Variation in herpetofauna detection probabilities: implications for study design

Population monitoring is fundamental for informing management decisions aimed at reducing the rapid rate of global biodiversity decline. Herpetofauna are experiencing declines worldwide and include species that are challenging to monitor. Raw counts and associated metrics such as richness indices are common for monitoring populations of herpetofauna; however, these methods are susceptible to bias as they fail to account for varying detection probabilities. Our goal was to develop a program for efficiently monitoring herpetofauna in southern Texas. Our objectives were to (1) estimate detection probabilities in an occupancy modeling framework using trap arrays for a diverse group of herpetofauna and (2) to evaluate the relative effectiveness of funnel traps, pitfall traps, and cover boards. We collected data with 36 arrays at 2 study sites in 2015 and 2016, for 2105 array-days resulting in 4839 detections of 51 species. We modeled occupancy for 21 species and found support for the hypothesis that detection probability varied over our sampling duration for 10 species and with rainfall for 10 species. For herpetofauna in our study, we found 14 and 12 species were most efficiently captured with funnel traps and pitfall traps, respectively, and no species were most efficiently captured with cover boards. Our results show that using methods that do not account for variations in detection probability are highly subject to bias unless the likelihood of false absences is minimized with exceptionally long capture durations. For monitoring herpetofauna in southern Texas, we recommend using arrays with funnel and pitfall traps and an analytical method such as occupancy modeling that accounts for variation in detection.

SARS-CoV-2 in Municipal Wastewater Treatment Plant, Collection Network and Hospital Wastewater

The current outbreak of coronavirus disease (COVID-19) has led to creating a public health emergency conditions since 2019. COVID-19, which is caused by SARS-CoV-2, is spread via human-to-human transmission by direct contact or droplets. Through conducting this study, we were looking for detecting SARS-CoV-2 in wastewater produced in Iran country (Ardabil, Nir, Khalkhal and Givi) (wastewater collection network, wastewater treatment plant and hospital wastewater). In this research, samples (n = 76) were collected from influent and effluent of municipal and hospital wastewater treatment plants and some samples were also collected from Ardabil municipal wastewater manholes. The sampling duration included the white (lower risk of covid-19) and red (high risk of covid-19) conditions. Samples were stored at -20°C for further diagnostic tests. Out of 76 samples, a total of 16 samples (21.05%) collected from wastewater in Ardabil province (Ardabil, Nir, Khalkhal, and Givi), were positive in terms of SARS-CoV-2. Wastewater epidemiology can facilitate detection of the incidence of pathogens through metropolises, measurement of population prevalence without direct testing, and provision of information to public health system about the efficiency of intervening efforts.

Air-Water Flow Properties in Hydraulic Jumps with Fully and Partially Developed Inflow Conditions

Novel air-water flow measurements were conducted in fully aerated hydraulic jumps with partially and fully developed supercritical inflow conditions. Irrespective of the inflow conditions, the hydraulic jumps resembled typical flow patterns with strong aeration and instabilities, albeit hydraulic jumps with fully developed inflow conditions had a more upwards directed roller motion and a larger clear water core in the second half of the roller. Hydraulic jumps with fully developed inflow conditions had comparatively larger void fractions in the first half of the jump roller and larger bubble count rates throughout, while a comparatively larger number of smaller bubble sizes suggested a stronger break-up of bubbles. This was consistent with slightly larger interfacial velocities and turbulence intensities in the first half of the jump roller with fully developed inflow conditions. An assessment of the required sampling duration for air-water flow properties indicated the requirement to sample for at least five times longer duration than applied in previous studies. These results highlighted the need to carefully consider the inflow conditions and sampling parameters for aerated hydraulic jumps.

Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission

Redondoviridae is a recently discovered DNA virus family consisting of two species, vientovirus and brisavirus. Here we used PCR amplification and sequencing to characterize redondoviruses in nasal/throat swabs collected longitudinally from a cohort of 58 individuals working with animals in Vietnam. We additionally analyzed samples from animals to which redondovirus DNA-positive participants were exposed. Redondoviruses were detected in approximately 60% of study participants, including 33% (30/91) of samples collected during episodes of acute respiratory disease and in 50% (29/58) of baseline samples (with no respiratory symptoms). Vientovirus (73%; 24/33) was detected more frequently in samples than brisaviruses (27%; 9/33). In the 23 participants with at least 2 redondovirus-positive samples among their longitudinal samples, 10 (43.5%) had identical redondovirus replication-gene sequences detected (sampling duration: 35–132 days). We found no identical redondovirus replication genes in samples from different participants, and no redondoviruses were detected in 53 pooled nasal/throat swabs collected from domestic animals. Phylogenetic analysis described no large-scale geographical clustering between viruses from Vietnam, the US, Spain, and China, indicating that redondoviruses are highly genetically diverse and have a wide geographical distribution. Collectively, our study provides novel insights into the Redondoviridae family in humans, describing a high prevalence, potentially associated with chronic shedding in the respiratory tract with lack of evidence of zoonotic transmission from close animal contacts. The tropism and potential pathogenicity of this viral family remain to be determined.

Use Of Canine Olfactory Detection For COVID-19 Testing Study On U.A.E. Trained Detection Dog Sensitivity

ABSTRACTThis study aimed to evaluate the sensitivity of 21 dogs belonging to different United Arab Emirates (UAE) Ministry of Interior (MOI), trained for COVID-19 olfactory detection.The study involved 17 explosives detection dogs, two cadaver detection dogs and two dogs with no previous detection training. Training lasted two weeks before starting the validation protocol. Sequential five and seven-cone line-ups were used with axillary sweat samples from symptomatic COVID-19 individuals (SARS-CoV-2 PCR positive) and from asymptomatic COVID-19 negative individuals (SARS-CoV-2 PCR negative). A total of 1368 trials were performed during validation, including 151 positive and 110 negative samples. Each line-up had one positive sample and at least one negative sample. The dog had to mark the positive sample, randomly positioned behind one of the cones. The dog, handler and data recorder were blinded to the positive sample location.The calculated overall sensitivities were between 71% and 79% for three dogs, between83% and 87% for three other dogs, and equal to or higher than 90% for the remaining 15 dogs (more than two thirds of the 21 dogs).After calculating the overall sensitivity for each dog using all line-ups, “matched” sensitivities were calculated only including line-ups containing COVID-19 positive and negative samples strictly comparable on confounding factors such as diabetes, anosmia, asthma, fever, body pain, diarrhoea, sex, hospital, method of sweat collection and sampling duration. Most of the time, the sensitivities increased after matching.Pandemic conditions in the U.A.E., associated with the desire to use dogs as an efficient mass-pretesting tool has already led to the operational deployment of the study dogs.Future studies will focus on comparatives fields-test results including the impact of the main COVID-19 comorbidities and other respiratory tract infections.

Use of Canine Olfactory Detection for Covid-19 Testing Study on U.A.E. Trained Detection Dog Sensitivity

This study aimed to evaluate the sensitivity of 21 dogs belonging to different united arab emirate administrations, trained for covid-19 olfactory detection. The study involved 17 explosives detection dogs, two cadaver detection dogs and two dogs with no previous detection training. Training lasted two weeks before starting the validation protocol. Sequential five and seven- cone line-ups were used with axillary sweat samples from 151 symptomatic covid-19 individuals (sars-cov-2 pcr positive) and from 110 asymptomatic covid-19 negative individuals (sars-cov-2 pcr negative). Each line-up had one positive sample and at least one negative sample. The dog had to mark the positive sample, randomly positioned behind one of the cones. The dog, handler and data recorder were blinded to the positive sample location. The calculated overall sensitivities were between 71% and 79% for three dogs, between 83% and 87% for three other dogs and equal to or higher than 90% for the remaining 15 dogs (more than two thirds of the 21 dogs). After calculating the overall sensitivity for each dog using all line- ups, “matched” sensitivities were calculated only including line-ups containing covid-19 positive and negative samples strictly comparable on confounding factors such as diabetes, anosmia, asthma, fever, body pain, diarrhoea, sex, hospital, method of sweat collection and sampling duration. Most of the time, the sensitivities increased after matching. Pandemic conditions in the U.A.E.., associated with the desire to use dogs as an efficient mass-pretesting tool has already led to the operational deployment of the study dogs. Future studies will focus on comparatives fields-test results including the impact of the main covid-19 comorbidities and other respiratory tract infections.

Macroinvertebrate Taxonomic Richness in Minimally Disturbed Streams on the Southeastern USA Coastal Plain

Collections made over 20 years with a multiple habitat sampling protocol and Hester–Dendy artificial substrate samplers were used to assess macroinvertebrate genera richness in first- to fourth-order streams on the Savannah River Site (SRS), a 780-km2, U.S. government reservation on the upper South Carolina, USA, coastal plain. We collected 312 genera representing 114 families including 268 genera and 87 families of insects. The total number of genera from each stream averaged 139 (97–194) with totals of 171–261 for drainages with more than one stream. Larger streams supported more macroinvertebrate genera, but small headwater streams supported genera not found in higher-order streams and contributed to drainage-wide richness. Sampling effort expressed as number of individuals collected or sites sampled and sampling duration influenced genera richness more than other factors. Genera accumulation curves showed that full representation of richness required several years of sampling and the inclusion of sampling sites that represented all habitats. Upper Three Runs, known for high insect species richness, was the most genera-rich stream, but richness was nearly comparable in other streams after adjusting for sampling effort. Some SRS streams are minimally exposed to anthropogenic disturbance, making them relatively unique in the southeastern USA Sand Hills and valuable as reference models.