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  1. Article ; Online: Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka [version 2; peer review

    Chitra Pattabiraman / Darshan Sreenivas / Anson K. George / Nakka Vijay Kiran Reddy / Pramada Prasad / Risha Rasheed / Anita Desai / Ravi Vasanthapuram

    Wellcome Open Research, Vol

    2 approved]

    2022  Volume 6

    Abstract: Background: As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and ... ...

    Abstract Background: As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and immune escape are a cause for concern. Such variants have been reported from the UK (B.1.1.7), South Africa (B.1.351) and, Brazil (P.1/B.1.1.28). We performed this study to track the importation, spread, and emergence of variants locally. Methods: We sequenced whole genomes of SARS-CoV-2 from international travellers (n=75) entering Karnataka, South India, between Dec 22, 2020 and Jan 31, 2021, and from positive cases in the city of Bengaluru (n=108), between Nov 22, 2020- Jan 22, 2021, as well as a local outbreak. We present the lineage distribution and analysis of these sequences. Results: Genomes from the study group into 34 lineages. Variant B.1.1.7 was introduced by international travel (24/73, 32.9%). Lineage B.1.36 and B.1 formed a major fraction of both imported (B.1.36: 20/73, 27.4%; B.1: 14/73, 19.2%), and circulating viruses (B.1.36: 45/103; 43.7%,. B.1: 26/103; 25.2%). The lineage B.1.36 was also associated with a local outbreak. We detected nine amino acid changes, previously associated with immune escape, spread across multiple lineages. The N440K change was detected in 45/162 (27.7%) of the sequences, 37 of these were in the B.1.36 lineage (37/65, 56.92%) Conclusions: Our data support the idea that variants of concern spread by travel. Viruses with amino acid replacements associated with immune escape are already circulating. It is critical to check transmission and monitor changes in SARS-CoV-2 locally.
    Keywords SARS-CoV-2 ; variants ; Variants of Concern ; VOC ; COVID-19 ; COVID-19 India ; eng ; Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Wellcome
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: KIAA1109 gene mutation in surviving patients with Alkuraya-Kučinskas syndrome

    Kishore Kumar / Anikha Bellad / Pramada Prasad / Satish Chandra Girimaji / Babylakshmi Muthusamy

    BMC Medical Genetics, Vol 21, Iss 1, Pp 1-

    a review of literature

    2020  Volume 11

    Abstract: Abstract Background Alkuraya-Kučinskas syndrome is an autosomal recessive disorder characterized by brain abnormalities associated with cerebral parenchymal underdevelopment, arthrogryposis, club foot and global developmental delay. KIAA1109, a ... ...

    Abstract Abstract Background Alkuraya-Kučinskas syndrome is an autosomal recessive disorder characterized by brain abnormalities associated with cerebral parenchymal underdevelopment, arthrogryposis, club foot and global developmental delay. KIAA1109, a functionally uncharacterized gene is identified as the molecular cause for Alkuraya-Kučinskas syndrome. Most of the reported mutations in KIAA1109 gene result in premature termination of pregnancies or neonatal deaths while a few mutations have been reported in surviving patients with global developmental delay and intellectual disability. To our knowledge, only three surviving patients from two families have been reported with missense variants in KIAA1109. In this study, we describe four surviving patients from two related families (a multiplex family) with global developmental delay and mild to severe intellectual disability with no other systemic manifestations. There were no miscarriages or neonatal deaths reported in these families. Methods X-chromosome exome panel sequencing was carried out in one patient and whole exome sequencing was carried out on the remaining three affected individuals and the unaffected father of the index family. Data analysis was carried out followed by variant filtering and segregation analysis. Sanger sequencing was carried out to validate the segregation of mutation in all four affected siblings and unaffected parents from both families. Results A novel homozygous missense mutation in a conserved region of KIAA1109 protein was identified. Sanger sequencing confirmed the segregation of mutation in both families in an autosomal recessive fashion. Conclusion Our study is the second study reporting a KIAA1109 variant in surviving patients with Alkuraya-Kučinskas syndrome. Our study expands the spectrum of phenotypic features and mutations associated with Alkuraya-Kučinskas syndrome.
    Keywords Neonatal death ; Premature termination of pregnancy ; Prenatal diagnosis ; KIAA clones ; Mental retardation ; Miscarriages ; Internal medicine ; RC31-1245 ; Genetics ; QH426-470
    Subject code 616
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka.

    Chitra Pattabiraman / Farhat Habib / Harsha P K / Risha Rasheed / Pramada Prasad / Vijayalakshmi Reddy / Prameela Dinesh / Tina Damodar / Kiran Hosallimath / Anson K George / Nakka Vijay Kiran Reddy / Banerjee John / Amrita Pattanaik / Narendra Kumar / Reeta S Mani / Manjunatha M Venkataswamy / Shafeeq K Shahul Hameed / Prakash Kumar B G / Anita Desai /
    Ravi Vasanthapuram

    PLoS ONE, Vol 15, Iss 12, p e

    2020  Volume 0243412

    Abstract: Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing ... ...

    Abstract Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing and genomic epidemiology to trace the spread of SARS-CoV-2 in the state up until May 21, 2020 (1578 cases). We obtained 91 genomes of SARS-CoV-2 which clustered into seven lineages (Pangolin lineages-A, B, B.1, B.1.80, B.1.1, B.4, and B.6). The lineages in Karnataka were known to be circulating in China, Southeast Asia, Iran, Europe and other parts of India and are likely to have been imported into the state both by international and domestic travel. Our sequences grouped into 17 contact clusters and 24 cases with no known contacts. We found 14 of the 17 contact clusters had a single lineage of the virus, consistent with multiple introductions and most (12/17) were contained within a single district, reflecting local spread. In most of the 17 clusters, the index case (12/17) and spreaders (11/17) were symptomatic. Of the 91 sequences, 47 belonged to the B.6 lineage, including eleven of 24 cases with no known contact, indicating ongoing transmission of this lineage in the state. Genomic epidemiology of SARS-CoV-2 in Karnataka suggests multiple introductions of the virus followed by local transmission in parallel with ongoing viral evolution. This is the first study from India combining genomic data with epidemiological information emphasizing the need for an integrated approach to outbreak response.
    Keywords Medicine ; R ; Science ; Q
    Subject code 950
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 [version 1; peer review

    Áine O'Toole / Verity Hill / Oliver G. Pybus / Alexander Watts / Issac I. Bogoch / Kamran Khan / Jane P. Messina / The COVID-19 Genomics UK (COG-UK) consortium / Network for Genomic Surveillance in South Africa (NGS-SA) / Brazil-UK CADDE Genomic Network / Houriiyah Tegally / Richard R. Lessells / Jennifer Giandhari / Sureshnee Pillay / Kefentse Arnold Tumedi / Gape Nyepetsi / Malebogo Kebabonye / Maitshwarelo Matsheka / Madisa Mine /
    Sima Tokajian / Hamad Hassan / Tamara Salloum / Georgi Merhi / Jad Koweyes / Jemma L. Geoghegan / Joep de Ligt / Xiaoyun Ren / Matthew Storey / Nikki E. Freed / Chitra Pattabiraman / Pramada Prasad / Anita S. Desai / Ravi Vasanthapuram / Thomas F. Schulz / Lars Steinbrück / Tanja Stadler / Swiss Viollier Sequencing Consortium / Antonio Parisi / Angelica Bianco / Darío García de Viedma / Sergio Buenestado-Serrano / Vítor Borges / Joana Isidro / Sílvia Duarte / João Paulo Gomes / Neta S. Zuckerman / Michal Mandelboim / Orna Mor / Torsten Seemann / Alicia Arnott

    Wellcome Open Research, Vol

    2 approved]

    2021  Volume 6

    Abstract: Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from ... ...

    Abstract Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Wellcome
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch [version 2; peer review

    Áine O'Toole / Verity Hill / Oliver G. Pybus / Alexander Watts / Issac I. Bogoch / Kamran Khan / Jane P. Messina / The COVID-19 Genomics UK (COG-UK) consortium / Network for Genomic Surveillance in South Africa (NGS-SA) / Brazil-UK CADDE Genomic Network / Houriiyah Tegally / Richard R. Lessells / Jennifer Giandhari / Sureshnee Pillay / Kefentse Arnold Tumedi / Gape Nyepetsi / Malebogo Kebabonye / Maitshwarelo Matsheka / Madisa Mine /
    Sima Tokajian / Hamad Hassan / Tamara Salloum / Georgi Merhi / Jad Koweyes / Jemma L. Geoghegan / Joep de Ligt / Xiaoyun Ren / Matthew Storey / Nikki E. Freed / Chitra Pattabiraman / Pramada Prasad / Anita S. Desai / Ravi Vasanthapuram / Thomas F. Schulz / Lars Steinbrück / Tanja Stadler / Swiss Viollier Sequencing Consortium / Antonio Parisi / Angelica Bianco / Darío García de Viedma / Sergio Buenestado-Serrano / Vítor Borges / Joana Isidro / Sílvia Duarte / João Paulo Gomes / Neta S. Zuckerman / Michal Mandelboim / Orna Mor / Torsten Seemann / Alicia Arnott

    Wellcome Open Research, Vol

    3 approved]

    2021  Volume 6

    Abstract: Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from ... ...

    Abstract Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Wellcome
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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