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Background: Reliable data on whooping cough, a highly contagious disease sometimes fatal for infants, are largely lacking in low- and middle-income countries., Methods: We conducted a hospital-based prospective study (PS) on infants, and a household contact-case investigation (CCI) for positive cases throughout Cambodia and in the city of Antananarivo, Madagascar, between 2017 and 2019. The PS, in which Bordetella diagnostics (qPCR) were performed, included infants aged ≤6 months presenting with ≥5 days of cough associated with one pertussis-like symptom. CCI was performed using qPCR and serology regardless of clinical signs., Results: In this study, 207 and 173 participants from Cambodia and Antananarivo were respectively enrolled. Respectively 26.1% (54/207) and 22.0% (38/173) of the infants were infected in the cohorts from Cambodia and Antananarivo. Cough longer than 10 days appeared as a risk factor in both countries, as well as coughing spells, apnea and normal pulmonary auscultation, having a coughing contact in Cambodia. In Antananarivo, being clinically well between coughing spells appeared as a risk factor. Five infants, all positive, died during the study. In Cambodia and Antananarivo respectively, 50.9% (118/232) and 67.8% (82/121) of the contact cases were positive. Respectively 94.4% (51/54) and 90.3% (28/31) of the households had at least one positive contact case., Conclusion: The data show that pertussis circulates at high levels among infants and in their households both in Cambodia and in Antananarivo. Given the vulnerability of youngest infants, who are too young to receive fully primary vaccination, they need to be protected through boosters breaking transmission chains. Molecular diagnosis, as well as trained medical human resources to detect the disease early, are absolutely key to protect populations., Competing Interests: Declarations. Ethics approval and consent to participate: The study was conducted under the sponsorship of the Institut Pasteur, Paris. The protocol was reviewed and approved by the IP’s Institutional Review Board, the National Biomedical Research Ethics Committee in Madagascar (N° 065-MSANP/CE), and the National Ethics Committee for Health Research in Cambodia (N° 019NECHR). All procedures were in accordance with the World Medical Association’s Declaration of Helsinki (2008). Authorization for data processing was obtained from the French Data Protection Authority (CNIL), and names were pseudonymized by assigning a study-specific code to each participant. The ClinicalTrials.gov identifier of the study is: NCT02983487, which was first registered on the 2nd of December 2016. Informed written consent was obtained from both the adult participants and the parent(s)/legal guardian(s) of all under-18s (minor children). The age under which parent(s)/legal guardian(s) consented for the individuals (i.e. 18 years) was determined by national ethics committee, which followed national regulations. Oral assent was obtained for all the children of age seven years or older. Only individuals who agreed to participate were included in the study. Consent for publication: Not Applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Background: Whooping cough due to Bordetella pertussis (BP) and/or B. parapertussis (BPP) is a highly contagious infection sometimes fatal for infants. Africa accounts for the largest share of cases and deaths worldwide. To evaluate pertussis circulation, we conducted a hospital-based prospective study (PS) including household contact-cases investigation (CCS) and a sero-epidemiological cross-sectional study (SECS)., Methods: The PS, in which Bordetella diagnostics (qPCR) were performed, included infants aged ≤6 months presenting with ≥5 days of cough associated with one pertussis-like symptom. CCS was performed using qPCR and serology regardless of clinical signs. In the SECS, serology was performed in children aged 3-15 years with primary pertussis immunization., Results: Study took place in Abidjan between April 2019 and July 2021. In the PS, 187 infants with median age of 2.8 months were enrolled. A total of 42 (22.5%) were confirmed as positive, including 29 (15.5%), 4 (2.1%) and 9 (4.8%) of BP, BPP and BP/BPP coinfections respectively. Age <3 months, low BMI, apnea and inclusion period were identified as risk factors of infection. In the CCIS, 36 households were investigated, representing 158 people with median age of 21.4 years. BP and/or BPP infection was confirmed for 77/157 (49.0%). Twenty-nine households (81%) had at least one positive case. Sixty-seven (42.7%) contact cases were categorized as possibly contaminated, mainly siblings older than five years (25.4%). Twenty-seven contact cases were considered as possible contaminators, primarily mothers (26%). In the SECS, 444 people were enrolled. Two hundred and thirty-eight (53.6%) and nine (2.0%) children had received one and two boosters, respectively. A positive serology was observed in 96 (21.7%) of children and adolescents., Conclusion: Our study highlighted high circulation of pertussis. Barriers to accessing boosters recommended by WHO need to be overcome. Laboratory capacities are key at individual level and to build an effective surveillance system., Competing Interests: Denis Macina is an employee of Sanofi and declares holding shares of the Sanofi group as part of his compensation. There are no patents, products in development or marketed products associated with this research to declare. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2024 Soumahoro et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

We provide the first diversity assessment of Iranian species of the genus Asaccus based on COI DNA-barcoding. We analyzed 53 samples of Iranian Asaccus representing nine OTU corresponding to 10 currently recognzied nominal species, and evaluated both morphological and genetic data to support the recognition of a new species from Bandar-e Jask, Hormozgan Province, southern Iran-Asaccus authenticus sp. nov. The new species is characterized by medium body size (SVL max 55.5 mm), elongated limbs, and relatively small dorsal tubercles arranged in 12-14 regular rows. Morphologically Asaccus authenticus sp. nov. resembles both Arabian and Iranian representatives of the genus; phylogenetically it forms a highly divergent lineage with sister relationships to all other Iranian congeners. We applied the geometric morphometrics method to compare the position and shape of postmental plates for almost all members of Asaccus and evaluated the importance of this character in species diagnostics in this group. We also critically evaluate the recent phylogenetic data on Asaccus and discuss the most problematic questions on taxonomy of this genus. We also revalidate Asaccus ingae (Eiselt, 1973) as a full species; overall our work raises the total number of species of the genus Asaccus to 20.

Snakebite is one of the largest risks from wildlife, however little is known about venomous snake distribution, spatial variation in snakebite risk, potential changes in snakebite risk pattern due to climate change, and vulnerable human population. As a consequence, management and prevention of snakebite is hampered by this lack of information. Here we used habitat suitability modeling for 10 medically important venomous snakes to identify high snakebite risk area under climate change in Iran. We identified areas with high snakebite risk in Iran and showed that snakebite risk will increase in some parts of the country. Our results also revealed that mountainous areas (Zagros, Alborz, Kopet-Dagh mountains) will experience highest changes in species composition. We underline that in order to improve snakebite management, areas which were identified with high snakebite risk in Iran need to be prioritized for the distribution of antivenom medication and awareness rising programs among vulnerable human population., (© 2023. The Author(s).)

The kukri snakes of the genus Oligodon Fitzinger, 1826 reach the westernmost limits of their distribution in Middle and Southwest Asia (Afghanistan, Iran, and Turkmenistan), and the Palearctic portions of Pakistan. In this article, we review the systematics and distribution of the two species native to this region, Oligodon arnensis (Shaw, 1802) and Oligodon taeniolatus (Jerdon, 1853) based on an integrative approach combining morphological, molecular, and species distribution modeling (SDM) data. Phylogenetic analyses recover O. taeniolatus populations from Iran and Turkmenistan in a clade with the O. arnensis species complex, rendering the former species paraphyletic relative to O. taeniolatus sensu stricto on the Indian subcontinent. To correct this, we resurrect the name Contia transcaspica Nikolsky, 1902 from the synonymy of O. taeniolatus and assign it to populations in Middle-Southwest Asia. So far, Oligodon transcaspicus comb. et stat. nov. is known only from the Köpet-Dag Mountain Range of northeast Iran and southern Turkmenistan, but SDM mapping suggests it may have a wider range. Genetic samples of O. "arnensis" from northern Pakistan are nested in a clade sister to the recently described Oligodon churahensis Mirza, Bhardwaj & Patel, 2021, and are phylogenetically separate from O. arnensis sensu stricto in south India and Sri Lanka. Based on morphological similarity, the Afghanistan and Pakistan populations are assigned to Oligodon russelius (Daudin, 1803) and we synonymize O. churahensis with this species. Our investigation leads us to remove O. taeniolatus from the snake fauna of Afghanistan, Iran, and Turkmenistan, with the consequence that only Oligodon transcaspicus comb. et stat. nov. and O. russelius are present in these countries. Additional studies are needed to resolve the taxonomy of the O. taeniolatus and O. arnensis species complexes on the Indian subcontinent, and an updated key for both groups is provided., Competing Interests: Nikolay A. Poyarkov is an Academic Editor for PeerJ., (© 2023 Lee et al.)

Objective: The studies evaluating the efficiency of fiber reinforce composite (FRC) retainers are few and contradictory. This study aimed to compare the debonding force of metal, glass FRC (GFRC) and polyethylene FRC (PFRC) retainers, assess the interactions between the materials and forces, and pattern of load distribution by finite element analysis (FEA)., Materials and Methods: Forty-eight sound lower incisors were collected and randomly assigned to 3 groups (n=8; each sample included 2 teeth). Next, 15mm of the three retainers (multi-stranded metal wire, GFRC, and PFRC) were bonded to the lingual surface of the teeth and debonding force was measured by a universal testing machine. For FEA, 3D models were designed. The data related to geometrical models and material properties were transferred to ANSYS software. A 187-Newton load was applied to the incisal edge of the two centrals. Then different parameters were assessed. The three groups were compared by one-way Anova and Tukey's test. Type one error was considered to be 0.05., Results: The debonding force decreased in the order: Metal (143.71N)≥GFRC (108.29N)>PFRC (45.08N). The difference between metal retainer and GFRC was not significant. In contrast, PFRC group showed significantly lower debonding force compared to other groups (P<0.05). FEA showed stress peak value in metal-composite interface. Maximum total deformation was noted in central, followed by lateral and canine., Conclusions: Glass-FRC can serve as an alternative to metal retainers as the difference in debonding force is not significant. However, the difficulty of repairing or replacing the Glass-FRC should be taken into account given the large number of failure in the interproximal dental area., (Copyright © 2022 Elsevier Masson SAS. All rights reserved.)

Automated snake image identification is important from different points of view, most importantly, snake bite management. Auto-identification of snake images might help the avoidance of venomous snakes and also providing better treatment for patients. In this study, for the first time, it's been attempted to compare the accuracy of a series of state-of-the-art machine learning methods, ranging from the holistic to neural network algorithms. The study is performed on six snake species in Lar National Park, Tehran Province, Iran. In this research, the holistic methods [k-nearest neighbors (kNN), support vector machine (SVM) and logistic regression (LR)] are used in combination with a dimension reduction approach [principle component analysis (PCA) and linear discriminant analysis (LDA)] as the feature extractor. In holistic methods (kNN, SVM, LR), the classifier in combination with PCA does not yield an accuracy of more than 50%, But the use of LDA to extract the important features significantly improves the performance of the classifier. A combination of LDA and SVM (kernel = 'rbf') is achieved to a test accuracy of 84%. Compared to holistic methods, convolutional neural networks show similar to better performance, and accuracy reaches 93.16% using MobileNetV2. Visualizing intermediate activation layers in VGG model reveals that just in deep activation layers, the color pattern and the shape of the snake contribute to the discrimination of snake species. This study presents MobileNetV2 as a powerful deep convolutional neural network algorithm for snake image classification that could be used even on mobile devices. This finding pave the road for generating mobile applications for snake image identification., (© 2021. The Author(s).)

As body size strongly determines the biology of an organism at all levels, it can be expected that miniaturization comes with substantial structural and functional constraints. Dwarf snakes of the genus Eirenis are derived from big, surface-dwelling ancestors, considered to be similar to those of the sister genus Dolichophis. To better understand the structural implications of miniaturization on the feeding apparatus in Eirenis, the morphology of the cranial musculoskeletal system of Dolichophis schmidti was compared with that of the miniature Eirenis punctatolineatus and E. persicus using high-resolution µCT data. The gape index was compared between D. schmidti and 14 Eirenis species. Our results show a relatively increased neurocranium size and decreased maximal jaw muscle force in E. persicus, compared with the D. schmidti, and an intermediate situation in E. punctatolineatus. A significant negative allometry in gape index relative to body size is observed across the transition from the Dolichophis to Pediophis and Eirenis subgenera. However, the gape index relative to head size showed a significant negative allometry only across the transition from the Dolichophis to Pseudocyclophis subgenus. In Dolichophis-Eirenis dwarfing lineages, different structural patterns are observed through miniaturization, indicating that overcoming the challenge of miniaturization has achieved via different adaptations., (© 2020 Anatomical Society.)

Spatial gradients of species richness can be shaped by the interplay between historical and ecological factors. They might interact in particularly complex ways in heterogeneous mountainous landscapes with strong climatic and geological contrasts. We mapped the distribution of 171 lizard species to investigate species richness patterns for all species (171), diurnal species (101), and nocturnal species (70) separately. We related species richness with the historical (past climate change, mountain uplifting) and ecological variables (climate, topography and vegetation). We found that assemblages in the Western Zagros Mountains, north eastern and north western parts of Central Iranian Plateau have the highest number of lizard species. Among the investigated variables, annual mean temperature explained the largest variance for all species (10%) and nocturnal species (31%). For diurnal species, temperature change velocity shows strongest explained variance in observed richness pattern (26%). Together, our results reveal that areas with annual temperature of 15-20 °C, which receive 400-600 mm precipitation and experienced moderate level of climate change since the Last Glacial Maximum (LGM) have highest number of species. Documented patterns of our study provide a baseline for understanding the potential effect of ongoing climate change on lizard diversity in Iran.

We describe a new species of the genus Eryx Daudin, 1803 from southern Iran that is morphologically closely related to the Indian sand boa, E. johnii. The new species, Eryx sistanensis sp. nov. has a distribution range from Zabol in the Sistan Region to the southern parts of Sistan Baluchistan, as well as Hormozgan Province of Iran. Morphologically, E. sistanensis sp. nov. differs from E. johnii by having fewer dorsal scale rows at midbody and the tail tip is not as blunt as E. johnii. The genetic distance (p-distance) between the new species and the Indian sand boa is considerable (9.1% for cytb and 11.8% for COI).

Reptiles are still being described worldwide at a pace of hundreds of species a year. While many discoveries are from remote tropical areas, biodiverse arid regions still harbor many novel taxa. Here, we present an updated phylogeny of colubrid snakes from the Western Palearctic by analyzing a supermatrix of all available global snake species with molecular data and report on the discovery of a new genus and species of colubrine snake from southeastern Iran. The new taxon, named Persiophis fahimii Gen. et sp. nov. , is nested within a clade containing Middle Eastern and South Asian ground racers ( Lytorhynchus , Rhynchocalamus, Wallaceophis , and Wallophis ). This species has a derived morphology including an edentulous pterygoid and occurrence of short and blunt teeth on the palatine, maxillae and dentary bones, an elongated snout and a relatively trihedral first supralabial scale that is slightly bigger than the second, and elongated toward the tip of rostral. We also report on the osteology and phylogenetic placement of several poorly studied colubrines: Hierophis andreanus (reassigned to Dolichophis ) and Muhtarophis barani., Competing Interests: Nikolay A. Poyarkov serves is an Academic Editor for PeerJ. The other authors declare that no conflicts of interest exist., (©2020 Rajabizadeh et al.)

We review the status of an Iranian gecko population previously referred to Tropiocolotes cf. steudneri and describe it as a new species, Tropiocolotes hormozganensis sp. nov. We discuss the taxonomic history of this population and compare its characters with those of the other species in the genus. The new species is distinguished from other species of Tropiocolotes by possessing weakly keeled dorsal scales and smooth ventral scales, having imbricate scales on dorsal and ventral tail, possessing clearly tricarinatesubdigital scales, 48-55 dorsal scales, two pairs of postmental shields, of which the second pair is about half of the size of the first, 100-107 scales longitudinally along underside of body, 15-19 scales across head and 16-19 subdigital lamellae.

The Near and Middle East is a hotspot of biodiversity, but the region remains underexplored at the level of genetic biodiversity. Here, we present an extensive molecular phylogeny of the viperid snake genus Montivipera, including all known taxa. Based on nuclear and mitochondrial data, we present novel insights into the phylogeny of the genus and review the status of its constituent species. Maximum likelihood methods revealed a montane origin of Montivipera at 12.3Mya. We then analyzed factors of mountain viper diversity. Our data support substantial changes in effective population size through Plio-Pleistocene periods. We conclude that climatic oscillations were drivers of allopatric speciation, and that mountain systems of the Near and Middle East have strongly influenced the evolution and survival of taxa, because climatic and topographical heterogeneities induced by mountains have played a crucial role as filters for dispersal and as multiple refugia. The wide diversity of montane microhabitats enabled mountain vipers to retain their ecological niche during climatic pessima. In consequence the varied geological and topographical conditions between refugia favoured genetic isolation and created patterns of species richness resulting in the formation of neoendemic taxa. Our data support high concordance between geographic distributions of Montivipera haplotypes with putative plant refugia., (Copyright © 2016. Published by Elsevier Inc.)

A new species of the lacertid genus Eremias Fitzinger, 1834 is described from northwest of Isfahan province, Central Iran. Two mitochondrial genes (cyt b and 12S DNA) were sequenced and analyzed as reliable molecular markers for the separation of this newly discovered species from closely related species within the genus Eremias: E. velox, E. persica, E. papenfussi, E. lalezharica, E. montana, E. strauchi, E. kopetdaghica and E. suphani. Genetic distances (K2-p) between any of these species with the newly described species are relatively high (27.5-32.8% for cyt b and 5.2-10.4% for 12S DNA). Phylogenetic analyses (MP, ML and BI) generated trees with very similar topologies. According to molecular and morphological data, Eremias isfahanica sp. nov. belongs to the subgenus Aspidorhinus, and is closely related to E. papenfussi. Because several new Eremias species have recently been described from the Iranian Plateau, we additionally provide an updated identification key.

We determined the effects of past and future climate changes on the distribution of the Montivipera raddei species complex (MRC) that contains rare and endangered viper species limited to Iran, Turkey and Armenia. We also investigated the current distribution of MRC to locate unidentified isolated populations as well as to evaluate the effectiveness of the current network of protected areas for their conservation. Present distribution of MRC was modeled based on ecological variables and model performance was evaluated by field visits. Some individuals at the newly identified populations showed uncommon morphological characteristics. The distribution map of MRC derived through modeling was then compared with the distribution of protected areas in the region. We estimated the effectiveness of the current protected area network to be 10%, which would be sufficient for conserving this group of species, provided adequate management policies and practices are employed. We further modeled the distribution of MRC in the past (21,000 years ago) and under two scenarios in the future (to 2070). These models indicated that climatic changes probably have been responsible for an upward shift in suitable habitats of MRC since the Last Glacial Maximum, leading to isolation of allopatric populations. Distribution will probably become much more restricted in the future as a result of the current rate of global warming. We conclude that climate change most likely played a major role in determining the distribution pattern of MRC, restricting allopatric populations to mountaintops due to habitat alterations. This long-term isolation has facilitated unique local adaptations among MRC populations, which requires further investigation. The suitable habitat patches identified through modeling constitute optimized solutions for inclusion in the network of protected areas in the region.