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Marine turtle fibropapillomatosis (FP) is a devastating neoplastic disease characterized by single or multiple cutaneous and visceral fibrovascular tumors. Chelonid alphaherpesvirus 5 (ChHV5) has been identified as the most likely etiologic agent. From 2010 to 2013, the presence of ChHV5 DNA was determined in apparently normal skin, tumors and swab samples (ocular, nasal and cloacal) collected from 114 olive ridley (Lepidochelys olivacea) and 101 green (Chelonia mydas) turtles, with and without FP tumors, on the Pacific coasts of Costa Rica and Nicaragua. For nesting olive ridley turtles from Costa Rica without FP, 13.5% were found to be positive for ChHV5 DNA in at least one sample, while in Nicaragua, all olive ridley turtles had FP tumors, and 77.5% tested positive for ChHV5 DNA. For green turtles without FP, 19.8% were found to be positive for ChHV5 DNA in at least one of the samples. In turtles without FP tumors, ChHV5 DNA was detected more readily in skin biopsies than swabs. Juvenile green turtles caught at the foraging site had a higher prevalence of ChHV5 DNA than adults. The presence of ChHV5 DNA in swabs suggests a possible route of viral transmission through viral secretion and excretion via corporal fluids.

Several highly infectious diseases can be transmitted through feces and cause elevated mortality among carnivore species. One such infectious agent, canine distemper virus (CDV; Paramyxoviridae: Morbillivirus), has been reported to affect wild carnivores, among them several felid species. We screened free-ranging and captive wild carnivores in Costa Rica for CDV. Between 2006 and 2012, we collected 306 fecal samples from 70 jaguars (Panther onca), 71 ocelots ( Leopardus pardalis ), five jaguarundis (Puma yaguaroundi), 105 pumas ( Puma concolor ), five margays ( Leopardus wiedii ), 23 coyotes ( Canis latrans ), and 27 undetermined Leopardus spp. We found CDV in six individuals: one captive jaguarundi (rescued in 2009), three free-ranging ocelots (samples collected in 2012), and two free-ranging pumas (samples collected in 2007). Phylogenetic analyses were performed using sequences of the phosphoprotein (P) gene. We provide evidence of CDV in wild carnivores in Costa Rica and sequence data from a Costa Rican CDV isolate, adding to the very few sequence data available for CDV isolates from wild Central American carnivores.

The non-invasive collection of biological samples has proven useful to study a diverse array of research topics worldwide. Here, we present a systematic bibliographical synthesis exploring how the non-invasive collection of genetic samples has been used to study avian populations in the Neotropics. We searched international online databases for scientific publications, spanning from 2007 to 2017, to describe the trends and identify the sample types used, species studied, and research questions addressed. The analysis of 21 articles showed that shed feathers were most frequently used (66.7% of articles), followed by carcasses (14.2%), eggs (9.5%), and non-invasively obtained blood (4.8%); one study used both feces and shed feathers. Most studies addressed population genetic issues (38.1%), followed by species identification (28.6%), phylogenetic questions (14.3%), molecular sexing (9.5%), and parentage analyses (9.5%). Brazil produced almost half (47.6%) of the publications retrieved. Despite an increasing interest in using non-invasive sampling to study Neotropical avifauna, its application is still largely concentrated in the most developed countries in this region and to explore a limited number of questions. A more regular use of non-invasive sampling would help advance the knowledge of ecological, behavioral, genetic, and evolutionary aspects of Neotropical birds. Investigating the extent of human–wildlife conflict, such as impact of road-kills, illegal traffic, and collision with aerial infrastructure or unmanned vehicles, is an underexplored avenue of research in which this method could be of much help. Non-invasive genetic sampling can help tackle conservation problems and pave the way to scientifically informed conservation policies in this avian biodiversity hotspot.

Once widely distributed throughout the lowland forests of Costa Rica, scarlet macaws (Ara macao) have been reduced to two major, geographically separated, populations along the Pacific slope. Past demographic declines raise conservation concerns regarding the detrimental effects of population fragmentation. This investigation aimed to evaluate the current status of scarlet macaws along the Pacific slope by examining levels of genetic variation and patterns of genetic structure within and among remnant populations. Statistical analyses using multilocus genotypes revealed strong differentiation between Central and South Pacific populations, suggesting local geographic barriers have historically restricted gene flow between these localities. High genetic diversity suggests neither population suffers from genetic erosion, likely resulting from relatively large population sizes and high dispersal capacity and longevity. However, evidence of disequilibrium within the Central Pacific population infers anthropogenic threats have disrupted natural population dynamics. These results advocate on focusing available resources on habitat restoration and nest protection, as a means to assist in reestablishing demographic stability and maintain the genetic health of wild scarlet macaws in Costa Rica.

We conducted a study of the two main populations of free-living Scarlet Macaws ( Ara macao) in Costa Rica to detect the causal agents of avian tuberculosis using noninvasive techniques. We analyzed 83 fecal samples collected between February and May 2016 from the central and southern Pacific areas in the country. Using PCR, we first amplified the 16S region of the ribosomal RNA, common to all Mycobacterium species. Then, products from the insertion sequence IS901 and from a 155-base pair DNA fragment evidenced the presence of the avian pathogenic Mycobacterium avium subsp. avium strain and a Mycobacterium genavense strain, respectively. Seven of 38 (18%) samples collected in the central Pacific area were positive for Mycobacterium spp. and 3 of 38 (8%) were positive for M. genavense, with one sample amplifying regions for both. Two of the 45 (4%) samples collected in the south Pacific area of Costa Rica were positive to M. a. avium. Our detection of avian tuberculosis pathogens in free-living Scarlet Macaws suggests that free-living macaws could excrete in their feces M. genavense, bird-pathogenic M. a. avium, and possibly other Mycobacteria (not detected in our study).

Parvoviruses in the genera Bocaparvovirus (HBoV), Erythroparvovirus (B19) and Tetraparvovirus (PARV4) are the only autonomous parvoviruses known to be associated with human and non‐human primates based on studies and clinical cases in humans worldwide and non‐human primates in Asia and Africa. Here, the presence of these agents with pathogenic potential was assessed by PCR in blood and faeces from 55 howler monkeys, 112 white‐face monkeys, 3 squirrel monkeys and 127 spider monkeys in Costa Rica and El Salvador. Overall, 3.7% (11/297) of the monkeys had HboV DNA, 0.67% (2/297) had B19 DNA, and 14.1% (42/297) had PARV4 DNA, representing the first detection of these viruses in New World Primates (NWP). Sex was significantly associated with the presence of HBoV, males having greater risk up to nine times compared with females. Captivity was associated with increased prevalence for PARV4 and when all viruses were analysed together. This study provides compelling molecular evidence of parvoviruses in NWPs and underscores the importance of future research aimed at understanding how these viruses behave in natural environments of the Neotropics and what variables may favour their presence and transmission.

West Nile virus (WNV) in the Americas is thought to be transported at large spatial scales by migratory birds and locally spread and amplified by resident birds. Local processes, including interspecific interactions and dominance of passerine species recognized as competent reservoirs, may boost infection and maintain endemic cycles. Change in species composition has been recognized as an important driver for infection dynamics. Due to migration and changes in species diversity and composition in wintering grounds, changes in infection prevalence are expected. To these changes, we used PCR to estimate the prevalence of WNV in wild resident birds during the dry and rainy seasons of 2012 in Yucatan, Mexico. Serum samples were obtained from 104 wild birds, belonging to six orders and 35 species. We detected WNV in 14 resident birds, representing 11 species and three orders. Prevalences by order was Passeriformes (27%), Columbiformes (6%), and Piciformes (33%). Resident birds positive to WNV from Yucatan may be indicative of local virus circulation and evidence of past virus transmission activity.