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.

Review: The status of the endangered Eld’s deer (Rucervus eldii) and conservation actions in Thailand

Abstract. Sukmasuang R, Bhumpakphan N, McShea WJ, Wajjwalku W, Siriaroonrat B, Kamolnoranart S, Yindee M, Nipanan T, Maleehuan B, Khanthathongsakuldee K, Pongcharoen C, Sutummawong N, Thomas W. 2022. Review: The status of the endangered Eld’s deer (Rucervus eldii) and conservation actions in Thailand. Biodiversitas 23: 5020-5034. The endangered Eld’s deer (Rucervus eldii) once roamed throughout the plains and dry forests of South and Southeast Asia. However, due to heavy poaching and habitat loss, the population has declined drastically and has disappeared from many of its historical ranges. They are presently found in some natural areas of India, Myanmar, Cambodia, Lao PDR, and Hainan Island, China. Thailand used to be the distribution center of the species, where two subspecies, the R.e. thamin and R.e. siamensis, were found. However, both subspecies have disappeared from the natural resources of Thailand since the early 1990s. Many conservation programs have been conducted to save this species in Thailand, such as captive breeding and reintroduction. Our literature review revealed that currently, more than a thousand R.e. thamin are housed in over 20 wildlife breeding facilities and 109 R.e. siamensis in 8 breeding facilities. Based on the workshops on conservation and restoration of the species, suitable genetic selection can create populations suitable for return to protected forest areas in Thailand. At present, more than 554 R.e. thamin have been released back into the wild in 8 wildlife sanctuaries, 3 national parks and 1 non-hunting area and 27 R.e. siamensis were released in 2 wildlife sanctuaries in Thailand. The follow-up of the deer in the release areas was flawed. Major knowledge gaps include recent trends in the population dynamics, habitat selection, diet items and threats. Identifying and restoring suitable dry forest habitats for reintroduction are also keys for species conservation.

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.

Maturation competence of swamp buffalo oocytes obtained by ovum pick-up and from slaughterhouse ovaries

This study was designed with the final goal of improving in vitro embryo production in the Thai swamp buffalo (Bubalus bubalis carabensis). Oocytes were collected by ovum pick-up (OPU) from six non-lactating multiparous swamp buffalo twice per week for 10 consecutive sessions followed by once-weekly collection for 10 consecutive sessions without hormone stimulation. In addition, oocytes were collected from slaughterhouse ovaries that were classified as follows: ovaries from non-pregnant cows with a visible corpus luteum (NPCL); pregnant cows with a corpus luteum (P); and non-pregnant cows without a corpus luteum (NP). Follicles in each group of ovaries were categorized as small (2-4 mm), medium-sized (5-8 mm) or large follicles (≥ 9 mm). The quality of the oocytes was assessed by their capacity to undergo in vitro maturation. The total number of observed follicles per session (all sizes combined) was larger in the once-weekly OPU group compared with the twice-weekly OPU group. In particular, the numbers of small and large follicles were higher in the once-weekly OPU group (5.2 ± 0.7 and 0.9 ± 0.2, respectively) than in the twice-weekly OPU group (3.9 ± 0.5 and 0.5 ± 0.1). The number of medium-sized follicles did not differ between the groups. The percentages of oocytes with an abnormal spindle morphology were not different between oocytes from the twice-weekly (30.0%) and the once-weekly (28.6%) OPU groups. A higher percentage of oocytes obtained in vitro (49.5%) exhibited nuclear abnormalities compared with those obtained in vivo (≤34.8%) after in vitro maturation. In conclusion, oocytes can be successfully collected by OPU in the swamp buffalo, without hormonal pretreatment, and per week more good-quality oocytes can be collected by twice-weekly OPU. In addition, oocytes collected from slaughterhouse ovaries can be used with the reproductive status of the cow having no influence on the maturation competence of oocytes.

Y-chromosomal variation confirms independent domestications of swamp and river buffalo

Y-chromosomal variation in the water buffalo was analysed by sequencing of DBY, ZFY and SRY gene segments. A clear separation of the paternal lineages of the river and swamp types parallels the differences between their maternal lineages and nuclear DNA. Sequence divergence was found to be comparable to the divergence of taurine cattle and zebu, and this divergence predated domestication, confirming that river and swamp buffalo originated from different wild populations. Within a sample of 23 Thai swamp buffaloes, we identified four haplotypes with different geographical distributions, two of which were shared by Thai wild buffaloes.