Correction: Kosoltanapiwat et al. A Novel Simian Adenovirus Associating with Human Adenovirus Species G Isolated from Long-Tailed Macaque Feces. Viruses 2023, 15, 1371.

After publication of the article, the authors received comments from a member of the Viruses editorial board who is an expert in the field of adenovirus concerning figures and references that should be included in the paper [...].

A Novel Simian Adenovirus Associating with Human Adeno-virus Species G Isolated from Long-Tailed Macaque Feces.

Metagenomics has demonstrated its capability in outbreak investigations and pathogen surveillance and discovery. With high-throughput and effective bioinformatics, many disease-causing agents, as well as novel viruses of humans and animals, have been identified using metagenomic analysis. In this study, a VIDISCA metagenomics workflow was used to identify potential unknown viruses in 33 fecal samples from asymptomatic long-tailed macaques (Macaca fascicularis) in Ratchaburi Province, Thailand. Putatively novel astroviruses, enteroviruses, and adenoviruses were detected and confirmed by PCR analysis of long-tailed macaque fecal samples collected from areas in four provinces, Ratchaburi, Kanchanaburi, Lopburi, and Prachuap Khiri Khan, where humans and monkeys live in proximity (total n = 187). Astroviruses, enteroviruses, and adenoviruses were present in 3.2%, 7.5%, and 4.8% of macaque fecal samples, respectively. One adenovirus, named AdV-RBR-6-3, was successfully isolated in human cell culture. Whole-genome analysis suggested that it is a new member of the species Human adenovirus G, closely related to Rhesus adenovirus 53, with evidence of genetic recombination and variation in the hexon, fiber, and CR1 genes. Sero-surveillance showed neutralizing antibodies against AdV-RBR-6-3 in 2.9% and 11.2% of monkeys and humans, respectively, suggesting cross-species infection of monkeys and humans. Overall, we reported the use of metagenomics to screen for possible new viruses, as well as the isolation and molecular and serological characterization of the new adenovirus with cross-species transmission potential. The findings emphasize that zoonotic surveillance is important and should be continued, especially in areas where humans and animals interact, to predict and prevent the threat of emerging zoonotic pathogens.

Day and night camera trap videos are effective for identifying individual wild Asian elephants.

Regular monitoring of wild animal populations through the collection of behavioral and demographic data is critical for the conservation of endangered species. Identifying individual Asian elephants (Elephas maximus), for example, can contribute to our understanding of their social dynamics and foraging behavior, as well as to human-elephant conflict mitigation strategies that account for the behavior of specific individuals involved in the conflict. Wild elephants can be distinguished using a variety of different morphological traits-e.g., variations in ear and tail morphology, body scars and tumors, and tusk presence, shape, and length-with previous studies identifying elephants via direct observation or photographs taken from vehicles. When elephants live in dense forests like in Thailand, remote sensing photography can be a productive approach to capturing anatomical and behavioral information about local elephant populations. While camera trapping has been used previously to identify elephants, here we present a detailed methodology for systematic, experimenter differentiation of individual elephants using data captured from remote sensing video camera traps. In this study, we used day and night video footage collected remotely in the Salakpra Wildlife Sanctuary in Thailand and identified 24 morphological characteristics that can be used to recognize individual elephants. A total of 34 camera traps were installed within the sanctuary as well as crop fields along its periphery, and 107 Asian elephants were identified: 72 adults, 11 sub-adults, 20 juveniles, and four infants. We predicted that camera traps would provide enough information such that classified morphological traits would aid in reliably identifying the adult individuals with a low probability of misidentification. The results indicated that there were low probabilities of misidentification between adult elephants in the population using camera traps, similar to probabilities obtained by other researchers using handheld cameras. This study suggests that the use of day and night video camera trapping can be an important tool for the long-term monitoring of wild Asian elephant behavior, especially in habitats where direct observations may be difficult.

Simian adenoviruses: Molecular and serological survey in monkeys and humans in Thailand.

Simian adenoviruses are in the genus Mastadenovirus of the family Adenoviridae. This family is composed of non-enveloped, double-stranded DNA viruses that infect a wide range of animals. Mastadenoviruses infect mammals, including non-human primates and humans. The close genetic relatedness between simian and human adenoviruses, with its associated potential for the cross-species transmission of zoonotic adenoviruses from monkeys to humans and vice versa, poses important health concerns and thus warrants research. In this study, we performed a molecular survey of adenoviruses in monkeys in Thailand. Most of the monkeys tested here were long-tailed macaques, free-ranging in areas close to human territories across four provinces: Ratchaburi, Kanchanaburi, Lopburi, and Prachuap Khiri Khan. A few fecal samples from captive wild monkeys (a stump-tailed macaque, pig-tailed macaques, gibbons, and a leaf monkey) were also tested. Adenoviruses were detected in 33.3% (70 out of 210) of the fecal or rectal swab samples. The viruses identified in these samples included Simian adenovirus (SAdV)-A, SAdV-B, SAdV-H, Human adenovirus (HAdV)-D, HAdV-G, and a bat adenovirus species. One SAdV-B, SAdV RBR-7-10, was isolated from a long-tailed macaque fecal sample and identified by mass spectrometry. Its full hexon gene and nearly complete DNA polymerase gene were sequenced and analyzed, and the virions were imaged by transmission electron microscopy. The SAdV RBR-7-10 virus was used in a microneutralization assay to identify virus-specific antibodies in monkey plasma and human serum samples collected from the same areas in Prachuap Khiri Khan Province. We detected neutralizing antibodies against SAdV RBR-7-10 in 6.8% (n = 103) of the monkey samples but in none of the 125 human serum samples, suggesting no cross-species transmission of SAdV RBR-7-10 occurred at this study site. Nevertheless, a continuing surveillance of pathogens in monkeys is warranted to quickly identify possible emerging zoonotic outbreaks.

Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis).

Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3' truncated and containing only 5' UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5' UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.

Investigating the use of sensory information to detect and track prey by the Sunda pangolin (Manis javanica) with conservation in mind.

Pangolins are of conservation concern as one of the most heavily poached, yet least understood mammals. The Sunda pangolin (Manis javanica) in particular is a critically endangered species. Here, we investigate the behaviour of these pangolins, for the first time, using a battery of cognitive tasks based on a manipulation of available sensory information. In an object-choice task in which only one of two containers was baited with food, the pangolins were able to find the food with olfactory information alone (N = 2), but not with visual or acoustic information alone (N = 1). The single subject tested on all three domains was further tested on how he used smell to find food by providing him with an opportunity to find it from a controlled distance or by using scent trails as a guide. The results suggest that our subject may have the capacity to exploit scent trails left by prey which can be tracked to a final source, though we found no evidence to suggest that he had the ability to initiate hunts based on distant prey odors. Despite the small sample size, this is the first controlled experiment to investigate pangolin foraging behaviour and cognition, which may have implications for the future protection of pangolin habitat based on the location of prey species.

Genetic variations in regions of bovine and bovine-like enteroviral 5'UTR from cattle, Indian bison and goat feces.

BACKGROUND: Bovine enteroviruses (BEV) are members of the genus Enterovirus in the family Picornaviridae. They are predominantly isolated from cattle feces, but also are detected in feces of other animals, including goats and deer. These viruses are found in apparently healthy animals, as well as in animals with clinical signs and several studies reported recently suggest a potential role of BEV in causing disease in animals. In this study, we surveyed the presence of BEV in domestic and wild animals in Thailand, and assessed their genetic variability. METHODS: Viral RNA was extracted from fecal samples of cattle, domestic goats, Indian bison (gaurs), and deer. The 5' untranslated region (5'UTR) was amplified by nested reverse transcription-polymerase chain reaction (RT-PCR) with primers specific to BEV 5'UTR. PCR products were sequenced and analyzed phylogenetically using the neighbor-joining algorithm to observe genetic variations in regions of the bovine and bovine-like enteroviral 5'UTR found in this study. RESULTS: BEV and BEV-like sequences were detected in the fecal samples of cattle (40/60, 67 %), gaurs (3/30, 10 %), and goats (11/46, 24 %). Phylogenetic analyses of the partial 5'UTR sequences indicated that different BEV variants (both EV-E and EV-F species) co-circulated in the domestic cattle, whereas the sequences from gaurs and goats clustered according to the animal species, suggesting that these viruses are host species-specific. CONCLUSIONS: Varieties of BEV and BEV-like 5'UTR sequences were detected in fecal samples from both domestic and wild animals. To our knowledge, this is the first report of the genetic variability of BEV in Thailand.

Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region.

The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY, SRY and DBY sequences. Swamp buffalo has a higher diversity of both maternal and paternal lineages than river buffalo, with also a remarkable contrast between a weak phylogeographic structure of river buffalo and a strong geographic differentiation of swamp buffalo. The highest diversity of the swamp buffalo maternal lineages was found in south China and north Indochina on both banks of the Mekong River, while the highest diversity in paternal lineages was in the China/Indochina border region. We propose that domestication in this region was later followed by introgressive capture of wild cows west of the Mekong. Migration to the north followed the Yangtze valley as well as a more eastern route, but also involved translocations of both cows and bulls over large distances with a minor influence of river buffaloes in recent decades. Bayesian analyses of various migration models also supported domestication in the China/Indochina border region. Coalescence analysis yielded consistent estimates for the expansion of the major swamp buffalo haplogroups with a credibility interval of 900 to 3900 years BP. The spatial differentiation of mtDNA and Y-chromosomal haplotype distributions indicates a lack of gene flow between established populations that is unprecedented in livestock.