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  • Recombination shapes the 2022 monkeypox outbreak
    Supplemental File 1. The Newick tree of the MPXV sequence dataset for Supplemental File 2. Supplemental File 2. Rooted phylogenetic tree of MPXV genomes during 2022 pandemics. Alignments of viral sequences were generated using MAFFT, and the phylogenetic tree was visualized using FigTree. Rooting was done by introducing the camelpox virus sequence (MZ300860) as an outgroup virus. Group U, M, and I of MPXV genomes is labeled in green, blue, and red, respectively. Recombinant MPXV isolates based on TR analysis are labeled in orange. Supplemental File 3. Genomic sequences of MPXV (B.1 clade) from January 1 to July 20, 2022 (N=415) in this study. The camelpox virus sequence (MZ300860) is included for phylogenetic analysis in Supplemental File 2. Supplemental File 4. TRAL analysis of the annotated TRs in MPXV genomic sequences of Supplemental File 3 and Figure S6. Supplemental Table 1. Summary of MPXV genome sequence information in this study. Figure S1. Sequences that contain SNP pairs with strong linkage disequilibrium, which the upper 95% confidence bound of the D’ is above 0.98 and the lower bound is above 0.7. Figure S2. TR C in the intergenic region of monkeypox A47R and A49R. (A) The map of TR C, A47R, and A49R gene. Arrows indicate the gene direction. (B) The location of TR C at the 3’-untranslated region of A47R transcript. The 3’ termination UUUUUNU sequence for adding poly(A) tail is boxed in red. Reference MPXV sequence is OP19276. Figure S3. TR B in the intergenic region of monkeypox A41L and A42R. (A) The map of TR B, A41L, and A42R gene. Arrows indicate the gene direction. Sequence b and c are shown in (B) and (C). (B) Sequence of TR B insertion in monkeypox genome as in (A) compared to vaccinia sequence. (C) Alignment of monkeypox and vaccinia in A42R promoter. TAAAT and AAAAAA element are boxed in red. Reference MPXV sequence is OP19276. Figure S4. TR D in the intergenic region of monkeypox B18R and B19R. (A) (A) The map of TR D, B18R, and B19R gene. Arrows indicate the gene direction. Sequence b, c and d are shown in (B), (C) and (D). (B) Alignment of monkeypox sequence B with vaccinia B19R promoter, including TAAAT and AAAAAAA element only found in vaccinia. (C and D) Sequences of B19R promoter of monkeypox. Sequence of TR D insertion in monkeypox genome as in (A). Reference MPXV sequence is OP19276. Figure S5. Comparison of vaccinia K3L and monkeypox C3L sequence. The stop codon was introduced at bp 130-132, causing C3L a truncated protein compared to K3L. Figure S6. (A) Table of divergence value ranges of TR A to F. The value of TR B is not available because its sequence is AT only. (B) Each box (TR A, C, D, E, F) contains individual TRNs with different colors associated with the parental viral sequences: IRBA22-14 (I, ON755040), MUW1527495 (M, ON019276) or USA_2022_CA002 (U, ON954773) as Figure 1F. TRs and TRNs were validated by the TRAL algorithm with p-value < 10-4.
    • Other
    • Tabular Data
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    • File Set
  • Demographics and Disease Associations of Patients with Monkeypox and Recipients of Monkeypox Vaccine from Safety Net Hospitals in New York City: A Cross-Sectional Study
    Supplementary Table 1. Monkeypox Cases. Inclusion criteria included all patients presenting to the NYC HHC system between 2/17/2022 and 8/16/2022 with either lab component: ORTHOPOXVIRUSPCR: Abnormal and Final or ORTHOPOXVIRUS DNA: Abnormal and Final AND Confirmed Diagnosis of HIV or Chief Complaint of Rash or Treatment with Tecovirimat, TECOVIRIMAT 200 MG PO CAPS, TECOVIRIMAT 200 MG/20ML IV SOL
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  • Monkeypox Skin Images Dataset (MSID)
    The latest outbreak of monkeypox has now become a source of concern for healthcare professionals throughout the world. It is essential to have an early diagnosis in order to slow down its rapid progression. For this purpose, we have created a new skin image-based dataset for the detection of monkeypox disease. This dataset consists of four classes: Monkeypox, Chickenpox, Measles, and Normal. All the image classes are collected from internet-based health website sources. The entire dataset has been developed by the Department of Computer Science and Engineering, Islamic University, Kushtia-7003, Bangladesh.
    • Dataset
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  • Monkeypox: Cutaneous Clues to Clinical Diagnosis
    Monkeypox: Cutaneous Clues to Clinical Diagnosis
    • Image
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  • MonkeyPox2022Tweets: The First Public Twitter Dataset on the 2022 MonkeyPox Outbreak
    Please cite the following paper when using this dataset: N. Thakur, “MonkeyPox2022Tweets: The first public Twitter dataset on the 2022 MonkeyPox outbreak,” Preprints, 2022, DOI: 10.20944/preprints202206.0172.v2 Abstract The world is currently facing an outbreak of the monkeypox virus, and confirmed cases have been reported from 28 countries. Following a recent “emergency meeting”, the World Health Organization just declared monkeypox a global health emergency. As a result, people from all over the world are using social media platforms, such as Twitter, for information seeking and sharing related to the outbreak, as well as for familiarizing themselves with the guidelines and protocols that are being recommended by various policy-making bodies to reduce the spread of the virus. This is resulting in the generation of tremendous amounts of Big Data related to such paradigms of social media behavior. Mining this Big Data and compiling it in the form of a dataset can serve a wide range of use-cases and applications such as analysis of public opinions, interests, views, perspectives, attitudes, and sentiment towards this outbreak. Therefore, this work presents MonkeyPox2022Tweets, an open-access dataset of Tweets related to the 2022 monkeypox outbreak that were posted on Twitter since the first detected case of this outbreak on May 7, 2022. The dataset is compliant with the privacy policy, developer agreement, and guidelines for content redistribution of Twitter, as well as with the FAIR principles (Findability, Accessibility, Interoperability, and Reusability) principles for scientific data management. Data Description The dataset consists of a total of 255,363 Tweet IDs of the same number of tweets about monkeypox that were posted on Twitter from 7th May 2022 to 23rd July 2022 (the most recent date at the time of dataset upload). The Tweet IDs are presented in 6 different .txt files based on the timelines of the associated tweets. The following provides the details of these dataset files. • Filename: TweetIDs_Part1.txt (No. of Tweet IDs: 13926, Date Range of the Tweet IDs: May 7, 2022 to May 21, 2022) • Filename: TweetIDs_Part2.txt (No. of Tweet IDs: 17705, Date Range of the Tweet IDs: May 21, 2022 to May 27, 2022) • Filename: TweetIDs_Part3.txt (No. of Tweet IDs: 17585, Date Range of the Tweet IDs: May 27, 2022 to June 5, 2022) • Filename: TweetIDs_Part4.txt (No. of Tweet IDs: 19718, Date Range of the Tweet IDs: June 5, 2022 to June 11, 2022) • Filename: TweetIDs_Part5.txt (No. of Tweet IDs: 47718, Date Range of the Tweet IDs: June 12, 2022 to June 30, 2022) • Filename: TweetIDs_Part6.txt (No. of Tweet IDs: 138711, Date Range of the Tweet IDs: July 1, 2022 to July 23, 2022) The dataset contains only Tweet IDs in compliance with the terms and conditions mentioned in the privacy policy, developer agreement, and guidelines for content redistribution of Twitter. The Tweet IDs need to be hydrated to be used.
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  • Publication Dataset of The COVID-19 Pandemic in Indonesia 2020
    The research and publication dataset of the COVID-19 pandemic in Indonesia, which was indexed by Scopus in 2020. The dataset contains data authors, authors ID Scopus, title, year, source title, volume, issue, article number in Scopus, DOI, link, affiliation, abstract, index keywords, references, correspondence Address, editors, publisher, conference name, conference date, conference code, ISSN, language, document type, access type, and EID.
    • Tabular Data
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  • Identifying and Tracking Low Frequency Virus-Specific TCR Clonotypes Using High-Throughput Sequencing
    Raw sequencing data from HLA-A2 transgenic mice before and after infection with either the ACAM2000 smallpox virus or highly releated monkeypox virus.
    • Tabular Data
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  • jmcastagnetto/paper-monkeypox-latam-caribbean: Code and data for the paper on Monkeypox outbreak in Latin America and the Caribbean
    Code and data for the paper: "Monkeypox in Latin America and the Caribbean: First response and challenge ahead after the first 100 days of the 2022 outbreak" (Paper authors: Antonio Quispe & Jesus M. Castagnetto) This release contains the code in R and the data used to generate the figures and table, using as sources the data from UN World Population Prospects, the World Bank country classification and the Monkeypox data from the Global Health Data Science Inititative (data donwloaded on 2022-08-31) Analysis, figures and table consider data from non-endemic countries from epidemiological week 2022W20 to 2022W34 (inclusive)
    • Software/Code
  • jmcastagnetto/paper-monkeypox-latam-caribbean: Code and data for the paper on Monkeypox outbreak in Latinamerica and the Caribbean
    Code and data for the paper: "Monkeypox in Latin America and the Caribbean: First response and challenge ahead after the first 100 days of the 2022 outbreak" (Paper authors: Antonio Quispe & Jesus M. Castagnetto) This release contains the code in R and the data used to generate the figures and table, using as sources the data from UN World Population Prospects, the World Bank country classification and the Monkeypox data from the Global Health Data Science Inititative (data donwloaded on 2022-08-23) Analysis, figures and table consider data from non-endemic countries from epidemiological week 2022W20 to 2022W33 (inclusive)
    • Software/Code
  • jmcastagnetto/paper-monkeypox-latam-caribbean: Code and data for the paper on Monkeypox outbreak in Latiamerica and the Caribbean
    Code and data for the paper: "Monkeypox in Latin America and the Caribbean: first response and challenge ahead after the first 12 weeks of the 2022 outbreak" (Paper authors: Antonio Quispe & Jesus M. Castagnetto) This release contains the code in R and the data used to generate the figures and table, using as sources the data from UN World Population Prospects, the World Bank country classification and the Monkeypox data from the Global Health Data Science Inititative
    • Software/Code
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