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The SARS‐CoV‐2 is the causative agent of COVID‐19 whose evolutionary path with geographical context forms the focus of present study. The first reported sequence from each of the 161 countries was downloaded from the GISAID database. Multiple sequence alignment was performed using MAFFT v.7, and a TCS‐based network was constructed using PopART v.1.7. A total of 27 proteins were analyzed including structural and non‐structural proteins. NSP3 and NSP12, responsible for viral replication and RNA synthesis, respectively, had the highest mutation incidence and frequency among non‐structural proteins. The spike (S) protein, critical for viral attachment and entry, had the highest prevalence and frequency of mutations. ORF3a had the highest mutation incidence and frequency among accessory proteins. The phylogeogenomic network identified six haplogroups containing 35 sequences, while the remaining sequences belonged to different haplotypes. The virus's genetic distinctiveness was higher in European genomes, with four haplogroups dominated by Europe‐linked sequences. The triangular‐shaped pattern observed in the virus's evolutionary path suggests that it spread to different continents from Asia. Multiple transmission pathways connecting different countries affirm the virus's ability to emerge in multiple countries by early 2020. The possibility of new species emergence through “saltation” due to the pandemic is also discussed. [ABSTRACT FROM AUTHOR]

Background Human papillomavirus (HPV)+ oropharynx cancer (OPC) has a more favorable prognosis than HPV-negative disease, but the impact of specific HPV genotype and phylogenic clade on patient outcomes is not well understood and has profound implications for treatment de-intensification. Methods The objective of this single-institution cohort study was to investigate the association of HPV genotype (16 vs high-risk non-16) and clade (A9 vs A7) with OPC outcomes. The primary endpoints were overall survival (OS) and event-free survival (EFS) in patients with M0 disease treated with curative intent. Results The cohort included 598 patients (87% HPV16, 98% A9). Compared to those with HPV16 OPC, individuals with non-HPV16 OPC had a higher age, comorbidity index, and proportion of non-whites, HIV+ patients, T4 tumors, and stage IV disease (AJCC 7th edition). Non-HPV16 genotype was associated with worse OS in univariate (HR = 2.17, 95% CI, 1.24-3.80, P  = .0066), but not in multivariate analysis (HRadj = 0.84, 95% CI, 0.43-1.62, P  = .5921). A7 clade was associated with worse OS in univariate (HR = 4.42, 95% CI, 1.60-12.30, P  = .0041), but not in multivariate analysis (HRadj = 2.39, 95% CI, 0.57-9.99, P  = .2325). Neither HPV genotype (HR = 1.60, 95% CI, 0.99-2.60, P  = .0566) nor phylogenic clade (HR = 2.47, 95% CI, 0.91-6.72, P  = .0761) was associated with EFS. Conclusion Non-HPV16 genotype and A7 clade were associated with worse OS and trended toward worse EFS in univariate analyses. The survival differences were more pronounced by phylogenic clade than by HPV16 status, suggesting that the former may be a more useful classification for future studies. However, neither HPV16 status nor phylogenic clade was prognostic when adjusting for patient and tumor covariates, raising the question as to whether possible differences in outcomes are related to distinct clinical profiles rather than inherent viral properties. [ABSTRACT FROM AUTHOR]

Abstract Many subtypes of SARS-CoV-2 have emerged since its early stages, with mutations showing regional and racial differences. These mutations significantly affected the infectivity and severity of the virus. This study aimed to predict the mutations that occur during the evolution of SARS-CoV-2 and identify the key characteristics for making these predictions. We collected and organized data on the lineage, date, clade, and mutations of SARS-CoV-2 from publicly available databases and processed them to predict the mutations. In addition, we utilized various artificial intelligence models to predict newly emerging mutations and created various training sets based on clade information. Using only mutation information resulted in low performance of the learning models, whereas incorporating clade differentiation resulted in high performance in machine learning models, including XGBoost (accuracy: 0.999). However, mutations fixed in the receptor-binding motif (RBM) region of Omicron resulted in decreased predictive performance. Using these models, we predicted potential mutation positions for 24C, following the recently emerged 24A and 24B clades. We identified a mutation at position Q493 in the RBM region. Our study developed effective artificial intelligence models and characteristics for predicting new mutations in continuously evolving infectious viruses.

As the global community continues to recover from the COVID-19 pandemic, the World Health Organization has issued a warning of another viral infection, mpox (monkeypox), that can pose a significant threat to public health. Mpox was once endemic in Africa but has spread globally, prompting the World Health Organization to declare it a public health emergency. In response, healthcare personnel must initiate timely, decisive, and robust action before the infection escalates. Moreover, accurate diagnosis is crucial, given the similarity between mpox and other rash-causing infections. This article provides a comprehensive overview of the symptoms, differentiating it from similar diseases, risk assessment, and treatment strategies. In addition, it aims to educate healthcare personnel with the necessary knowledge to educate others and take preventative measures when handling cases, thereby avoiding the spread of infection.

Background: The omicron variants have been classified as variants of concern by the world health organization due to their initial emergence with a notable mutations that affect on the transmissibility, immune escape and virulence of the SARS-CoV-2 virus. We conducted a cross-sectional analysis study to detect the most common strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Egypt during the 4th wave of the COVID-19 pandemic and used the next genaration sequencing to characterize the SARS CoV-2 omicron variant genome and find the significant mutation influencing the virus's virulence, immune evasion, and transmissibility. Material and methods: This study started during the 4th wave of the COVID-19 pandemic by collecting nasopharyngeal swabs (n = 39) from individuals having COVID-19 symptoms. SARSCoV-2 was molecularly identified using reverse transcription PCR (RT-PCR). For every sample, whole genome sequencing (WGS) was carried out using next generation sequencing Illumina Iseq100 system. Clade assignment, Pangolin lineages, phylogenetic placement, and mutation calling were all carried out using Nextclade tool V3.4.0, Coronavirus Typing Tool V 1.25 and CoVsurver mutation application. Result: Sequencing data analysis proved that all the involved samples in the study belong to the Omicron variant with different clade and Pangolin lineage, the most common strain in Egypt during the 4th wave of the COVID-19 pandemic was Omicron clade 22B and BA.5.2 Pango lineage. Mutation analysis showed that the S gene of the omicron variant accumulated with significant mutations that affect viral immune escape. Conclusion: The omicron variant in Egypt during the 4th wave of the pandemic showed a high ability to escape from the immune system because of newly mutation on the antibodies recognized sites of the S gene, so it is very important to perform continuous monitoring for omicron genome mutations using next-generation sequencing to help the scientific community in the development of appropriate vaccine for this variant. [ABSTRACT FROM AUTHOR]

The slug moth family Limacodidae is a cosmopolitan group of economic importance, but its higher level systematics remains poorly understood. Here, we present a robust, higher level phylogenetic framework for Palaearctic and Indomalayan members of the family using sequence capture data of 148 nuclear protein‐coding and 13 mitochondrial markers from 145 samples of 126 species in 67 genera representing all five morphologically delineated limacodid lineages. Our results strongly support the monophyly of Limacodidae in which six major clades are recognized. The relationships among these clades are revealed, with Phrixolepia‐clade being the most basal group followed by Apoda‐clade, Euphlyctinides‐clade, Cania‐clade and Phlossa‐clade + Parasa‐clade, respectively. We also add publicly available DNA barcode sequences from additional species worldwide to this phylogenetic framework to infer the most completely sampled phylogeny of Limacodidae to date. Our work provides a major step towards understanding the systematics and evolution of slug moths. [ABSTRACT FROM AUTHOR]

Mpox is an important emerging infectious disease spreading rapidly with a changing geographical, clinical, epidemiological, virological, and clinical manifestations. The identification of clade I virus, the variant associated with severe disease and higher risk of death outside Africa in August 2024 is alarming. It is vital to document its changing epidemiology, clinical manifestations, and outcome to better understand how to prevent and treat the disease. We aimed to describe the clinical features and disease outcome of patients with mpox from 1970 to 2023. We performed a systematic search of peer-reviewed publications and grey literature using PubMed, MEDLINE, CINAHL, and EMBASE, published between 1973 and 2023. Thirty-seven articles met the inclusion criteria. We pooled data from 19 studies with at least 10 cases to enhance the appreciation of the review findings. A clear distinction was observed regarding the age, gender, sexual orientation, and HIV status distribution of mpox cases before and after May 2022. From May 2022 onwards, a high prevalence of mpox, almost exclusively, was observed among individuals identifying as men who have sex with men (MSM) 20–40 years with high-risk sexual behaviour and/or HIV immunosupression. No change in the common clinical manifestations – mucocutaneous rash, fever, lymphadenopathy, headache, and generalized malaise, typically during prodrome. However, certain symptoms such as myalgia/arthralgia, oropharyngitis, proctitis, and depression/anxiety were typically reported from May 2022 onwards. We could not establish from the review if the observed symptomatology change was real or resulting from an observation bias. Notably, a clear change in symptomatology was observed among individuals with immunosuppression who do not necessarily experience the prodromal stage and present with significantly more and larger mucocutaneous lesions that sometimes coalesced to form ulcers. Our pooled data report a CFR of 8.3 % before May 2022 and 1.2 % from May 2022 onwards. We show that mental health in patients with mpox has not received the attention required. There is a need for a strategic and strong approach to revamp mpox services to improve clinical suspicion and treatment, protect individuals most at risk including healthcare workers in high risk areas.

ABSTRACT Outbreaks of influenza A viruses are generally seasonal and cause annual epidemics worldwide. Due to their frequent reassortment and evolution, annual surveillance is of paramount importance to guide vaccine strategies. The aim of this study was to explore the molecular epidemiology of influenza A virus and nasopharyngeal microbiota composition in infected patients in Saudi Arabia. A total of 103 nasopharyngeal samples from 2015 and 12 samples from 2022 were collected from patients positive for influenza A. Sequencing of influenza A as well as metatranscriptomic analysis of the nasopharyngeal microbiota was conducted using Oxford Nanopore sequencing. Phylogenetic analysis of hemagglutinin, neuraminidase segments, and concatenated influenza A genomes was performed using MEGA7. Whole-genome sequencing analysis revealed changing clades of influenza A virus: from 6B.1 in 2015 to 5a.2a in 2022. One sample containing the antiviral resistance-mediating mutation S247N toward oseltamivir and zanamivir was found. Phylogenetic analysis showed the clustering of influenza A strains with the corresponding vaccine strains in each period, thus suggesting vaccine effectiveness. Principal component analysis and alpha diversity revealed the absence of a relationship between hospital admission status, age, or gender of infected patients and the nasopharyngeal microbial composition, except for the infecting clade 5a.2a. The opportunistic pathogens Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis were the most common species detected. The molecular epidemiology appears to be changing in Saudi Arabia after the COVID-19 pandemic. Antiviral resistance should be carefully monitored in future studies. In addition, the disease severity of patients as well as the composition of the nasopharyngeal microbiota in patients infected with different clades should also be assessed.IMPORTANCEIn this work, we have found that the clade of influenza A virus circulating in Riyadh, KSA, has changed over the last few years from 6B.1 to 5a.2a. Influenza strains clustered with the corresponding vaccine strains in our population, thus emphasizing vaccine effectiveness. Metatranscriptomic analysis showed no correlation between the nasopharyngeal microbiome and the clinical and/or demographic characteristics of infected patients. This is except for the 5a.2a strains isolated post-COVID-19 pandemic. The influenza virus is among the continuously evolving viruses that can cause severe respiratory infections. Continuous surveillance of its molecular diversity and the monitoring of anti-viral-resistant strains are thus of vital importance. Furthermore, exploring potential microbial markers and/or dysbiosis of the nasopharyngeal microbiota during infection could assist in the better management of patients in severe cases.

ABSTRACT Clostridioides difficile (C. difficile) is widely distributed in the intestinal tract of humans, animals, and in the environment. It is the most common cause of diarrhea associated with the use of antimicrobials in humans and among the most common healthcare-associated infections worldwide. Its pathogenesis is mainly due to the production of toxin A (TcdA), toxin B (TcdB), and a binary toxin (CDT), whose genetic variants may be associated with disease severity. We studied genetic diversity in 39 C. difficile isolates from adults and children attended at two Mexican hospitals, using different gene and genome typing methods and investigated their association with in vitro expression of toxins. Whole-genome sequencing in 39 toxigenic C. difficile isolates were used for multilocus sequence typing, tcdA, and tcdB typing sequence type, and phylogenetic analysis. Strains were grown in broth media, and expression of toxin genes was measured by real-time PCR and cytotoxicity in cell-culture assays. Clustering of strains by genome-wide phylogeny matched clade classification, forming different subclusters within each clade. The toxin profile tcdA+/tcdB+/cdt+ and clade 2/ST1 were the most prevalent among isolates from children and adults. Isolates presented two TcdA and three TcdB subtypes, of which TcdA2 and TcdB2 were more prevalent. Prevalent clades and toxin subtypes in strains from children differed from those in adult strains. Toxin gene expression or cytotoxicity was not associated with genotyping or toxin subtypes. In conclusion, genomic and phenotypic analysis shows high diversity among C. difficile isolates from patients with healthcare-associated diarrhea.IMPORTANCEClostridioides difficile is a toxin-producing bacterial pathogen recognized as the most common cause of diarrhea acquired primarily in healthcare settings. This bacterial species is diverse; its global population has been divided into five different clades using multilocus sequence typing, and strains may express different toxin subtypes that may be related to the clades and, importantly, to the severity and progression of disease. Genotyping of children strains differed from adults suggesting toxins might present a reduced toxicity. We studied extensively cytotoxicity, expression of toxins, whole genome phylogeny, and toxin typing in clinical C. difficile isolates. Most isolates presented a tcdA+/ tcdB+/cdt+ pattern, with high diversity in cytotoxicity and clade 2/ST1 was the most prevalent. However, they all had the same TcdA2/TcdB2 toxin subtype. Advances in genomics and bioinformatics tools offer the opportunity to understand the virulence of C. difficile better and find markers for better clinical use

Background: The coronavirus disease 2019 (COVID-19) pandemic has had a severe impact on population health. The genetic determinants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in southern Bangladesh are not well understood. Methods: This study aimed to determine the genomic variation in SARS-CoV-2 genomes that have evolved over 2 years of the pandemic in southern Bangladesh and their association with disease outcomes and virulence of this virus. We investigated demographic variables, disease outcomes of COVID-19 patients and genomic features of SARS-CoV-2. Results: We observed that the disease severity was significantly higher in adults (85.3%) than in children (14.7%), because the expression of angiotensinconverting enzyme-2 (ACE-2) diminishes with ageing that causes differences in innate and adaptive immunity. The clade GK (n = 66) was remarkable between June 2021 and January 2022. Because of the mutation burden, another clade, GRA started a newly separated clustering in December 2021. The burden was significantly higher in GRA (1.5-fold) highlighted in mild symptoms of COVID-19 patients than in other clades (GH, GK, and GR). Mutations were accumulated mainly in S (22.15 mutations per segment) and ORF1ab segments. Missense (67.5%) and synonymous (18.31%) mutations were highly noticed in adult patients with mild cases rather than severe cases, especially in ORF1ab segments. Moreover, we observed many unique mutations in S protein in mild cases compared to severe, and homology modeling revealed that those might cause more folding in the protein's alpha helix and beta sheets. Conclusion: Our study identifies some risk factors such as age comorbidities (diabetes, hypertension, and renal disease) that are associated with severe COVID-19, providing valuable insight regarding prioritizing vaccination for high-risk individuals and allocating health care and resources. The findings of this work outlined the knowledge and mutational basis of SARS-CoV-2 for the next treatment steps. Further studies are needed to confirm the effects of structural and functional proteins of SARS-CoV-2 in detail for monitoring the emergence of new variants in future. [ABSTRACT FROM AUTHOR]

The human immunodeficiency virus type 1 (HIV‐1) A6 sub‐subtype is highly prevalent in Eastern Europe. Over the past decade, the dissemination of the A6 lineage has been expanding in Poland. The recent Russian invasion of Ukraine may further escalate the spread of this sub‐subtype. While evolutionary studies using viral sequences have been instrumental in identifying the HIV epidemic patterns, the origins, and dynamics of the A6 sub‐subtype in Poland remain to be explored. We analyzed 1185 HIV‐1 A6 pol sequences from Poland, along with 8318 publicly available sequences from other countries. For analyses, phylogenetic tree construction, population dynamics inference, Bayesian analysis, and discrete phylogeographic modeling were employed. Of the introduction events to Poland, 69.94% originated from Ukraine, followed by 29.17% from Russia. Most A6 sequences in Poland (53.16%) formed four large clades, with their introductions spanning 1993−2008. Central and Southern Polish regions significantly influenced migration events. Transmissions among men who have sex with men (MSM) emerged as the dominant risk group for virus circulation, representing 72.92% of migration events. Sequences from migrants were found primarily outside the large clades. Past migration from Ukraine has fueled the spread of the A6 sub‐subtype and the current influx of war‐displaced people maintains the growing national epidemic. [ABSTRACT FROM AUTHOR]

An animal with a large body can have larger sense organs than a smaller one, collecting more sensory information. However, many structures scale with body size to be relatively smaller in larger animals. This occurs with eyes, however the situation for mechanosensory organs is less clear. I investigated scaling of particular mechanosensory organs unique to dipteran flies, halteres, which replace hind wings and are important for the aerobatic ability underlying the success and diversity of dipterans. Halteres are shaped like drumsticks and beat up and down in time with the wings, acting as gyroscopes because yawing, pitching or rolling generate twisting forces in them. These forces are detected by campaniform sensilla (CS), dome‐shaped sensory cells in the cuticle that are mainly clustered into three fields. Unusually for a sense organ, individual CS are visible on the cuticle surface. I compared how haltere size, shape and CS number scale with body size in four clades representing different branches of dipteran phylogeny: tipulids (craneflies); tabanids (horseflies); syrphids (hoverflies) and calyptrates (e.g. houseflies, blowflies). In all clades, haltere length scaled with body mass raised to the power 0.23, similar to that for eyes of insects and other animals. It was directly proportional to wing length, probably enabling halteres to beat in time with wings. In relation to body size or wing length, tipulids had longer halteres than other clades. In contrast to haltere length, the number of CS was not related to body size within each clade but did vary between clades, suggesting a basic pattern for each clade was laid down early in its evolution. Tipulids had the smallest number, associated with relatively ponderous flight. Tabanids had more CS than calyptrates or syrphids, reasons for which require further investigation. [ABSTRACT FROM AUTHOR]

The idea that birds are maniraptoran theropod dinosaurs is now considered an evolutionary consensus. An "open" (i.e., completely or substantially perforate) acetabulum is considered an important synapomorphy verifying the bird–dinosaur nexus. Here, I present anatomical evidence from the acetabulum and its important appurtenances, the supracetabular crest and the antitrochanter, that hip anatomy differs substantially between dinosaurs and birds. Given the thin bone of the acetabular walls and the varied tissue, both hard and soft, in the acetabular region and especially the lower part of the basin, it is apparent that many avian skeletons exhibit some anatomical loss of soft tissue and thin bone, some perhaps related to changes in gait, but also in part related to the dramatic trend in bone reduction associated with flight, especially in more advanced crown taxa. Many basal birds and early diverging neornithines tend to have a nearly closed or partially closed acetabula, thus rendering the current terms "open" or "closed" acetabula inaccurate; they should be modified or replaced. Given new evidence presented here, the relationship of "dinosaurs" and birds must be re-evaluated. [ABSTRACT FROM AUTHOR]

Abstract Background The coronavirus disease 2019 (COVID‐19) pandemic has had a severe impact on population health. The genetic determinants of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in southern Bangladesh are not well understood. Methods This study aimed to determine the genomic variation in SARS‐CoV‐2 genomes that have evolved over 2 years of the pandemic in southern Bangladesh and their association with disease outcomes and virulence of this virus. We investigated demographic variables, disease outcomes of COVID‐19 patients and genomic features of SARS‐CoV‐2. Results We observed that the disease severity was significantly higher in adults (85.3%) than in children (14.7%), because the expression of angiotensin‐converting enzyme‐2 (ACE‐2) diminishes with ageing that causes differences in innate and adaptive immunity. The clade GK (n = 66) was remarkable between June 2021 and January 2022. Because of the mutation burden, another clade, GRA started a newly separated clustering in December 2021. The burden was significantly higher in GRA (1.5‐fold) highlighted in mild symptoms of COVID‐19 patients than in other clades (GH, GK, and GR). Mutations were accumulated mainly in S (22.15 mutations per segment) and ORF1ab segments. Missense (67.5%) and synonymous (18.31%) mutations were highly noticed in adult patients with mild cases rather than severe cases, especially in ORF1ab segments. Moreover, we observed many unique mutations in S protein in mild cases compared to severe, and homology modeling revealed that those might cause more folding in the protein's alpha helix and beta sheets. Conclusion Our study identifies some risk factors such as age comorbidities (diabetes, hypertension, and renal disease) that are associated with severe COVID‐19, providing valuable insight regarding prioritizing vaccination for high‐risk individuals and allocating health care and resources. The findings of this work outlined the knowledge and mutational basis of SARS‐CoV‐2 for the next treatment steps. Further studies are needed to confirm the effects of structural and functional proteins of SARS‐CoV‐2 in detail for monitoring the emergence of new variants in future.

The multi-country mpox outbreak across the globe has led to the systematic surveillance of mpox cases in India. During the surveillance of mpox, we encountered cases of Varicella Zoster Virus (VZV) in suspected mpox cases amongst children & adults. This study focused on the genomic characterization of VZV in India. A total of 331 mpox suspected cases were tested for VZV through real-time PCR, and the positive samples were subjected to next-generation sequencing to retrieve the whole genome of VZV using CLC genomics software. Phylogenetic analysis has been done in MEGA 11.0 software to identify circulating clades. Of the 331 suspected cases, 28 cases with vesicular rashes were found to be positive for VZV. The maximum genome could be retrieved from the clinical specimens of 16 cases with coverage greater than 98% when mapped with reference strain Dumas (NC 001348). The phylogenetic analyses of these sequences determined the circulation of clades 1, 5, and 9 in India. Further, the sequence analysis demonstrated non-synonymous single nucleotide polymorphism (SNPs) among specific ORF of VZV including ORF 14, ORF 22, ORF 36, ORF 37 and ORF 51. Although clade 1 and 5 has been reported earlier, the circulation of clade 9 of VZV has been determined for the first time in India. Although the circulation of different clades of VZV was reported from India, the presence of clade 9 was detected for the first time during the mpox surveillance. [ABSTRACT FROM AUTHOR]

Candida auris is an emerging fungal pathogen that is feared to spread of infection because of its propensity for multidrug resistance and high mortality rate. This pathogenic yeast is classified into four major clades by phylogenetic analyses, which are referred to the South Asia clade (clade I), East Asia clade (clade II), South Africa clade (clade III), and South America clade (clade IV), based on the location of the initial isolate. In this study, we evaluated the virulence of C. auris strains belonging to four major clades and the therapeutic effects of micafungin in a silkworm infection model. The highest mortality rate at 21 h after C. auris inoculation was observed for strains from clade IV (80% or more). In contrast, it was 20% or less in those from other clades. Antifungal susceptibility tests indicated resistance to fluconazole and sensitivity to echinocandins in the blood-derived strains. Micafungin prolonged the survival of blood-derived C. auris infected silkworms. These results suggest that the silkworm infection model is useful for evaluating the virulence of C. auris and determining its therapeutic effects. [ABSTRACT FROM AUTHOR]

BackgroundThe prevalence of community-acquired Clostridioides difficile infection (CA-CDI) has been rising, due to changes in antibiotics prescribing practices, emergence of hypervirulent strains and improved diagnostics. This study explored CA-CDI epidemiology by examining strain diversity and virulence factors of CA-CDI isolates collected across several geographical regions in Israel.MethodsStool samples of 126 CA-CDI patients were subjected to PCR and an immunoassay to identify toxin genes and proteins, respectively. Toxin loci PaLoc and PaCdt were detected by whole-genome sequencing (WGS). Biofilm production was assessed by crystal violet-based assay. Minimum inhibitory concentration was determined using the Etest technique or agar dilution. WGS and multi-locus sequence typing (MLST) were used to classify strains and investigate genetic diversity.ResultsSequence types (ST) 2 (17, 13.5%), ST42 (13, 10.3%), ST104 (10, 8%) and ST11 (9, 7.1%) were the most common. All (117, 92.8%) but ST11 belonged to Clade 1. No associations were found between ST and gender, geographic area or antibiotic susceptibility. Although all strains harbored toxins genes, 34 (27%) produced toxin A only, and 54 (42.9%) strains produced toxin B only; 38 (30.2%) produced both toxins. Most isolates were biofilm-producers (118, 93.6%), primarily weak producers (83/118, 70.3%). ST was significantly associated with both biofilm and toxin production.ConclusionC. difficile isolates in Israel community exhibit high ST diversity, with no dominant strain. Other factors may influence the clinical outcomes of CDI such as toxin production, antibiotic resistance and biofilm production. Further studies are needed to better understand the dynamics and influence of these factors on CA-CDI.

AbstractBackground The multi-country mpox outbreak across the globe has led to the systematic surveillance of mpox cases in India. During the surveillance of mpox, we encountered cases of Varicella Zoster Virus (VZV) in suspected mpox cases amongst children & adults. This study focused on the genomic characterization of VZV in India.Methods A total of 331 mpox suspected cases were tested for VZV through real-time PCR, and the positive samples were subjected to next-generation sequencing to retrieve the whole genome of VZV using CLC genomics software. Phylogenetic analysis has been done in MEGA 11.0 software to identify circulating clades.Result Of the 331 suspected cases, 28 cases with vesicular rashes were found to be positive for VZV. The maximum genome could be retrieved from the clinical specimens of 16 cases with coverage greater than 98% when mapped with reference strain Dumas (NC 001348). The phylogenetic analyses of these sequences determined the circulation of clades 1, 5, and 9 in India. Further, the sequence analysis demonstrated non-synonymous single nucleotide polymorphism (SNPs) among specific ORF of VZV including ORF 14, ORF 22, ORF 36, ORF 37 and ORF 51. Although clade 1 and 5 has been reported earlier, the circulation of clade 9 of VZV has been determined for the first time in India.Conclusion Although the circulation of different clades of VZV was reported from India, the presence of clade 9 was detected for the first time during the mpox surveillance.

In African countries where mpox (monkeypox) is endemic, infection is caused by two genetically related clades—Clade I (formerly Congo Basin), and Clade IIa (formerly West Africa), both of which are potentially life-threatening infections. Prior to the 2022–2023 global outbreak, mpox infections among pregnant women caused by Clade I were reported to have a 75% perinatal case fatality rate in the Democratic Republic of Congo, including the only documented case of placental infection and stillbirth from the Congenital Mpox Syndrome, and the Clade IIa mpox infection was associated with stillbirths in Nigeria. The 2022–2023 global mpox outbreak, caused by a genetically distinct strain, Clade IIb, has focused attention on the effects of mpox on pregnant women and fetal outcomes. There have been at least 58 cases of mpox infection occurring in pregnant women during the 2022–2023 outbreak. No confirmed cases of adverse perinatal outcome, including stillbirth, have been reported. The absence of perinatal morbidity and mortality from Clade IIb corresponds to the overall case fatality rate among non-pregnant women of <0.1%, as this clade has been demonstrated to produce a less-severe disease than the mpox Clade I or IIa variants. Thus, there are apparently important differences between mpox clades affecting pregnant women and perinatal outcomes. [ABSTRACT FROM AUTHOR]

Introduction: Prolonged COVID-19 pandemic accelerates the emergence and transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants through the accumulation of adaptive mutations. Particularly, adaptive mutations in spike (S) protein of SARS-CoV-2 leads to increased viral infectivity, severe morbidity and mortality, and immune evasion. This study focuses on the phylodynamic distribution of SARS-CoV-2 variants during the year 2021 in India besides analyzing the functional significance of mutations in S-protein of SARS-CoV-2 variants. Methods: Whole genome of SARS-CoV-2 sequences (n = 87957) from the various parts of India over the period of January to December 2021 was retrieved from Global Initiative on Sharing All Influenza Data. All the S-protein sequences were subjected to clade analysis, variant calling, protein stability, immune escape potential, structural divergence, Furin cleavage efficiency, and phylogenetic analysis using various in silico tools. Results: Delta variant belonging to 21A, 21I, and 21J clades was found to be predominant throughout the year 2021 though many variants were also present. A total of 4639 amino acid mutations were found in S-protein. D614G was the most predominant mutation in the S-protein followed by P681R, L452R, T19R, T478K, and D950N. The highest number of mutations was found in the N-terminal domain of S-protein. Mutations in the crucial sites of S-protein impacting pathogenicity, immunogenicity, and fusogenicity were identified. Intralineage diversity analysis showed that certain variants of SARS-CoV-2 possess high diversification. Conclusions: The study has disclosed the distribution of various variants including the Delta, the predominant variant, in India throughout the year 2021. The study has identified mutations in S-protein of each SARS-CoV-2 variant that can significantly impact the virulence, immune evasion, increased transmissibility, high morbidity, and mortality. In addition, it is found that mutations acquired during each viral replication cycle introduce new sub-lineages as studied by intralineage diversity analysis.

In the study, we evaluated the genetic specificity of haplotypes in the population of hybrid gilts (Large White × Landrace), (Landrace × Large White) from the SPE “Globinsky Pig Complex” LLC and breeding sows of the Large White breed from the SE “DG named after January 9th” using polymorphism of the lengths of the restricted fragments of mtDNA. The purpose of the study was to determine if the process of creating specialized parent lines (of modern cross-border breeds) reduces haplotype diversity. As a genetic material, bristles from sows of the Large White breed (n=7) were used and epithelial tissue of pigs (Large White × Landrace), (Landrace × Large White) — (n=37). DNA release from bristle samples was carried out using ion exchange resin Chelex-100. For the study of the D-loop of the mitochondrial genome of hybrid pigs (n=37) from the epithelial tissue of the auricle, a set of DNA-sorb-B nucleic acid extraction kit from “InterLabService-Ukraine” LLC was used. The samples of epithelial tissue of pigs’ ears were treated with fire from fuel tablet. For the analysis of the mitochondrial genome, the method of polymorphism of the lengths of restricted fragments was used, amplified with PCR. Genotyping of DNA samples of experimental pigs according to mitochondrial markers was carried out with the involvement of the polysite method in accordance with the methodological recommendations of K. F. Pochernyaev and M. D. Berezovsky (2014). The use of maternal inheritance type markers (mtDNA) allowed to identify 2 maternal lines with specific haplotypes, which participated in the creation of hybrid pigs and the formation of their haplogroup. The genetic diversity of mtDNA subspecies of wild and domesticated pigs is limited by the existing lines. Therefore, one haplotype of the mitochondrial genome does not indicate a specific breed, since, several breeds have the same haplotype mtDNA — A, G, C, N, and O. The concentration of haplotype A in tribal sows of Large White breed with a frequency (16%). In the hybrid gilts (Large White × Landrace), (Landrace × Large White) the concentration of detected haplotypes is: C (n=9) — Landrace, Hampshire, Wales, wild pig (20.5%); G — (n=5) Wales, wild pig (11.4%); O (n=5) — Landrace, wild pig (11.4%); N (n=11) — Large White, Berkshire, Asian wild pig (25%); D 9%, K 6.8% (n=7) — unknown among the breeds of domestic pig. We assume that pigs of a Large White breed with haplotype A and hybrid pigs (Large White × Landrace), (Landrace × Large White) with haplotype G, O, in particular D, K contain aboriginal genetic resources. However, in the middle of the XX century, subspecies of wild and domesticated pig breeds became less population-like due to decrease in the area of cultivation and increased pressure from foreign breeds with high growth rates and breeding grounds. Thus, there is a risk of extinction — existing haplotypes and those which have not yet been identified among domesticated pigs (D, K). This suggests that the study should focus on classifying and identifying the phylogenetic origin of pigs and the creation of a molecular genetic bank of producer boars for environmental activities. The domestication process puts strong selective pressure on Sus scrofa species through genetic processes such as inbreeding, genetic drift, natural and artificial selection according to the desired signs. Over the past 9–10,000 years, human intervention has led to domesticated species that are morphologically, behaviorally, and genetically different from their ancestors’ relatives. We believe that the “hybrid” subspecies of wild pigs with some morphological features of a domesticated pig had a higher proportion of the full-genomic ancestors of a domestic pig compared to the morphologically pure subspecies of wild pigs. Animals with haplotypes D, K are the result of hybridization with European boars. Representatives of haplotypes A (Large White, European-type Duroc, Mangalica); G (Wales, wild pig) — Italy; C (Landrace, Wales, Hampshire, wild pig) — Ukraine, Poland, France; O (landrace, wild pig) — Sweden, grouped into the European cluster of “mt-E” haplogroup. Pigs with the haplotype N — Large White (Asian type), Berkshire, a wild pig belongs to the Asian cluster of “mt-A” haplogroup. Over time, this led to almost complete disappearance of primary Middle Eastern ancestors in the nuclear genomes of European domesticated pigs. Phylogenetic reconstruction of mitochondrial genome data from hybrid pigs reflects a clear geographical division of mtDNA data — Eastern Europe and Asia. In particular, the subspecies of European and Asian wild pigs is the ancestral foundation on the maternal line, which preceded domestication and breeding pigs by hybridization. European and Asian haplotypes of wild pigs have shown that wild pigs from regions such as Italy, Poland, France, Scandinavia, and Ukraine were also either domesticated or at least initially included in domesticated pigs. The results of the study of the S. s. domestica mitochondrial genome showed an intra-breed genetic diversity of hybrid gilts. This is due to the selection strategy of international genetic centers, where, despite the consolidation of the genetic structure in the inside of the center, significant general genetic diversity of the breed is ensured. In addition, the above results indicate a connection between the frequency distribution of mtDNA haplotypes and adaptation to different climate conditions. As a whole, the presented results are an incentive to continue research on the study of the mitochondrial genome of modern lines of hybrid pigs. Carriers of haplotype C, O, G, and N are the basis of maternal breeding and improvement of the lines of hybrid pigs of the XXI century. It is necessary to take into account the fact that the cleanest mother nuclei (Wild pig, Great Yorkshire, Landrace) are really clean foundation for use in hybridization schemes, in the crossing over, in the formation and development of modern hybrid lines of pigs. Despite this, the diversity of the mitochondrial genome in the population of transboundary breeds persists.

Avian Influenza (AI) has become the largest animal epidemic in the world. So far hundreds of millions birds have died or been culled due to the disease. A novel highly-pathogenic avian influenza (HPAI) subtype H5N1 virus, which emerged in 1996 in domestic geese in China, passed from wild waterfowl as a lowpathogenic (LP) virus, and in the domestic birds was modified to a High Pathogenic (HP) virus due to mutational addition of basic amino acids to the cleavage site of the Hemagglutinin (HA) protein. This "A/ goose/Guangdong/1/1996" virus killed poultry but also infected at least 18 people of whom 6 died. In 2003-6 the virus spread to Asia, Europe, Africa and the Middle East. Mass mortality of migratory birds at the Salt Qinghai Lake in West China in 2005 was a turning point in the understanding of the virus co-circulation between poultry and wild birds. Israel is situated on migratory routes for over a billion birds each year in the autumn migration from Europe to Africa and in the northwards spring migration, thus the potential for virus transmission is high. The 1996's parental virus emerged in Israel in 2006, following the Qinghai Lake event, and included meat turkeys, heavy breeders and broilers. Since then, several focal outbreaks occurred in Israel every 1-3 years. In 2012, the same AIV-H5N1 was detected in meat turkeys and found also in alley cats following consumption of the bird carcasses, with 100% identity of the HA gene. A second multi-focal outbreak of AIV-H5N1 appeared in 2015 following the worldwide wave in 2014-15. This outbreak included meat turkeys, heavy breeders and egg layers. These viruses belonged phylogenetically to clade 2.2.1.2, emerged from previous clades 2.2 and 2.2.1.1. Reassortment of viral segments of a descendant-H5 AIV of the Chinese parental virus with AIV-N8 viruses created novel H5N8 viruses, first detected in China in 2010. An 2016's variant of this virus (group-B Gochang-like, clade 2.3.4.4), was discovered in May-June 2016 in wild swans at Lake Ubsu-Nur on the Russian-Mongolian border, and reached Central Asia, Europe, Africa, Middle East and Israel. The Ubsu-Nur 2016's AIV-H5N8 was genetically identical to an AIV-H5N8 that emerged in Israel six months later during the autumn migration. This was the first H5N8 outbreak in Israel, which included meat and breeder turkeys, heavy and light breeders, layers, breeder ducks and backyard poultry, but also many wild birds, not seen in the previous H5N1 outbreaks, of at least 16 species mostly waterfowl and raptors. The cleavage site of HA gene showed similarity between poultry and wild birds, as well as to grp B-2.3.4.4 European-Asian H5N8 viruses. Since October 2020, new H5 reassortants with LPAI viruses from wild birds contributed the Neuraminidase (NA) glycoprotein, have appeared in Europe and created new H5 strains. A second global outbreak of a new H5 variant occurred in 2020-21 in Russia and the Palearctic region. Following this global outbreak, a second AIV-H5N8 outbreak appeared in Israel in 2020 during the autumn migration. The outbreak included meat and breeder turkeys, heavy breeders, broilers, game birds mainly black swans (Cygnus atratus), and wild birds. The 2021--22's AIV-H5N1 epidemic season was the largest so far in Europe and Eurasia, with about 2500 outbreaks in poultry and culling of 50 million birds, and about 3600 detections in wild birds. That outbreak followed the 2020's wave of the new AIV-H5N8. Following this epidemic, a third multi-focal outbreak of AIV-H5N1 occurred in Israel in 2021, in meat and breeder turkeys, heavy breeders, organic egg layers and meat ducks. The 2021's outbreak was characterized also by affecting many wild birds, not seen before in H5N1's outbreaks in Israel, while the largest affected population was Common cranes (Grus grus) on their migration routes from Russia and Scandinavia to Ethiopia and Sudan through Israel, undergoing mass mortality of almost 10,000 birds. Other threatened species like Marbled teal (Marmaronetta angustirostris) have died also due to this virus, as well as hundreds of Great white pelicans (Pelecanus onocrotalus), and several species of waterfowl and raptors. Classification of the viruses by whole genome sequencing (WGS) revealed the same group B-2.3.4.4 clade as in the H5N8 events and similarity between poultry and wild birds. This virus probably came from Russia in the autumn migration. A new outbreak of AIV-H5N1 began emerging in Israel from November 2022, in meat turkeys, heavy and light breeders, broilers. Unlike the 2021's outbreak, this virus affected only a few wild birds. HA gene sequencing revealed the virus belonged to the same group B-2.3.4.4 clade as in previous outbreaks. In conclusion, all avian influenza subtype H5 outbreaks in Israel followed the European-Eurasian outbreaks. The virus origin was from South East Asia, reaching Israel through spillover with migrating birds via Eurasia and Europe. [ABSTRACT FROM AUTHOR]

Genomic epidemiology has proven to be a useful tool for investigating pandemic outbreaks and tracking pathogen spread and evolution. This study describes the circulation of SARS-CoV-2 strains in N. Macedonia during a period of one year, encompassing three waves of the COVID-19 pandemic. A certain percentage (2-3%) of positive cases were continuously selected and analyzed by whole genome sequencing (WGS) technology. Using this approach, a total of 337 SARS-CoV-2 genomes were sequenced and 26 different lineages belonging to 7 clades were detected. During the first wave of the pandemic, the most dominant lineage was B.1.1, followed by B.1.1.70, which became the most dominant in the second wave. The B.1.1.7 lineage completely overpassed all other variants in the third wave. Our study strengthens the notion that the progression of COVID-19 pandemic is associated with emergence of new SARS-CoV-2 variants with increased virulence. The measure of the impact of this viral dynamic on the spread of the pandemic should be evaluated in association with other factors that might influence the transmission. [ABSTRACT FROM AUTHOR]

Introduction: Prolonged COVID-19 pandemic accelerates the emergence and transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants through the accumulation of adaptive mutations. Particularly, adaptive mutations in spike (S) protein of SARS-CoV-2 leads to increased viral infectivity, severe morbidity and mortality, and immune evasion. This study focuses on the phylodynamic distribution of SARS-CoV-2 variants during the year 2021 in India besides analyzing the functional significance of mutations in S-protein of SARS-CoV-2 variants. Methods: Whole genome of SARS-CoV-2 sequences (n = 87957) from the various parts of India over the period of January to December 2021 was retrieved from Global Initiative on Sharing All Influenza Data. All the S-protein sequences were subjected to clade analysis, variant calling, protein stability, immune escape potential, structural divergence, Furin cleavage efficiency, and phylogenetic analysis using various in silico tools. Results: Delta variant belonging to 21A, 21I, and 21J clades was found to be predominant throughout the year 2021 though many variants were also present. A total of4639 amino acid mutations were found in S-protein. D614G was the most predominant mutation in the S-protein followed by P681R, L452R, T19R, T478K, and D950N. The highest number of mutations was found in the N-terminal domain of S-protein. Mutations in the crucial sites of S-protein impacting pathogenicity, immunogenicity, and fusogenicity were identified. Intralineage diversity analysis showed that certain variants of SARS-CoV-2 possess high diversification. Conclusions: The study has disclosed the distribution of various variants including the Delta, the predominant variant, in India throughout the year 2021. The study has identified mutations in S-protein of each SARS-CoV-2 variant that can significantly impact the virulence, immune evasion, increased transmissibility, high morbidity, and mortality. In addition, it is found that mutations acquired during each viral replication cycle introduce new sub-lineages as studied by intralineage diversity analysis. [ABSTRACT FROM AUTHOR]

Background and Aims: Since the beginning of the SARS‐CoV‐2 pandemic, multiple new variants have emerged posing an increased risk to global public health. This study aimed to investigate SARS‐CoV‐2 variants, their temporal dynamics, infection rate (IFR) and case fatality rate (CFR) in Bangladesh by analyzing the published genomes. Methods: We retrieved 6610 complete whole genome sequences of the SARS‐CoV‐2 from the GISAID (Global Initiative on Sharing all Influenza Data) platform from March 2020 to October 2022, and performed different in‐silico bioinformatics analyses. The clade and Pango lineages were assigned by using Nextclade v2.8.1. SARS‐CoV‐2 infections and fatality data were collected from the Institute of Epidemiology Disease Control and Research (IEDCR), Bangladesh. The average IFR was calculated from the monthly COVID‐19 cases and population size while average CFR was calculated from the number of monthly deaths and number of confirmed COVID‐19 cases. Results: SARS‐CoV‐2 first emerged in Bangladesh on March 3, 2020 and created three pandemic waves so far. The phylogenetic analysis revealed multiple introductions of SARS‐CoV‐2 variant(s) into Bangladesh with at least 22 Nextstrain clades and 107 Pangolin lineages with respect to the SARS‐CoV‐2 reference genome of Wuhan/Hu‐1/2019. The Delta variant was detected as the most predominant (48.06%) variant followed by Omicron (27.88%), Beta (7.65%), Alpha (1.56%), Eta (0.33%) and Gamma (0.03%) variant. The overall IFR and CFR from circulating variants were 13.59% and 1.45%, respectively. A time‐dependent monthly analysis showed significant variations in the IFR (p = 0.012, Kruskal–Wallis test) and CFR (p = 0.032, Kruskal–Wallis test) throughout the study period. We found the highest IFR (14.35%) in 2020 while Delta (20A) and Beta (20H) variants were circulating in Bangladesh. Remarkably, the highest CFR (1.91%) from SARS‐CoV‐2 variants was recorded in 2021. Conclusion: Our findings highlight the importance of genomic surveillance for careful monitoring of variants of concern emergence to interpret correctly their relative IFR and CFR, and thus, for implementation of strengthened public health and social measures to control the spread of the virus. Furthermore, the results of the present study may provide important context for sequence‐based inference in SARS‐CoV‐2 variant(s) evolution and clinical epidemiology beyond Bangladesh. [ABSTRACT FROM AUTHOR]

Bat species in Mongolia have received a relatively low conservation priority compared to avian and other mammalian species. This might partially result from their understudied ecologies, distributions, and population sizes in Mongolia. Additionally, Mongolia hosts a relatively small assembly of bat species. In this study, we investigated the genetic characteristics of 14 species of bats (n = 61) from six genera (Myotis, Vespertilio, Eptesicus, Hypsugo, Plecotus, and Murina) using a 598 bp long mitochondrial DNA cytochrome c oxidase subunit 1 gene. We reconstructed Maximum likelihood and Bayesian-inference trees, together with estimated molecular divergence times on nodes of interest using an HKY substitution model. Our findings clearly showed four distinct clades (I–IV). Through the partial fragment mitochondrial DNA cytochrome c oxidase subunit 1 gene, 26 haplotypes (Hd = 0.94 ± 0.0001) were identified overall from 61 individuals. We estimated a divergence time of 31.71–55.84 mya (95% highest posterior density (HPD)) on the node of clade I (genus Myotis) and the other three clades (other genera). Interestingly, in clade II, we no longer considered animals in haplotype 2 (H2) of Hypsugo alaschanicus as H. alaschanicus. Instead, this haplotype was recently described as H. stubbei. Additional molecular genetic studies are required to clarify intraspecific divergences of some vesper bats in Mongolia, particularly, M. ikonnikovi, M. davidii, H. alaschanicus, and P. ognevi.

Abstract Background and Aims Since the beginning of the SARS‐CoV‐2 pandemic, multiple new variants have emerged posing an increased risk to global public health. This study aimed to investigate SARS‐CoV‐2 variants, their temporal dynamics, infection rate (IFR) and case fatality rate (CFR) in Bangladesh by analyzing the published genomes. Methods We retrieved 6610 complete whole genome sequences of the SARS‐CoV‐2 from the GISAID (Global Initiative on Sharing all Influenza Data) platform from March 2020 to October 2022, and performed different in‐silico bioinformatics analyses. The clade and Pango lineages were assigned by using Nextclade v2.8.1. SARS‐CoV‐2 infections and fatality data were collected from the Institute of Epidemiology Disease Control and Research (IEDCR), Bangladesh. The average IFR was calculated from the monthly COVID‐19 cases and population size while average CFR was calculated from the number of monthly deaths and number of confirmed COVID‐19 cases. Results SARS‐CoV‐2 first emerged in Bangladesh on March 3, 2020 and created three pandemic waves so far. The phylogenetic analysis revealed multiple introductions of SARS‐CoV‐2 variant(s) into Bangladesh with at least 22 Nextstrain clades and 107 Pangolin lineages with respect to the SARS‐CoV‐2 reference genome of Wuhan/Hu‐1/2019. The Delta variant was detected as the most predominant (48.06%) variant followed by Omicron (27.88%), Beta (7.65%), Alpha (1.56%), Eta (0.33%) and Gamma (0.03%) variant. The overall IFR and CFR from circulating variants were 13.59% and 1.45%, respectively. A time‐dependent monthly analysis showed significant variations in the IFR (p = 0.012, Kruskal–Wallis test) and CFR (p = 0.032, Kruskal–Wallis test) throughout the study period. We found the highest IFR (14.35%) in 2020 while Delta (20A) and Beta (20H) variants were circulating in Bangladesh. Remarkably, the highest CFR (1.91%) from SARS‐CoV‐2 variants was recorded in 2021. Conclusion Our findings highlight the importance of genomic surveillance for careful monitoring of variants of concern emergence to interpret correctly their relative IFR and CFR, and thus, for implementation of strengthened public health and social measures to control the spread of the virus. Furthermore, the results of the present study may provide important context for sequence‐based inference in SARS‐CoV‐2 variant(s) evolution and clinical epidemiology beyond Bangladesh.

The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive sequencing protocol for 384 samples by adapting the use of an Illumina NovaSeq library to an Illumina MiSeq flow cell instrument. The SARS-CoV-2 genome sequences obtained with Illumina NovaSeq and those obtained using MiSeq instruments were compared with the objective to validate the new, modified protocol. A total of 356 (94.6%) samples yielded interpretable sequences using the modified Illumina COVIDSeq protocol, with an average coverage of 91.6%. By comparison, 357 (94.9%) samples yielded interpretable sequences with the standard COVIDSeq protocol, with an average coverage of 95.6%. Our modified COVIDSeq protocol could save 14,155 euros per run and yield results from 384 samples in 53.5 h, compared to four times 55.5 h with the standard Illumina MiSeq protocol. The modified COVIDSeq protocol thus provides high quality results comparable to those obtained with the standard COVIDSeq protocol, four times faster, while saving money. [ABSTRACT FROM AUTHOR]

HEV genotype (gt) 3 infections are prevalent in high-income countries and display a wide spectrum of clinical presentations. Host – but not viral – factors are reported to be associated with worse clinical outcomes. Demographic, clinical, and biochemical data laboratory-confirmed HEV infections (by PCR and/or a combination of IgM and IgG serology) at the Belgian National Reference Centre between January 2010 and June 2018 were collected using standardised case report forms. Genotyping was based on HEV open reading frame 2 sequences. Serum CXCL10 levels were measured by a magnetic bead-based assay. H&E staining was performed on liver biopsies. A total of 274 HEV-infected individuals were included. Subtype assignment was possible for 179/218 viraemic cases, confirming gt3 as dominant with an almost equal representation of clades abchijklm and efg. An increased hospitalisation rate and higher peak serum levels of alanine aminotransferase, bilirubin, and alkaline phosphatase were found in clade efg-infected individuals in univariate analyses. In multivariable analyses, clade efg infections remained more strongly associated with severe disease presentation than any of the previously identified host risk factors, being associated with a 2.1-fold higher risk of hospitalisation (95% CI 1.1–4.4, p = 0.034) and a 68.2% higher peak of bilirubin levels (95% CI 13.3–149.9, p = 0.010), independently of other factors included in the model. In addition, acute clade efg infections were characterised by higher serum CXCL10 levels (p = 0.0005) and a more pronounced liver necro-inflammatory activity (p = 0.022). In symptomatic HEV gt3 infections, clade efg is associated with a more severe disease presentation, higher serum CXCL10 levels, and liver necro-inflammatory activity, irrespective of known host risk factors. The protocol was submitted to clinicaltrials.gov (NCT04670419). HEV genotype (gt) 3 infections display a wide spectrum of clinical presentations currently ascribed to host factors. Here we examined the role of viral factors on liver disease outcomes by combining viral phylogeny with clinical, biochemical, cytokine, and histological data from 274 Belgian adults infected with HEV presenting between 2010 and 2018. HEV gt 3 clade efg infections were associated with a more severe disease presentation, higher serum CXCL10 levels and liver necro-inflammatory activity, irrespective of known host risk factors. HEV gt3 clade-dependent clinical outcomes call for broad HEV gt3 subtyping in clinical practice and research to help identify those at higher risk for worse outcomes and to further unravel underlying virus–host interactions. [Display omitted] • This is a study of clinical outcome, CXCL10 level, and viral phylogenetic analysis of 274 HEV infections in Belgium. • HEV gt3 clade is the strongest predictor for outcomes in symptomatic infections. • HEV gt3 clade efg is linked to higher hospitalisation rates, peak bilirubin levels, serum CXCL10 levels, and liver necro-inflammatory activity. [ABSTRACT FROM AUTHOR]

Background and Aim: Characterization of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) based on analyzing the evolution and mutations of viruses is crucial for tracking viral infections, potential mutants, and other pathogens. The purpose was to study the complete sequences of SARS‐CoV‐2 to reveal genetic distance and mutation rate among different provinces of Iran. Methods: As of March 2020–April 2021, a total of 131 SARS‐CoV‐2 whole genome sequences submitted from Tehran and 133 SARS‐CoV‐2 full‐length sequences from 24 cities with high coverage submitted to EpiCoV GISAID database were analyzed to infer clades and mutation annotation compared with the wild‐type variant Wuhan‐Hu‐1. Results: The results of variant annotation were revealed 11,204 and 9468 distinct genomes were identified among the samples from different cities and Tehran, respectively. The phylogenetic analysis of genomic sequences showed the presence of eight GISAID clades, namely GH, GR, O, GRY, G, GK, L, and GV, and six Nextstrain clades; that is, 19A, 20A, 20B, 20I (alpha, V1), 20H (Beta, V2), and 21I (Delta) in Iran. The GH (GISAID clade), 20A (Nextstrain clade), and B.1 (Pango lineage) were predominant in Iran. Notably, analysis of the spike protein revealed D614G mutation (S_D614G) in 56% of the sequences. Also, the delta variant of the coronavirus, the super‐infectious strain that was first identified among the sequences submitted from the southern cities of the country such as Zahedan, Yazd and Bushehr, and most likely from these places to other cities of Iran as well has expanded. Conclusions: Our results indicate that most of the circulated viruses in Iran in the early time of the pandemic had collected in eight GISAID clades. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS‐CoV‐2 in Iran. [ABSTRACT FROM AUTHOR]

Abstract Background A global pandemic has been declared for coronavirus disease 2019 (COVID-19), which has serious impacts on human health and healthcare systems in the affected areas, including Vietnam. None of the previous studies have a framework to provide summary statistics of the virus variants and assess the severity associated with virus proteins and host cells in COVID-19 patients in Vietnam. Method In this paper, we comprehensively investigated SARS-CoV-2 variants and immune responses in COVID-19 patients. We provided summary statistics of target sequences of SARS-CoV-2 in Vietnam and other countries for data scientists to use in downstream analysis for therapeutic targets. For host cells, we proposed a predictive model of the severity of COVID-19 based on public datasets of hospitalization status in Vietnam, incorporating a polygenic risk score. This score uses immunogenic SNP biomarkers as indicators of COVID-19 severity. Result We identified that the Delta variant of SARS-CoV-2 is most prevalent in southern areas of Vietnam and it is different from other areas in the world using various data sources. Our predictive models of COVID-19 severity had high accuracy (Random Forest AUC = 0.81, Elastic Net AUC = 0.7, and SVM AUC = 0.69) and showed that the use of polygenic risk scores increased the models’ predictive capabilities. Conclusion We provided a comprehensive analysis for COVID-19 severity in Vietnam. This investigation is not only helpful for COVID-19 treatment in therapeutic target studies, but also could influence further research on the disease progression and personalized clinical outcomes.

Abstract Background We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondrial DNA (mtDNA) haplogroup U5, which appears at high frequencies in northern Europe. Methods Haplogroup U5 mitogenome sequences were gathered from GenBank. The hierarchal Bayesian Analysis of Population Structure (hierBAPS) method was used to generate groups of sequences that were then projected onto a rooted maximum likelihood (ML) phylogenetic tree to visualize the pattern of clustering. The haplogroup statuses of the individual sequences were assessed using Haplogrep2. Results A total of 23 hierBAPS groups were identified, all of which corresponded to subclades defined in Phylotree, v.17. The hierBAPS groups projected onto the ML phylogeny accurately clustered all haplotypes belonging to a specific haplogroup in accordance with Haplogrep2. By incorporating the geographic source of each sequence and subclade age estimates into this framework, inferences about the diversification of U5 mtDNAs were made. Haplogroup U5 has been present in northern Europe since the Mesolithic, and spread in both eastern and western directions, undergoing significant diversification within Scandinavia. A review of historical and archeological evidence attests to some of the population interactions contributing to this pattern. Conclusions The hierBAPS algorithm accurately grouped mitogenome sequences into subclades in a phylogenetically robust manner. This analysis provided new insights into the phylogeographic structure of haplogroup U5 diversity in northern Europe, revealing a detailed perspective on the diversity of subclades in this region and their distribution in Scandinavian populations.

The idea that birds are maniraptoran theropod dinosaurs is now considered an evolutionary consensus. An “open” (i.e., completely or substantially perforate) acetabulum is considered an important synapomorphy verifying the bird–dinosaur nexus. Here, I present anatomical evidence from the acetabulum and its important appurtenances, the supracetabular crest and the antitrochanter, that hip anatomy differs substantially between dinosaurs and birds. Given the thin bone of the acetabular walls and the varied tissue, both hard and soft, in the acetabular region and especially the lower part of the basin, it is apparent that many avian skeletons exhibit some anatomical loss of soft tissue and thin bone, some perhaps related to changes in gait, but also in part related to the dramatic trend in bone reduction associated with flight, especially in more advanced crown taxa. Many basal birds and early diverging neornithines tend to have a nearly closed or partially closed acetabula, thus rendering the current terms “open” or “closed” acetabula inaccurate; they should be modified or replaced. Given new evidence presented here, the relationship of “dinosaurs” and birds must be re-evaluated.

Abstract Background and Aim Characterization of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) based on analyzing the evolution and mutations of viruses is crucial for tracking viral infections, potential mutants, and other pathogens. The purpose was to study the complete sequences of SARS‐CoV‐2 to reveal genetic distance and mutation rate among different provinces of Iran. Methods As of March 2020–April 2021, a total of 131 SARS‐CoV‐2 whole genome sequences submitted from Tehran and 133 SARS‐CoV‐2 full‐length sequences from 24 cities with high coverage submitted to EpiCoV GISAID database were analyzed to infer clades and mutation annotation compared with the wild‐type variant Wuhan‐Hu‐1. Results The results of variant annotation were revealed 11,204 and 9468 distinct genomes were identified among the samples from different cities and Tehran, respectively. The phylogenetic analysis of genomic sequences showed the presence of eight GISAID clades, namely GH, GR, O, GRY, G, GK, L, and GV, and six Nextstrain clades; that is, 19A, 20A, 20B, 20I (alpha, V1), 20H (Beta, V2), and 21I (Delta) in Iran. The GH (GISAID clade), 20A (Nextstrain clade), and B.1 (Pango lineage) were predominant in Iran. Notably, analysis of the spike protein revealed D614G mutation (S_D614G) in 56% of the sequences. Also, the delta variant of the coronavirus, the super‐infectious strain that was first identified among the sequences submitted from the southern cities of the country such as Zahedan, Yazd and Bushehr, and most likely from these places to other cities of Iran as well has expanded. Conclusions Our results indicate that most of the circulated viruses in Iran in the early time of the pandemic had collected in eight GISAID clades. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS‐CoV‐2 in Iran.

Mucorales are ubiquitous environmental molds responsible for mucormycosis in diabetic, immunocompromised, and severely burned patients. Small outbreaks of invasive wound mucormycosis (IWM) have already been reported in burn units without extensive microbiological investigations. We faced an outbreak of IWM in our center and investigated the clinical isolates with whole-genome sequencing (WGS) analysis. We analyzed M. circinelloides isolates from patients in our burn unit (BU1, Hôpital Saint-Louis, Paris, France) together with nonoutbreak isolates from Burn Unit 2 (BU2, Paris area) and from France over a 2-year period (2013 to 2015). A total of 21 isolates, including 14 isolates from six BU1 patients, were analyzed by whole-genome sequencing (WGS). Phylogenetic classification based on de novo assembly and assembly free approaches showed that the clinical isolates clustered in four highly divergent clades. Clade 1 contained at least one of the strains from the six epidemiologically linked BU1 patients. The clinical isolates were specific to each patient. Two patients were infected with more than two strains from different clades, suggesting that an environmental reservoir of clonally unrelated isolates was the source of contamination. Only two patients from BU1 shared one strain, which could correspond to direct transmission or contamination with the same environmental source. In conclusion, WGS of several isolates per patients coupled with precise epidemiological data revealed a complex situation combining potential cross-transmission between patients and multiple contaminations with a heterogeneous pool of strains from a cryptic environmental reservoir.IMPORTANCE Invasive wound mucormycosis (IWM) is a severe infection due to environmental molds belonging to the order Mucorales. Severely burned patients are particularly at risk for IWM. Here, we used whole-genome sequencing (WGS) analysis to resolve an outbreak of IWM due to Mucor circinelloides that occurred in our hospital (BU1). We sequenced 21 clinical isolates, including 14 from BU1 and 7 unrelated isolates, and compared them to the reference genome (1006PhL). This analysis revealed that the outbreak was mainly due to multiple strains that seemed patient specific, suggesting that the patients were more likely infected from a pool of diverse strains from the environment rather than from direct transmission among them. This study revealed the complexity of a Mucorales outbreak in the settings of IWM in burn patients, which has been highlighted based on WGS combined with careful sampling.

The ongoing SARS-CoV-2 evolution process has generated several variants due to its continuous mutations, making pandemics more critical. The present study illustrates SARS-CoV-2 evolution and its emerging mutations in five directions. First, the significant mutations in the genome and S-glycoprotein were analyzed in different variants. Three linear models were developed with the regression line to depict the mutational load for S-glycoprotein, total genome excluding S-glycoprotein, and whole genome. Second, the continent-wide evolution of SARS-CoV-2 and its variants with their clades and divergence were evaluated. It showed the region-wise evolution of the SARS-CoV-2 variants and their clustering event. The major clades for each variant were identified. One example is clade 21K, a major clade of the Omicron variant. Third, lineage dynamics and comparison between SARS-CoV-2 lineages across different countries are also illustrated, demonstrating dominant variants in various countries over time. Fourth, gene-wise mutation patterns and genetic variability of SARS-CoV-2 variants across various countries are illustrated. High mutation patterns were found in the ORF10, ORF6, S, and low mutation pattern E genes. Finally, emerging AA point mutations (T478K, L452R, N501Y, S477N, E484A, Q498R, and Y505H), their frequencies, and country-wise occurrence were identified, and the highest event of two mutations (T478K and L452R) was observed. [ABSTRACT FROM AUTHOR]

Fasciolopsiasis caused by Fasciolopsis buski, is a significant cause of morbidity. In the present study F. buski detected during endoscopy of a 50-year-old male patient form Uttar Pradesh, India was used for phylogenetic analysis based on 28S rDNA and ITS2 regions. The parasite was genetically similar to an isolate of pig from Meghalaya. The intra-species genetic variation for 28S rDNA was 1-3% (India), 5% (Vietnam) and for ITS2, 1-2% (India) while 17 % from Vietnam. Thus, F. buski from humans or pigs from India were closely related than those from Vietnam and China which were grouped into separate clades., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

The world health organization has announced that SARS-CoV-2 Omicron variant (B.1.1.529), including the three versions; 21K (BA.1), 21L (BA.2) and 21M (BA.3) as a variant of concern (VOC) on November 2022. In this study, we used the specialized computational platforms to predict the stability and flexibility of the spike protein of Omicron. The aim of this study was to investigate the expected effect of Omicron spike mutations on its physiochemical properties. Findings of this study revealed 16 stabilizing mutations that might explain a newly gained environmental stability. We expect the new mutations to play a crucial role in changing the physiochemical properties of epitopes of the spike protein. The notable finding of SuerPose work was the potential linear B-cells epitope G252 → S255 that has been changed in the spike protein of the Omicron 21L to a helix structure which might confer an escape from human monoclonal antibodies. • Thermodynamics prediction showed 16 stabilizing Omicron spike protein mutations. • Physiochemical attributes of spike protein are crucial to characterize. • Omicron clade 21L is expected to be more transmissible than 21K and 21M. • Spike linear B-cells epitope G252.→ S255 has been changed to a helix structure [ABSTRACT FROM AUTHOR]

• Multiple sequence alignment of 18392 SARS-CoV-2 genomes for 71 countries. • Phylogenetic analysis to identify virus clades. • Mutation points as SNPs are identified in each clade. • Top 10 signature SNPs are identified in each clade. • Signature SNPs are characterized using PROVEAN, Polyphen-2 and I-Mutant 2.0. Since the emergence of SARS-CoV-2 in Wuhan, China more than a year ago, it has spread across the world in a very short span of time. Although, different forms of vaccines are being rolled out for vaccination programs around the globe, the mutation of the virus is still a cause of concern among the research communities. Hence, it is important to study the constantly evolving virus and its strains in order to provide a much more stable form of cure. This fact motivated us to conduct this research where we have initially carried out multiple sequence alignment of 15359 and 3033 global dataset without Indian and the dataset of exclusive Indian SARS-CoV-2 genomes respectively, using MAFFT. Subsequently, phylogenetic analyses are performed using Nextstrain to identify virus clades. Consequently, the virus strains are found to be distributed among 5 major clades or clusters viz. 19A, 19B, 20A, 20B and 20C. Thereafter, mutation points as SNPs are identified in each clade. Henceforth, from each clade top 10 signature SNPs are identified based on their frequency i.e. number of occurrences in the virus genome. As a result, 50 such signature SNPs are individually identified for global dataset without Indian and dataset of exclusive Indian SARS-CoV-2 genomes respectively. Out of each 50 signature SNPs, 39 and 41 unique SNPs are identified among which 25 non-synonymous signature SNPs (out of 39) resulted in 30 amino acid changes in protein while 27 changes in amino acid are identified from 22 non-synonymous signature SNPs (out of 41). These 30 and 27 amino acid changes for the non-synonymous signature SNPs are visualised in their respective protein structure as well. Finally, in order to judge the characteristics of the identified clades, the non-synonymous signature SNPs are considered to evaluate the changes in proteins as biological functions with the sequences using PROVEAN and PolyPhen-2 while I-Mutant 2.0 is used to evaluate their structural stability. As a consequence, for global dataset without Indian sequences, G251V in ORF3a in clade 19A, F308Y and G196V in NSP4 and ORF3a in 19B are the unique amino acid changes which are responsible for defining each clade as they are all deleterious and unstable. Such changes which are common for both global dataset without Indian and dataset of exclusive Indian sequences are R203M in Nucleocapsid for 20B, T85I and Q57H in NSP2 and ORF3a respectively for 20C while for exclusive Indian sequences such unique changes are A97V in RdRp, G339S and G339C in NSP2 in 19A and Q57H in ORF3a in 20A. [ABSTRACT FROM AUTHOR]

Cryptococcosis is a potentially lethal disease of humans/animals caused by Cryptococcus neoformans and Cryptococcus gattii. Distinction between the two species is based on phenotypic and genotypic characteristics. Recently, it was proposed that C. neoformans be divided into two species and C. gattii into five species based on a phylogenetic analysis of 115 isolates. While this proposal adds to the knowledge about the genetic diversity and population structure of cryptococcosis agents, the published genotypes of 2,606 strains have already revealed more genetic diversity than is encompassed by seven species. Naming every clade as a separate species at this juncture will lead to continuing nomenclatural instability. In the absence of biological differences between clades and no consensus about how DNA sequence alone can delineate a species, we recommend using "Cryptococcus neoformans species complex" and "C. gattii species complex" as a practical intermediate step, rather than creating more species. This strategy recognizes genetic diversity without creating confusion.

Cryptococcosis is a potentially lethal disease of humans/animals caused by Cryptococcus neoformans and Cryptococcus gattii. Distinction between the two species is based on phenotypic and genotypic characteristics. Recently, it was proposed that C. neoformans be divided into two species and C. gattii into five species based on a phylogenetic analysis of 115 isolates. While this proposal adds to the knowledge about the genetic diversity and population structure of cryptococcosis agents, the published genotypes of 2,606 strains have already revealed more genetic diversity than is encompassed by seven species. Naming every clade as a separate species at this juncture will lead to continuing nomenclatural instability. In the absence of biological differences between clades and no consensus about how DNA sequence alone can delineate a species, we recommend using "Cryptococcus neoformans species complex" and "C. gattii species complex" as a practical intermediate step, rather than creating more species. This strategy recognizes genetic diversity without creating confusion.

Members of the Orthonairovirus genus (family Nairoviridae) include many tick-borne viruses of significant human and animal health impact, with several recently-documented pathogenic viruses lacking sufficient epidemiological information. We screened 215 adult ticks of seven species collected in Bulgaria, Georgia, Latvia and Poland for orthonairoviruses, followed by nanopore sequencing (NS) for genome characterization. Initial generic amplification revealed Sulina virus (SULV, Orthonairovirus sulinaense), for which an updated amplification assay was used, revealing an overall prevalence of 2.7% in Ixodes ricinus ticks from Latvia. Three complete and additional partial SULV genomes were generated, that consistently formed a separate, distinct clade with further intragroup divergence in the maximum likelihood analyses. Comparisons with previously described viruses from Romania exhibited similar genome topologies, albeit with divergent motifs and cleavage sites on the glycoprotein precursor. Preliminary evidence of recombination involving the S segment was documented, in addition to variations in predicted viral glycoproteins. Generic screening further identified Tacheng tick virus 1 (TCTV1, Orthonairovirus tachengense), with documented human infections, in Dermacentor reticulatus ticks from Poland, with a prevalence of 0.9%. Subsequent NS and assembly provided the first complete TCTV1 genome outside of China, where it was originally described. Phylogenetic analysis of virus genome segments revealed TCTV1-Poland as a discrete taxon within the TCTV1 cluster in the Orthonairovirus genus, representing a geographically segregated clade. Comparable genome topology with TCTV1 from China was observed, aside from minor variations in the M segment. Similar to SULV, TCTV1 exhibited several mismatches on previously described screening primer binding sites, likely to prevent amplification. These findings indicate presence of novel TCTV1 and SULV clades in Eastern Europe, confirming the expansion of orthonairoviruses with pathogenic potential. • We documented first complete SULV and TCTV1 genomes outside original locations. • SULV and TCTV1 genomes constituted novel clades within respective species. • Preliminary evidence for genetic exchange between SULV genomes was noted. • Expansion of the TCTV1 into Europe is confirmed. [ABSTRACT FROM AUTHOR]

Background: We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondrial DNA (mtDNA) haplogroup U5, which appears at high frequencies in northern Europe. Methods: Haplogroup U5 mitogenome sequences were gathered from GenBank. The hierarchal Bayesian Analysis of Population Structure (hierBAPS) method was used to generate groups of sequences that were then projected onto a rooted maximum likelihood (ML) phylogenetic tree to visualize the pattern of clustering. The haplogroup statuses of the individual sequences were assessed using Haplogrep2. Results: A total of 23 hierBAPS groups were identified, all of which corresponded to subclades defined in Phylotree, v.17. The hierBAPS groups projected onto the ML phylogeny accurately clustered all haplotypes belonging to a specific haplogroup in accordance with Haplogrep2. By incorporating the geographic source of each sequence and subclade age estimates into this framework, inferences about the diversification of U5 mtDNAs were made. Haplogroup U5 has been present in northern Europe since the Mesolithic, and spread in both eastern and western directions, undergoing significant diversification within Scandinavia. A review of historical and archeological evidence attests to some of the population interactions contributing to this pattern. Conclusions: The hierBAPS algorithm accurately grouped mitogenome sequences into subclades in a phylogenetically robust manner. This analysis provided new insights into the phylogeographic structure of haplogroup U5 diversity in northern Europe, revealing a detailed perspective on the diversity of subclades in this region and their distribution in Scandinavian populations. [ABSTRACT FROM AUTHOR]

Background: A global pandemic has been declared for coronavirus disease 2019 (COVID-19), which has serious impacts on human health and healthcare systems in the affected areas, including Vietnam. None of the previous studies have a framework to provide summary statistics of the virus variants and assess the severity associated with virus proteins and host cells in COVID-19 patients in Vietnam.Method: In this paper, we comprehensively investigated SARS-CoV-2 variants and immune responses in COVID-19 patients. We provided summary statistics of target sequences of SARS-CoV-2 in Vietnam and other countries for data scientists to use in downstream analysis for therapeutic targets. For host cells, we proposed a predictive model of the severity of COVID-19 based on public datasets of hospitalization status in Vietnam, incorporating a polygenic risk score. This score uses immunogenic SNP biomarkers as indicators of COVID-19 severity.Result: We identified that the Delta variant of SARS-CoV-2 is most prevalent in southern areas of Vietnam and it is different from other areas in the world using various data sources. Our predictive models of COVID-19 severity had high accuracy (Random Forest AUC = 0.81, Elastic Net AUC = 0.7, and SVM AUC = 0.69) and showed that the use of polygenic risk scores increased the models' predictive capabilities.Conclusion: We provided a comprehensive analysis for COVID-19 severity in Vietnam. This investigation is not only helpful for COVID-19 treatment in therapeutic target studies, but also could influence further research on the disease progression and personalized clinical outcomes. [ABSTRACT FROM AUTHOR]

1. In recent months, several outbreaks with clinical signs of MDV-1 were reported in Iranian parent and laying hen farms, in addition to backyard chickens. Several meq gene sequences from these outbreaks were amplified and molecularly characterised. 2. The meq protein sequences revealed three different sizes, namely the standard 339 aa, a shorter form of 338 aa lacking a proline residue at position 191, and a very short (vs) size of 265 aa. Based on sequence and size, the 265 aa meq has never been reported from international research groups before. The protein has only one PPPP repeat motif suggesting it belongs to a highly virulent strain. 3. The standard meq sequences showed 100% BLAST identity to the vv+ isolate Polen5. However, the 338 aa form clustered to the clade usually reported from North America. 4. This is the first report on genetic analysis of MDV-1 from Iran, but further study is required to obtain a better picture of the diversity and prevalence of different MDV-1 strains circulating in the country's farms, backyard poultry and other bird species. [ABSTRACT FROM AUTHOR]

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Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been proven to be lethal to human health, which affects almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficiency of the contact tracing system in Oman. Methods: We combined epidemiological data and whole-genome sequence data from 94 samples of SARS-CoV-2 in Oman to understand the origins, genetic variation, and transmissibility. The whole-genome size of sequence data was obtained through a customized SARS-COV-2 research panel. Amplifier methods ranged from 26 Kbp to 30 Kbp and were submitted to GISAID. Findings: The study found that P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). In addition, the study revealed a good agreement between genetic and epidemiological data. Interpretation: Oman’s robust surveillance system was very efficient in guiding the outbreak investigation processes in the country, the study illustrates the future importance of molecular epidemiology in leading the national response to outbreaks and pandemics.