies caused by Arctic-like rabies virus in Inner Mongolia, China

An outbreak of rabies affected domestic raccoon dogs on an animal farm in Inner Mongolia, China in 2007. A study was conducted to characterize the aetiological agent and clarify the origin of the rabies virus. Brain tissues were obtained from five rabid raccoon dogs. Viral nucleoprotein antigen was detected in the brain tissues and five rabies viruses were isolated from these rabid animals. Phylogenetic analysis of the N and G gene sequences showed that these isolates were closely related to Arctic-like rabies viruses isolated from the far-eastern region of Russia and South Korea, but distinct from the rabies viruses that are widely distributed in endemic areas in China. Epidemiological data suggested that the likely source of infection was from one wild raccoon dog that was captured and placed in the same type of pen used for domestic raccoon dogs.

The origin and phylogeography of dog rabies virus

Rabies is a progressively fatal and incurable viral encephalitis caused by a lyssavirus infection. Almost all of the 55 000 annual rabies deaths in humans result from infection with dog rabies viruses (RABV). Despite the importance of rabies for human health, little is known about the spread of RABV in dog populations, and patterns of biodiversity have only been studied in limited geographical space. To address these questions on a global scale, we sequenced 62 new isolates and performed an extensive comparative analysis of RABV gene sequence data, representing 192 isolates sampled from 55 countries. From this, we identified six clades of RABV in non-flying mammals, each of which has a distinct geographical distribution, most likely reflecting major physical barriers to gene flow. Indeed, a detailed analysis of phylogeographic structure revealed only limited viral movement among geographical localities. Using Bayesian coalescent methods we also reveal that the sampled lineages of canid RABV derive from a common ancestor that originated within the past 1500 years. Additionally, we found no evidence for either positive selection or widespread population bottlenecks during the global expansion of canid RABV. Overall, our study reveals that the stochastic processes of genetic drift and population subdivision are the most important factors shaping the global phylogeography of canid RABV.

Arctic and Arctic-like rabies viruses: distribution, phylogeny and evolutionary history

Forty-one newly sequenced isolates of Arctic and Arctic-like rabies viruses, were genetically compared to each other and to those available from GenBank. Four phylogenetic lineages of Arctic viruses were identified. Arctic-1 viruses circulate in Ontario, Arctic-2 viruses circulate in Siberia and Alaska, Arctic-3 viruses circulate circumpolarly, and a newly described lineage Arctic-4 circulates locally in Alaska. The oldest available isolates from Siberia (between 1950 and 1960) belong to the Arctic-2 and Arctic-3 lineages and share 98.6-99.2% N gene identity with contemporary viruses. Two lineages of Arctic-like viruses were identified in southern Asia and the Middle East (Arctic-like-1) and eastern Asia (Arctic-like-2). A time-scaled tree demonstrates that the time of the most recent common ancestor (TMRCA) of Arctic and Arctic-like viruses is dated between 1255 and 1786. Evolution of the Arctic viruses has occurred through a northerly spread. The Arctic-like-2 lineage diverged first, whereas Arctic viruses share a TMRCA with Arctic-like-1 viruses.

Emergence of Arctic-like rabies lineage in India

A collection of 37 rabies-infected samples, 10 human saliva and 27 animal brain, were recovered during 2001-2004 from the cities of Bangalore and Hyderabad in southern India and from Kasauli, a mountainous region in Himachal Pradesh, northern India. Phylogenetic analysis of partial N gene nucleotide sequences of these 37 specimens and 1 archival specimen identified 2 groups, divided according to their geographic (north or south) origins. Comparison of selected Indian viruses with representative rabies viruses recovered worldwide showed a close association of all Indian isolates with the circumpolar Arctic rabies lineage distributed throughout northern latitudes of North America and Europe and other viruses recovered from several Asian countries.

Molecular characterization of rabies virus isolates in China during 2004

Human rabies cases have been on the rise during the past few years in China and a total of 2651 cases were reported in 2004. To better understand the current rabies epidemics in China, we isolated rabies viruses from dogs and humans from five provinces and characterized these isolates genetically by sequencing the entire nucleoprotein (N) gene. Comparison of the N genes among these isolates revealed 86.6-99.9% homology and these viruses can be grouped into three lineages. Phylogenetic analysis indicates that all the Chinese isolates have a close relationship with viruses circulating in Asian canine population. When compared with rabies viruses isolated previously, the three lineages were similar to three of the four groups. Thus, our data suggest that rabies viruses currently circulating in China were similar, if not identical, to those reported in the previous epidemics.

Molecular epidemiology of rabies virus isolates from South Korea

A molecular epidemiological study was performed on 13 Korean virus isolates, which were collected from wild and domestic animals diagnosed as rabid between 1998 and 2004. Seven samples were from domestic animals such as dogs and cattle infected by rabid raccoon dogs (Nyctereutes procyonoides koreensis), and the rest of the six samples were from raccoon dogs in the wild. The study was carried out based on the comparison of nucleotide and amino acid sequences of nucleoprotein (N) and glycoprotein (G) coding regions and nucleotide sequence of the G-L intergenic (Psi) non-coding region of the isolates. The similarities of nucleotide and amino acid sequence were at least 97.8 and 98.5%, respectively, between all Korean isolates. Phylogenetic analyses of the isolate showed that they formed a monophyletic group closely related to the Arctic strains but distant from other Asian strains, including Chinese strains. The fact that the raccoon dog is the main epidemic carrier of rabies in Korea and the results of these studies supported the conclusion of previous studies (Kuzmin et al.) that the raccoon dogs take part in the circulation of rabies virus within their natural territories in the Far East. The Korean isolates can be divided into two subgroups. All the topology of the most likelihood tree of Korean isolates using nucleotide and amino acid sequences of N, G and G-L region reflected not the species but the year of isolation and geographical location of the virus isolates. This study presents the detailed description of the molecular epidemiology of rabies virus in Korea.