Seroevidence of SARS-CoV-2 spillback to rodents in Sarawak, Malaysian Borneo.

BACKGROUND: SARS-CoV-2 is believed to have originated from a spillover event, where the virus jumped from bats to humans, leading to an epidemic that quickly escalated into a pandemic by early 2020. Despite the implementation of various public health measures, such as lockdowns and widespread vaccination efforts, the virus continues to spread. This is primarily attributed to the rapid emergence of immune escape variants and the inadequacy of protection against reinfection. Spillback events were reported early in animals with frequent contact with humans, especially companion, captive, and farmed animals. Unfortunately, surveillance of spillback events is generally lacking in Malaysia. Therefore, this study aims to address this gap by investigating the presence of SARS-CoV-2 neutralising antibodies in wild rodents in Sarawak, Malaysia. RESULTS: We analysed 208 archived plasma from rodents collected between from 2018 to 2022 to detect neutralising antibodies against SARS-CoV-2 using a surrogate virus neutralisation test, and discovered two seropositive rodents (Sundamys muelleri and Rattus rattus), which were sampled in 2021 and 2022, respectively. CONCLUSION: Our findings suggest that Sundamys muelleri and Rattus rattus may be susceptible to natural SARS-CoV-2 infections. However, there is currently no evidence supporting sustainable rodent-to-rodent transmission.

Detection of novel coronaviruses from dusky fruit bat (Penthetor lucasi) in Sarawak, Malaysian Borneo.

BACKGROUND: Sarawak has one of the highest diversity of fruit bats species (family Pteropodidae) in Malaysia, with 19 species described. Most coronavirus (CoV) studies have mainly focused on insectivorous bats, resulting in a lack of information on CoVs present in frugivorous bats. In addition, bat CoV surveillance activities are lacking in Malaysia. OBJECTIVES: Our study focuses on determining the presence of bat CoVs in dusky fruit bat (Penthetor lucasi). METHODS: Guano samples belonging to P. lucasi were collected from Wind Cave Nature Reserve. The samples were screened for the presence of CoVs using validated hemi-nested consensus RNA-dependent RNA polymerase consensus primers. RESULTS: The bat CoV positivity rate was 38.5% (n = 15/39), with the viruses belonging to two subgenera: Alphacoronavirus (α-CoV) and Betacoronavirus (ß-CoV). Phylogenetic analysis revealed that CoVs from 14 samples of P. lucasi belong to the genus α-CoV and may represent previously described genetic lineages in insectivorous bats in Wind Cave. However, only one sample of P. lucasi was detected with ß-CoV which is closely related to subgenus Nobecovirus, which is commonly seen in frugivorous bats. CONCLUSIONS: This study provides the first available data on CoVs circulating in P. lucasi.

Serosurveillance of SARS-CoV-2 in companion animals in Sarawak, Malaysia.

SARS-CoV-2 is a zoonotic betacoronavirus that was first reported at the dawn of 2019 in Wuhan, China and has since spread globally, causing an ongoing pandemic. Anthroponotic transmission was reported early, with confirmed infections reported in 26 species to date, including dogs and cats. However, there is a paucity of reports on the transmission of SARS-CoV-2 to companion animals, and thus, we aimed to estimate the seroprevalence of SARS-CoV-2 in dogs and cats in Sarawak, Malaysia. From August 2022 to 2023, we screened plasma samples of 172 companion animals in Sarawak, Malaysia, using a species-independent surrogate virus neutralization test. Our findings revealed the presence of neutralizing antibodies of SARS-CoV-2 in 24.5% (27/110) of dogs and 24.2% (15/62) of cats. To the best of our knowledge, this is the first report of the seroprevalence of SARS-CoV-2 in companion animals in Malaysia. Our findings emphasize the need for pet owners to distance themselves from their pets when unwell, and a strategy must be in place to monitor SARS-CoV-2 in companion animals to assess the potential impact of the virus on companion animals.

A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2

BackgroundCOVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rigorous detection and treatment strategies against SARS-CoV-2 have become very challenging due to continuous evolutions to the viral genome. Therefore, careful genomic analysis is sorely needed to understand transmission, the cellular mechanism of pathogenicity, and the development of vaccines or drugs. ObjectiveIn this study, we intended to identify SARS-CoV-2 genome variants that may help understand the cellular and molecular foundation of coronavirus infections required to develop effective intervention strategies. MethodsSARS-CoV-2 genome sequences were downloaded from an open-source public database, processed, and analyzed for variants in target detection sites and genes. ResultsWe have identified six unique variants, G---AAC, T---AAC---T; AAC---T; C----C; C-------C; and C--------T at the nucleocapsid region and eleven major hotspot mutant genes: nsp3, surface glycoprotein, nucleocapsid phosphoprotein, ORF8, nsp6, nsp2, nsp4, helicase, membrane glycoprotein, 3-5 exonuclease, and 2-O-ribose methyltransferases. In addition, we have identified eleven major mutant genes that may have a crucial role in SARS-CoV-2 pathogenesis. ConclusionStudying haplotype variants and 11 major mutant genes to understand the mechanism of action of fatal pathogenicity and inter-individual variations in immune responses is inevitable for managing target patient groups with identified variants and developing effective anti-viral drugs and vaccines.

Loss of p53 suppresses replication stress-induced DNA damage in ATRX-deficient neuroblastoma.

Genetic aberrations are present in the ATRX gene in older high-risk neuroblastoma (NB) patients with very poor clinical outcomes. Its loss-of-function (LoF) facilitates the alternative lengthening of telomeres (ALT) pathway in tumor cells and is strongly linked to replication stress (RS) and DNA damage through G-quadruplex (G4) DNA secondary structures. However, limited information is available on ATRX alteration-related NB tumorigenesis. We herein knocked out (KO) ATRX in MYCN-amplified (NGP) and MYCN single copy (SK-N-AS) NB cells with wild-type (wt) and truncated TP53 at the C terminus, respectively, using CRISPR/Cas9 technologies. The loss of ATRX increased DNA damage and G4 formation related to RS in TP53 wt isogenic ATRX KO NGP cells, but not in SK-N-AS clones. A gene set enrichment analysis (GSEA) showed that the gene sets related to DNA double-strand break repair, negative cell cycle regulation, the G2M checkpoint, and p53 pathway activation were enriched in NGP clones. The accumulation of DNA damage activated the ATM/CHK2/p53 pathway, leading to cell cycle arrest in NGP clones. Interestingly, ATRX loss did not induce RS related to DNA damage response (DDR) in TP53-truncated SK-N-AS cells. p53 inactivation abrogated cell cycle arrest and reduced G4 accumulation in NGP clones. The loss of p53 also induced G4 DNA helicases or Fanconi anemia group D2 protein (FANCD2) with ATRX deficiency, suggesting that ATRX maintained genome integrity and p53 deficiency attenuated RS-induced DNA damage in NB cells featuring inactivated ATRX by regulating DNA repair mechanisms and replication fork stability.

The systematic position of Hypsugo macrotis (Chiroptera: Vespertilionidae) and a new record from Peninsular Malaysia.

The Southeast Asian species of Hypsugo are rare bats, except for H. cadornae and H. pulveratus, which are distributed throughout the Indomalayan region. Hypsugo macrotis is restricted to Peninsular Malaysia, Sumatra, Java and adjacent islands, and is known only from a handful of specimens. Here we report a new locality record of the species from Seremban, Peninsular Malaysia, which also represents the first known building-dweller colony of any Hypsugo from the region. We discuss the taxonomic status of two morphologically similar species, H. macrotis and H. vordermanni, and provide the first COI and cyt b gene sequences for H. macrotis and reconstruct the species' phylogenetic relationships.

Optical precursors in coupled-resonator-induced transparency.

We experimentally examined the propagation of temporally square modulated optical pulses through a coupled ring resonator. Sharp transient spikes appeared as the square pulses entered the system. The main signal gradually grew up through coupled-resonator-induced transparency (CRIT), with the time constant determined by a second resonator. Transient spikes were attributed to the higher and lower spectral components of the incident pulse, to which the resonators cannot respond; hence, they were interpreted as optical precursors. The experiments, therefore, demonstrated that precursors and the main signal can be observed separately, with amplitudes comparable to that of the incident step in CRIT.

Delayed optical images through coupled-resonator-induced transparency.

We propagated transverse two-dimensional images encoded on optical pulses through a frequency window of a coupled-image-resonator-induced transparency. The optical images are stored and delayed by 10.6ns, reflecting the tunable dispersion of the coupled resonator. The k-space bandwidth of the amplitude transfer function of the system is discussed in the presence of the off-resonance Fano interference effect between the two resonators.

Advanced and delayed images through an image resonator.

We performed optical image propagation experiments in an image resonator consisting of a Fabry-Perot resonator in reflection geometry. Two-dimensional images encoded on optical pulses of 32ns were stored, and either advanced, -6.0ns, or delayed, 10.9ns, using the dispersion relation relevant to the image resonator, in the under- or over- coupling condition, respectively. The overall images are propagated through the resonator clearly, while the diffraction effects were analyzed both in real-space and in k-space.

Effectiveness of participatory planning for community management of fisheries in Bangladesh.

This study provides statistical evidence that support for community-based management of resources was more effective when initiated through a process known as participatory action plan development (PAPD). Thirty-six sites were studied where community management of fisheries was facilitated by NGOs. All involved community participation and establishing local fisheries management institutions. However, communities were able to take up more conservation-related interventions and faced fewer conflicts in the 18 sites where a PAPD was the basis for collective action and institution development. This indicates the value and effectiveness of adopting good practice in participatory planning, such as PAPD, which helps diverse stakeholders find common problems and solutions for natural resource management.

Fate of maize intrinsic and recombinant genes in calves fed genetically modified maize Bt11.

The presence of maize intrinsic and recombinant cry1Ab genes in the gastrointestinal (GI) contents, peripheral blood mononuclear cells (PBMC), and visceral organs of calves fed genetically modified Bt11 maize was examined by PCR in a subchronic 90-day performance study. Samples were collected from six Japanese Black/Holstein calves fed Bt11 maize and from six calves fed non-Bt maize. Fragments of maize zein (Ze1), invertase, chloroplast, and cry1Ab were detected inconsistently in the rumen fluid and rectal contents 5 and 18 h after feeding. The chloroplast DNA fragments of ribulose-1,5-bisphosphate carboxylase/oxygenase and tRNA were detected inconsistently in the PBMC, the visceral organs, and the longissimus muscle, while the cry1Ab gene was never detected in PBMC or in the visceral organs. These results suggest that feed-derived maize DNA was mostly degraded in the GI tract but that fragmented DNA was detectable in the GI contents as a possible source of transfer to calf tissues. These results also suggest that the recombinant cry1Ab genes were not transferred to the PBMC and tissues of calves fed Bt11 maize.

Lessons from community based management of floodplain fisheries in Bangladesh.

Inland (floodplain) fisheries remain the most important contributor to fish production in Bangladesh. They have in the past been administered to generate government revenue without due concern for sustainability or equity. Community Based Fisheries Management (CBFM) is a possible solution and was tested in 19 waterbodies (rivers and beels) during 1996-2000. The outcomes so far are assessed with respect to social, institutional, and physical context, and the interactions that arose in establishing CBFM. The lessons drawn are that: it was essential that communities obtained rights over the fisheries, strong facilitation was necessary, taking up visible resource management actions greatly helped, success was more likely in homogeneous communities, external threats were a strong limiting factor, clear boundaries and small fisheries were not so critical, and new institutions could be built with as much ease (or difficulty) as modifying existing ones. Effective well-defined partnerships of NGOs and government were not easy to establish but were sufficiently beneficial that in several locations new community institutions for fisheries management were established. This is a slow process, the sustainability of local management institutions is not yet established, although they continued during an interim period without funding, further phased support is planned to strengthen these organizations and to generate evidence of impacts and momentum to influence wider fisheries policy in and beyond Bangladesh.