Uncovering the magnitude of African pangolin poaching with extensive nanopore DNA genotyping of seized scales.

Trade in pangolins is illegal, and yet tons of their scales and products are seized at various ports. These large seizures are challenging to process and comprehensively genotype for upstream provenance tracing and species identification for prosecution. We implemented a scalable DNA barcoding pipeline in which rapid DNA extraction and MinION sequencing were used to genotype a substantial proportion of pangolin scales subsampled from 2 record shipments seized in Singapore in 2019 (37.5 t). We used reference sequences to match the scales to phylogeographical regions of origin. In total, we identified 2346 cytochrome b (cytb) barcodes of white-bellied (Phataginus tricuspis) (from 1091 scales), black-bellied (Phataginus tetradactyla) (227 scales), and giant (Smutsia gigantea) (1028 scales) pangolins. Haplotype diversity was higher for P. tricuspis scales (121 haplotypes, 66 novel) than that for P. tetradactyla (22 haplotypes, 15 novel) and S. gigantea (25 haplotypes, 21 novel) scales. Of the novel haplotypes, 74.2% were likely from western and west-central Africa, suggesting potential resurgence of poaching and newly exploited populations in these regions. Our results illustrate the utility of extensively subsampling large seizures and outline an efficient molecular approach for rapid genetic screening that should be accessible to most forensic laboratories and enforcement agencies.

Revelación de la magnitud de la caza furtiva del pangolín africano mediante el genotipo extenso de nanoporos de ADN de escamas incautadas Resumen Aunque el mercado de pangolines es ilegal, se incautan toneladas de sus escamas y productos derivados en varios puertos comerciales. Es un reto procesar estas magnas incautaciones y obtener el genotipo completo para usarlo en la trazabilidad logística ascendente e identificación de la especie y así imponer sanciones. Implementamos una canalización escalable del código de barras de ADN en el cual usamos la extracción rápida de ADN y la secuenciación MinION para obtener el genotipo de una proporción sustancial de las escamas de pangolín submuestreadas en dos cargamentos incautados en 2019 en Singapur (37.5 t). Usamos secuencias referenciales para emparejar las escamas con las regiones filogeográficas de origen. Identificamos en total 2,346 códigos de citocromo b (cytb) del pangolín de vientre blanco (Phataginus tricuspis) (de 1,091 escamas), de vientre negro (P. tetradactyla) (227 escamas) y del pangolín gigante (Smutsia gigantea) (1,028 escamas). La diversidad de haplotipos fue mayor en las escamas de P. tricuspis (121 haplotipos, 66 nuevos) que en las de P. tetradactyla (22 haplotipos, 15 nuevos) y S. gigantea (25 haplotipos, 21 nuevos). De los haplotipos nuevos, el 74.2% probablemente provenía del occidente y centro­occidente de África, lo que sugiere un resurgimiento potencial de la caza furtiva y poblaciones recién explotadas en estas regiones. Nuestros resultados demuestran la utilidad de submuestrear extensivamente las grandes incautaciones y esboza una estrategia molecular eficiente para un análisis genético rápido que debería ser accesible para la mayoría de los laboratorios forenses y las autoridades de aplicación.

Anthropogenic Transmission of SARS-CoV-2 from Humans to Lions, Singapore, 2021.

In Singapore, 10 captive lions tested positive for SARS-CoV-2 by real-time PCR. Genomic analyses of nanopore sequencing confirmed human-to-animal transmission of the SARS-CoV-2 Delta variant. Viral genomes from the lions and zookeeper shared a unique spike protein substitution, S:A1016V. Widespread SARS-CoV-2 transmission among humans can increase the likelihood of anthroponosis.

Detection of African Swine Fever Virus from Wild Boar, Singapore, 2023.

We detected African swine fever virus (ASFV) from a wild boar in Singapore. In <72 hours, we confirmed and reported ASFV p72 genotype II, CD2v serogroup 8, and IGR-II variant by using a combination of real-time PCR and whole-genome sequencing. Continued biosurveillance will be needed to monitor ASFV in Singapore.

The influence of the COVID-19 pandemic on the demand for different shades of green.

COVID-19 has heightened the dependence of urban dwellers on cultural ecosystem services provided by urban green spaces (UGS), specifically in regard to the provision of recreational opportunities, and psychological and physical health benefits arising from their use.As different types and levels of cultural ecosystem services are provided by different types of UGS, people may seek out different UGS to satisfy personal needs over various phases of COVID-19 mobility restrictions imposed by cities. We report on a study that took advantage of the different phases of COVID-19 mobility restrictions to assess the demand for and perception of different types of UGS in Singapore.The study utilised four datasets to compare demand for and visitorship patterns of UGS before the pandemic (Pre-Circuit Breaker), the duration of the strictest mobility restrictions (Circuit Breaker), and after the measures were relaxed (Post-Circuit Breaker). We used Google Search trends as a proxy for UGS demand, Google mobility data for an overview of population visitorship trends, visitor counts for granular insights on actual visitorship trends, and qualitative data on perception of parks by park visitors after restrictions eased. Parks were categorised as manicured and less manicured UGS for analysis.Search interest for UGS overall fell by more than 50% from during Circuit Breaker but the post-Circuit Breaker levels exceeded pre-Circuit Breaker, with a 70.9% increase for less manicured UGS compared to 20.8% for manicured UGS. This corroborated with Google mobility and visitor counts, which showed a steep decrease in park use followed by a rapid increase in the same periods, and with increased visitorship in the less manicured UGS. The perception study also showed that more than 50% of respondents reported visiting parks that they have never visited before, and there was a greater appreciation and use of UGS after the pandemic and preference for less manicured and more naturalistic landscapes.The pandemic has heightened the demand for cultural ecosystem services provided by UGS. Our study showed that this demand is not uniform across different types of UGS, with an increase visitorship and preference for less manicured green spaces. Read the free Plain Language Summary for this article on the Journal blog.