Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions.

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers

The Primate Habituation Programme, Dzanga Sangha Protected Areas, Central African Republic: An overview

Dzanga Sangha Protected Areas (DSPA), including Dzanga-Ndoki National Park (DNNP), are located in SW Central African Republic (CAR) and are managed by the government and WWF. DSPA is CAR’s largest remaining nearly intact forest block and known for its outstanding biodiversity, including most of CAR's gorillas (G. g. gorilla). In 2012, DNNP, and its neighbouring NPs, were designated a World Heritage Site, the Sangha Tri-National complex (TNS) – classified as an exceptional priority area for western lowland gorilla and central chimpanzee (Pan t. troglodytes) conservation in the IUCN Regional Action Plan. The Primate Habituation Programme (PHP) was established in 1997 and plays a key role in DSPA’s conservation management strategy, generating significant revenue for the programme and tangible local community benefits. Now recognized as the most successful western lowland gorilla tourism and research programme, it has successfully habituated three groups, with another two undergoing habituation, and developed a controlled tourism programme. The habituated gorillas are regularly visited by tourists and are subjects of numerous scientific articles and film documentaries that have greatly contributed to our knowledge of this elusive species. Strong measures are in place to combat habitat loss and poaching in DSPA, but increased tourism, while providing income, can also negatively impact gorilla population health. Added to potential emerging diseases, human contact may increase stress and expose gorillas to human-borne pathogens, to which they may have little immunity. A PHP priority is to develop the programme into a model of sustainable best-practice with reduced risk of negative impacts from tourism/research. Current IUCN great ape tourism best practices (PHP is partly/fully compliant on ~90% of 156 criteria) include ongoing observational gorilla health monitoring, prohibiting visitors who are/have recently been ill and regular staff screening. However, disease risk, especially from asymptomatic pathogens, is a real threat and in order to monitor and mitigate these risks, the PHP set up a Wildlife Health Laboratory (WHL) in 2012. The main aim of this presentation is to give an overview of the PHP’s past, present and future activities (including habituation, research, tourism, and WHL), most of which continue despite the current political instability in CAR

Influence of food availability on the diet and activity budget of two western lowland gorilla (Gorilla gorilla gorilla) groups of differing size in the Dzanga-Ndoki National Park, Central African Republic

Variation in food availability, body size and group size are known to influence primate diet and activity budgets. Here we report how seasonal food availability shapes the diet and activity patterns of two habituated western lowland gorilla (WLG) groups of differing size. WLGs are ripe fruit opportunists, showing dietary flexibility when preferred foods are scarce. However, as fruit can be rare/ patchily distributed, as intra-group feeding competition increases with group size, access to individual patches may be limited. We thus predicted that frugivory decreases with increased group size and influences diet and activity budgets accordingly (increased diet breadth and time feeding since relying on alternative/lower quality food). First, we compared food availability between home-ranges by monitoring leafing/fruiting patterns of major gorilla food trees. Second, we compared the groups’ activity budgets and diet composition/diversity, testing for differences between high (HF) and low fruit seasons (LF). We measured gorilla activity over six months by continuous focal sampling of 16 target animals rotated daily from both groups (N=9 and N=15). Our results confirm that WLG diet consisted mainly of fruits (36%, then: stems 24%; leaves 21%; insects 14%; other food types 3%, and bark 2%) and spend most of their time feeding (39%, then: resting 33%; traveling 19%; social 5%, and other activities 4%). However, contrary to our predictions, we found no group differences within or between seasons: irrespective of group size both spent significantly less time feeding, but more time traveling and socializing, and consumed significantly more fruits, less leaves and bark during the HF compared to the LF. Our results show that WLG activity budgets and diet appear to vary more in response to ripe fruit availability than group size. We suggest that WLGs may cope with increased group size costs through other mechanisms such as group spread, rather than lowering diet quality or further changing activity patterns. Such flexibility may better allow WLG groups to track ripe fruits when available but, unlike sympatric chimpanzees, switch to more herbivorous diets when necessary, adjusting activity budgets accordingly ; WLGs thus may be considered more resilient faced with environmental change such as forest degradation

A Novel Orthohepadnavirus Identified in a Dead Maxwell’s Duiker (Philantomba maxwellii) in Taï National Park, Côte d’Ivoire

New technologies enable viral discovery in a diversity of hosts, providing insights into viral evolution. We used one such approach, the virome capture sequencing for vertebrate viruses (VirCapSeq-VERT) platform, on 21 samples originating from six dead Maxwell’s duikers (Philantomba maxwellii) from Taï National Park, Côte d’Ivoire. We detected the presence of an orthohepadnavirus in one animal and characterized its 3128 bp genome. The highest viral copy numbers were detected in the spleen, followed by the lung, blood, and liver, with the lowest copy numbers in the kidney and heart; the virus was not detected in the jejunum. Viral copy numbers in the blood were in the range known from humans with active chronic infections leading to liver histolytic damage, suggesting this virus could be pathogenic in duikers, though many orthohepadnaviruses appear to be apathogenic in other hosts, precluding a formal test of this hypothesis. The virus was not detected in 29 other dead duiker samples from the Côte d’Ivoire and Central African Republic, suggesting either a spillover event or a low prevalence in these populations. Phylogenetic analysis placed the virus as a divergent member of the mammalian clade of orthohepadnaviruses, though its relationship to other orthohepadnaviruses remains uncertain. This represents the first orthohepadnavirus described in an artiodactyl. We have tentatively named this new member of the genus Orthohepadnavirus (family Hepadnaviridae), Taï Forest hepadnavirus. Further studies are needed to determine whether it, or some close relatives, are present in a broader range of artiodactyls, including livestock.Peer Reviewe

Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers

Tropical field stations yield high conservation return on investment

Conservation funding is currently limited; cost-effective conservation solutions are essential. We suggest that the thousands of field stations worldwide can play key roles at the frontline of biodiversity conservation and have high intrinsic value. We assessed field stations’ conservation return on investment and explored the impact of COVID-19. We surveyed leaders of field stations across tropical regions that host primate research; 157 field stations in 56 countries responded. Respondents reported improved habitat quality and reduced hunting rates at over 80% of field stations and lower operational costs per km2 than protected areas, yet half of those surveyed have less funding now than in 2019. Spatial analyses support field station presence as reducing deforestation. These ‘earth observatories’ provide a high return on investment; we advocate for increased support of field station programs and for governments to support their vital conservation efforts by investing accordingly