Mortality in sea lions is associated with the introduction of the H5N1 clade 2.3.4.4b virus in Brazil October 2023: whole genome sequencing and phylogenetic analysis.

Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) H5N1 virus was detected in the South American sea lions found dead in Santa Catarina, Brazil, in October 2023. Whole genome sequencing and comparative phylogenetic analysis were conducted to investigate the origin, genetic diversity, and zoonotic potentials of the H5N1 viruses. The H5N1 viruses belonged to the genotype B3.2 of clade 2.3.4.4b H5N1 virus, which was identified in North America and disseminated to South America. They have acquired new amino acid substitutions related to mammalian host affinity. Our study provides insights into the genetic landscape of HPAI H5N1 viruses in Brazil, highlighting the continuous evolutionary processes contributing to their possible adaptation to mammalian hosts.

Long-term stability in the circumpolar foraging range of a Southern Ocean predator between the eras of whaling and rapid climate change.

Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis), that forages on copepods and krill from ~30°S to the Antarctic ice edge (>60°S). We analyzed carbon and nitrogen isotope values of 1,002 skin samples from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude (>60°S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.

Crassicaudiasis in three geographically and chronologically distant Cuvier's beaked whales (Ziphius cavirostris) stranded off Brazil.

The Cuvier's beaked whale (CBW; Ziphius cavirostris) is a cosmopolitan marine mammal found in deep tropical and temperate waters of all oceans. CBW strandings have been recorded sporadically in Brazil; however, there is lack of information available regarding their causes of stranding and/or death. Herein, we report the epidemiologic, pathologic, morphologic parasitologic features and molecular identification of arterial and renal crassicaudiasis by Crassicauda sp. in three geographically and chronologically distant CBW stranded off Brazil. CBW-1 was an adult male stranded dead in Rio Grande do Sul State. CBW-2 was an adult female that stranded alive in Sergipe State and died shortly after. CBW-3 was and adult male that stranded dead in Santa Catarina State. The most relevant pathologic findings in these three CBW were severe, chronic proliferative mesenteric and caudal aortic endarteritis and chronic granulomatous and fibrosing interstitial nephritis with renicular atrophy and loss, and numerous intralesional Crassicauda sp. nematodes. Furthermore, CBW-1 had concomitant gram-negative bacterial pneumonia and pulmonary and hepatic thromboembolism. Morphologic analysis of renal adult nematodes identified Crassicauda sp. in the three CBW. Molecular analyses targeting the 18S and ITS-2 ribosomal loci of renal nematodes in CBW-2 and CBW-3 identified C. anthonyi. It is believed that severe arterial and renal crassicaudiasis likely resulted or contributed significantly to morbidity and death of these animals. These results expand the known geographical range of occurrence of crassicaudiasis in CBW. Specifically, the present study provides the first accounts of arterial and renal crassicaudiasis in CBW off the southern hemisphere, specifically in CBW off Brazil, and to the authors' knowledge, it is the first record of C. anthonyi in the southern Atlantic Ocean.

The northernmost haulout site of South American sea lions and fur seals in the western South Atlantic.

We present estimates of the seasonal and spatial occupation by pinnipeds of the Wildlife Refuge of Ilha dos Lobos (WRIL), based on aerial photographic censuses. Twenty aerial photographic censuses were analysed between July 2010 and November 2018. To assess monthly differences in the numbers of pinnipeds in the WRIL we used a Generalized Linear Mixed Model. Spatial analysis was carried out using Kernel density analysis of the pinnipeds on a grid plotted along the WRIL. Subadult male South American sea lions (Otaria flavescens) were the most abundant pinniped in the WRIL. Potential females of this species were also recorded during half of the census. The maximum number of pinnipeds observed in the WRIL was 304 in September 2018, including an unexpected individual southern elephant seal (Mirounga leonina), and a high number of South American fur seal yearlings (Arctocephalus australis). However, there was no statistically significant difference in counts between months. In all months analysed, pinnipeds were most often found concentrated in the northern portion of the island, with the highest abundances reported in September. This study confirms the importance of the WRIL as a haulout site for pinnipeds in Brazil, recommends that land research and recreational activities occur in months when no pinnipeds are present, and encourages a regulated marine mammal-based tourism during winter and spring months.

Animal-borne tags provide insights into the acoustic communication of southern right whales (Eubalaena australis) on the calving grounds.

This study investigated the repertoire, call-type variability and call rates of southern right whales on a calving ground off Brazil in the western South Atlantic. Acoustic tag data were collected from four lactating females and one juvenile. Pulsive, hybrid, and upcalls showed the greatest variability among call-types with up to 23% of non-standard forms detected. Quiet sounds (grunt, single, and double pulse) were detected for the first time in this species on the calving grounds. Although the sample size was limited, results suggest that social interaction increased call-type diversity and call rates, in line with other acoustic studies on right whales.

Genetic Diversity and Connectivity of Southern Right Whales (Eubalaena australis) Found in the Brazil and Chile-Peru Wintering Grounds and the South Georgia (Islas Georgias del Sur) Feeding Ground.

As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile-Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile-Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile-Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile-Peru.

Pathologic findings and causes of death in southern right whales Eubalaena australis, Brazil.

Southern right whales Eubalaena australis (SRWs) migrate to southern Brazil for breeding and calving from June through November. Overall, there is scarce knowledge on health status and pathologic conditions in SRWs. We report the pathologic and molecular investigation results of 8 SRWs that were necropsied between 2010 and 2017 within a breeding and calving ground in Santa Catarina state, Brazil. The animals were of various ages (7 newborns/calves, 1 adult) and sex (3 females, 5 males). Five whales stranded dead; 3 stranded alive and died shortly after (n = 2) or were euthanized (n = 1). The causes of stranding and/or death were neonatal respiratory distress syndrome with meconium aspiration (n = 3) with concomitant congenital hepatopathy in one of them; trauma of unknown origin (n = 3), infectious renal and lung disease with presumed sepsis (n = 1), and euthanasia (n = 1). Three animals were PCR-positive for cetacean morbillivirus; one of them also had morbilliviral antigen in kidney via immunohistochemical analysis. These results, integrating novel findings and a published report, contribute to the pathology knowledge of this species.

Cetacean morbillivirus in Southern Right Whales, Brazil.

Cetacean morbillivirus (CeMV) has caused repeated epizootics and interepizootic fatalities in a variety of cetacean species worldwide. Recently, a novel CeMV strain (GD-CeMV) was linked to a mass die-off of Guiana dolphins (Sotalia guianensis) in Brazil. Southern right whales (SRWs; Eubalaena australis) migrate to the southern Brazilian coast during austral winter and spring (June through November) for breeding and calving. Because unexplained high calf mortality rates have recurrently been documented in SRWs, we hypothesized they could be infected with CeMV. We developed a novel real-time RT-PCR method based on SYBR® GREEN for detection of CeMV and identified the virus in three out of five stranded SRWs from Santa Catarina state, Brazil. The partial sequences of the morbillivirus phosphoprotein gene suggest that the virus is similar to the GD-CeMV strain. Our results indicate CeMV can infect SRWs and should be considered in the differential aetiologic diagnosis of infectious diseases in this species. It also raises concern for potential conservation implications for this species in its main coastal breeding area off Southern Brazil.

The recovery of North Atlantic right whales, Eubalaena glacialis, has been constrained by human-caused mortality.

North Atlantic right whales (NARW), Eubalaena glacialis, were nearly exterminated by historical whaling. Their abundance slowly increased up until 2010, to a maximum of fewer than 500 whales, and since then they have been in decline. We assessed the extent to which the relatively slow increase demonstrated by NARW was intrinsic, and how much could be due to anthropogenic impacts. In order to do so, we first compared calf counts of three populations of Southern right whales (SRW), E. australis, with that of NARW, over the period 1992-2016. By this index, the annual rate of increase of NARW was approximately one-third of that of SRW. Next we constructed a population projection model for female NARW, using the highest annual survival estimates available from recent mark-resight analysis, and assuming a four-year calving interval. The model results indicated an intrinsic rate of increase of 4% per year, approximately twice that observed, and that adult female mortality is the main factor influencing this rate. Necropsy records demonstrate that anthropogenic mortality is the primary cause of known mortality of NARW. Anthropogenic mortality and morbidity has limited the recovery of NARW, and baseline conditions prior to their recent decline were already jeopardizing NARW recovery.

Vocalizations produced by southern right whale (Eubalaena australis) mother-calf pairs in a calving ground off Brazil.

Aiming to gather information on southern right whale (Eubalaena australis) mother-calf pairs' vocal behavior, archival acoustic recorders were deployed at a calving area off Brazil. Manual inspection of spectrograms revealed seven call classes: upcall, downcall, down-upcall, tonal variable, tonal constant, hybrid, and pulsive calls, which are consistent with those previously described for this species in Argentina. Gunshots and warbles, vocalizations described from other right whale species, were not detected. Mean values of start, end, maximum, minimum and peak frequencies, frequency bandwidth and duration were calculated for each call class. Start and end frequencies, frequency bandwidth and duration of upcalls recorded off Brazil were compared to those from other right whale populations and species. Only mean duration of upcalls from Brazil were significantly different from upcalls from all other populations. Differences in call duration may be driven by differences in demographic factors or background noise features among study areas. The repertoire characterization presented in this study will contribute to increase the utility of passive acoustic monitoring as a tool for conservation and research of southern right whales off Brazil as it provides important baseline information on the vocal behavior of this species.

Southern Right Whale (Eubalaena australis) Reproductive Success is Influenced by Krill (Euphausia superba) Density and Climate.

The reproductive success of southern right whale (Eubalaena australis) depends on body condition and, therefore, on foraging success. This, in turn, might be affected by climatically driven change in the abundance of the species main prey, krill (Euphausia superba), on the feeding grounds. Annual data on southern right whale number of calves were obtained from aerial surveys carried out between 1997 and 2013 in southern Brazil, where the species concentrate during their breeding season. The number of calves recorded each year varied from 7 to 43 ( = 21.11 ± 11.88). Using cross-correlation analysis we examined the response of the species to climate anomalies and krill densities. Significant correlations were found with krill densities (r = 0.69, p = 0.002, lag 0 years), Oceanic Niño Index (r = -0.65, p = 0.03, lag 6 years), Antarctic Oscillation (r = 0.76, p = 0.01, lag 7 years) and Antarctic sea ice area (r = -0.68, p = 0.002, lag 0 years). Our results suggest that global climate indices influence southern right whale breeding success in southern Brazil by determining variation in food (krill) availability for the species. Therefore, increased frequency of years with reduced krill abundance, due to global warming, is likely to reduce the current rate of recovery of southern right whales from historical overexploitation.

Humans, Fish, and Whales: How Right Whales Modify Calling Behavior in Response to Shifting Background Noise Conditions.

This study investigates the role of behavioral plasticity in the variation of sound production of southern right whales (Eubalaena australis) in response to changes in the ambient background noise conditions. Data were collected from southern right whales in Brazilian waters in October and November 2011. The goal of this study was to quantify differences in right whale vocalizations recorded in low background noise as a control, fish chorus noise, and vessel noise. Variation in call parameters were detected among the three background noise conditions and have implications for future studies of noise effects on whale sound production.