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  1. Article ; Online: Expanding repertoire of SARS-CoV-2 deletion mutations contributes to evolution of highly transmissible variants.

    Venkatakrishnan, A J / Anand, Praveen / Lenehan, Patrick J / Ghosh, Pritha / Suratekar, Rohit / Silvert, Eli / Pawlowski, Colin / Siroha, Abhishek / Chowdhury, Dibyendu Roy / O'Horo, John C / Yao, Joseph D / Pritt, Bobbi S / Norgan, Andrew P / Hurt, Ryan T / Badley, Andrew D / Halamka, John / Soundararajan, Venky

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 257

    Abstract: The emergence of highly transmissible SARS-CoV-2 variants and vaccine breakthrough infections globally mandated the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed 2.13 million SARS-CoV-2 genomes from 188 ... ...

    Abstract The emergence of highly transmissible SARS-CoV-2 variants and vaccine breakthrough infections globally mandated the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed 2.13 million SARS-CoV-2 genomes from 188 countries/territories (up to June 2021) and performed whole-genome viral sequencing from 102 COVID-19 patients, including 43 vaccine breakthrough infections. We identified 92 Spike protein mutations that increased in prevalence during at least one surge in SARS-CoV-2 test positivity in any country over a 3-month window. Deletions in the Spike protein N-terminal domain were highly enriched for these 'surge-associated mutations' (Odds Ratio = 14.19, 95% CI 6.15-32.75, p value = 3.41 × 10
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; COVID-19/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Breakthrough Infections ; Mutation ; Sequence Deletion ; Vaccines
    Chemical Substances Spike Glycoprotein, Coronavirus ; Vaccines ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2023-01-05
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-26646-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Normative blood pressure data for Indian neonates.

    Samanta, Moumita / Mondal, Rakesh / Ray, Somosri / Sabui, Tapas / Hazra, Avijit / Kundu, Chanchal / Sarkar, Debolina / Chowdhury, Dibyendu Roy

    Indian pediatrics

    2015  Volume 52, Issue 8, Page(s) 669–673

    Abstract: Objective: To establish the normative blood pressure (BP) values in healthy Indian neonates using oscillometric method, and to develop BP percentile charts.: Design: Prospective observational study.: Setting: Neonatal unit of a teaching hospital ... ...

    Abstract Objective: To establish the normative blood pressure (BP) values in healthy Indian neonates using oscillometric method, and to develop BP percentile charts.
    Design: Prospective observational study.
    Setting: Neonatal unit of a teaching hospital in Eastern India.
    Participants: 1617 hemodynamically stable inborn neonates without birth asphyxia, major congenital anomaly, maternal complications (e.g. preeclampsia, hypertension, diabetes) or critical neonatal illness.
    Procedure: Quite state measurements of systolic BP (SBP), diastolic BP (DBP) and mean arterial pressure (MAP) were recorded by oscillometric method on day 4, 7 and 14 of postnatal life. The averages of three readings at 2-minute intervals were used.
    Results: Percentile charts (providing 5th, 10th, 25th, 50th, 75th, 95th, and 99th percentile values) have been developed. SBP, DBP and MAP showed a steady rise from day 4 to day 14, and were comparable between males and females, but were significantly lower in preterms than in term neonates.
    Conclusions: Normative neonatal BP data along with gestational age-wise percentile charts shall be of help for decision-making and planning for sick newborns.
    MeSH term(s) Blood Pressure/physiology ; Blood Pressure Determination/standards ; Female ; Gestational Age ; Humans ; India ; Infant, Newborn ; Male ; Reference Values
    Language English
    Publishing date 2015-09-18
    Publishing country India
    Document type Journal Article
    ZDB-ID 402594-5
    ISSN 0974-7559 ; 0019-6061
    ISSN (online) 0974-7559
    ISSN 0019-6061
    DOI 10.1007/s13312-015-0694-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Antigenic minimalism of SARS-CoV-2 is linked to surges in COVID-19 community transmission and vaccine breakthrough infections

    Venkatakrishnan, AJ / Anand, Praveen / Lenehan, Patrick / Ghosh, Pritha / Suratekar, Rohit / Siroha, Abhishek / Chowdhury, Dibyendu Roy / OHoro, John C / Yao, Joseph D / Pritt, Bobbi S / Norgan, Andrew / Hurt, Ryan T / Badley, Andrew D / Halamka, John D / Soundararajan, Venky

    medRxiv

    Abstract: The raging COVID-19 pandemic in India and reports of vaccine breakthrough infections globally have raised alarm mandating the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed over 1.3 million SARS-CoV-2 ... ...

    Abstract The raging COVID-19 pandemic in India and reports of vaccine breakthrough infections globally have raised alarm mandating the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed over 1.3 million SARS-CoV-2 genomes from 178 countries and performed whole-genome viral sequencing from 53 COVID-19 patients, including 20 vaccine breakthrough infections. We identified 116 Spike protein mutations that increased in prevalence during at least one surge in SARS-CoV-2 test positivity in any country over a three-month window. Deletions in the Spike protein N-terminal domain (NTD) are highly enriched for these surge-associated mutations (Odds Ratio = 18.2, 95% CI: 7.53-48.7; p=1.465x10-18). In the recent COVID-19 surge in India, an NTD deletion (ΔF157/R158) increased over 10-fold in prevalence from February 2021 (1.1%) to April 2021 (15%). During the recent surge in Chile, an NTD deletion (Δ246-253) increased rapidly over 30-fold in prevalence from January 2021 (0.86%) to April 2021 (33%). Strikingly, these simultaneously emerging deletions associated with surges in different parts of the world both occur at an antigenic supersite that is targeted by neutralizing antibodies. Finally, we generated clinically annotated SARS-CoV-2 whole genome sequences and identified deletions within this NTD antigenic supersite in a patient with vaccine breakthrough infection (Δ156-164) and other deletions from unvaccinated severe COVID-19 patients that could represent emerging deletion-prone regions. Overall, the expanding repertoire of NTD deletions throughout the pandemic and their association with case surges and vaccine breakthrough infections point to antigenic minimalism as an emerging evolutionary strategy for SARS-CoV-2 to evade immune responses. This study highlights the urgent need to sequence viral genomes at a larger scale globally and to mandate that sequences are deposited with more granular and transparent clinical annotations to ensure that therapeutic development keeps pace with the evolution of SARS-CoV-2.
    Keywords covid19
    Language English
    Publishing date 2021-05-31
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.05.23.21257668
    Database COVID19

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