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Article ; Online: SARS-CoV-2 variants and spike mutations involved in second wave of COVID-19 pandemic in India.

Muttineni, Radhakrishna / R N, Binitha / Putty, Kalyani / Marapakala, Kavitha / K P, Sandra / Panyam, Jaslin / Vemula, Aravind / Singh, Shashi Mohan / Balachandran, Subin / S T, Viroji Rao / Kondapi, Anand Kumar

Transboundary and emerging diseases

2022 Volume 69, Issue 5, Page(s) e1721–e1733

Abstract: Against the backdrop of the second wave of COVID-19 pandemic in India that started in March 2021, we have monitored the spike (S) protein mutations in all the reported (GISAID portal) whole-genome sequences of SARS-CoV-2 circulating in India from 1 ... ...

Abstract	Against the backdrop of the second wave of COVID-19 pandemic in India that started in March 2021, we have monitored the spike (S) protein mutations in all the reported (GISAID portal) whole-genome sequences of SARS-CoV-2 circulating in India from 1 January 2021 to 31 August 2021. In the 43,102 SARS-CoV-2 genomic sequences analysed, we have identified 24,260 amino acid mutations in the S protein, based on which 265 Pango lineages could be categorized. The dominant lineage in most of the 28 states of India and its 8 union territories was B.1.617.2 (the delta variant). However, the states Madhya Pradesh, Jammu & Kashmir, and Punjab had B.1.1.7 (alpha variant) as the major lineage, while the Himachal Pradesh state reported B.1.36 as the dominating lineage. A detailed analysis of various domains of S protein was carried out for detecting mutations having a prevalence of >1%; 70, 18, 7, 3, 9, 4, and 1 (N = 112) such mutations were observed in the N-terminal domain, receptor binding domain, C -terminal domain, fusion peptide region, heptapeptide repeat (HR)-1 domains, signal peptide domain, and transmembrane region, respectively. However, no mutations were recorded in the HR-2 and cytoplasmic domains of the S protein. Interestingly, 13.39% (N = 15) of these mutations were reported to increase the infectivity and pathogenicity of the virus; 2% (N = 3) were known to be vaccine breakthrough mutations, and 0.89% (N = 1) were known to escape neutralizing antibodies. The biological significance of 82% (N = 92) of the reported mutations is yet unknown. As SARS-CoV-2 variants are emerging rapidly, it is critical to continuously monitor local viral mutations to understand national trends of virus circulation. This can tremendously help in designing better preventive regimens in the country, and avoid vaccine breakthrough infections.
MeSH term(s)	Amino Acids ; Animals ; Antibodies, Neutralizing ; COVID-19/epidemiology ; COVID-19/veterinary ; Pandemics ; Peptides/chemistry ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Amino Acids ; Antibodies, Neutralizing ; Peptides ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-03-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2414822-2
ISSN	1865-1682 ; 1865-1674
ISSN (online)	1865-1682
ISSN	1865-1674
DOI	10.1111/tbed.14508
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: SARS‐CoV‐2 variants and spike mutations involved in second wave of COVID‐19 pandemic in India

Muttineni, Radhakrishna / R.N., Binitha / Putty, Kalyani / Marapakala, Kavitha / K.P., Sandra / Panyam, Jaslin / Vemula, Aravind / Singh, Shashi Mohan / Balachandran, Subin / S.T., Viroji Rao / Kondapi, Anand Kumar

Transboundary and emerging diseases. 2022 Sept., v. 69, no. 5

2022

Abstract: Against the backdrop of the second wave of COVID‐19 pandemic in India that started in March 2021, we have monitored the spike (S) protein mutations in all the reported (GISAID portal) whole‐genome sequences of SARS‐CoV‐2 circulating in India from 1 ... ...

Abstract	Against the backdrop of the second wave of COVID‐19 pandemic in India that started in March 2021, we have monitored the spike (S) protein mutations in all the reported (GISAID portal) whole‐genome sequences of SARS‐CoV‐2 circulating in India from 1 January 2021 to 31 August 2021. In the 43,102 SARS‐CoV‐2 genomic sequences analysed, we have identified 24,260 amino acid mutations in the S protein, based on which 265 Pango lineages could be categorized. The dominant lineage in most of the 28 states of India and its 8 union territories was B.1.617.2 (the delta variant). However, the states Madhya Pradesh, Jammu & Kashmir, and Punjab had B.1.1.7 (alpha variant) as the major lineage, while the Himachal Pradesh state reported B.1.36 as the dominating lineage. A detailed analysis of various domains of S protein was carried out for detecting mutations having a prevalence of >1%; 70, 18, 7, 3, 9, 4, and 1 (N = 112) such mutations were observed in the N‐terminal domain, receptor binding domain, C ‐terminal domain, fusion peptide region, heptapeptide repeat (HR)‐1 domains, signal peptide domain, and transmembrane region, respectively. However, no mutations were recorded in the HR‐2 and cytoplasmic domains of the S protein. Interestingly, 13.39% (N = 15) of these mutations were reported to increase the infectivity and pathogenicity of the virus; 2% (N = 3) were known to be vaccine breakthrough mutations, and 0.89% (N = 1) were known to escape neutralizing antibodies. The biological significance of 82% (N = 92) of the reported mutations is yet unknown. As SARS‐CoV‐2 variants are emerging rapidly, it is critical to continuously monitor local viral mutations to understand national trends of virus circulation. This can tremendously help in designing better preventive regimens in the country, and avoid vaccine breakthrough infections.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; amino acids ; genomics ; pathogenicity ; peptides ; signal peptide ; vaccines ; viruses ; India
Language	English
Dates of publication	2022-09
Size	p. e1721-e1733.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2414822-2
ISSN	1865-1682 ; 1865-1674
ISSN (online)	1865-1682
ISSN	1865-1674
DOI	10.1111/tbed.14508
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Clinical and whole genome characterization of SARS-CoV-2 in India.

Muttineni, Radhakrishna / Kammili, Nagamani / Bingi, Thrilok Chander / Rao M, Raja / Putty, Kalyani / Dholaniya, Pankaj Singh / Puli, Ravi Kumar / Pakalapati, Sunitha / S, Saritha / K, Shekar / Doodipala, Mallikarjuna Reddy / Upadhyay, Amit A / Bosinger, Steven E / Amara, Rama R / Kondapi, Anand K

PloS one

2021 Volume 16, Issue 2, Page(s) e0246173

Abstract: We report clinical profile of hundred and nine patients with SARS CoV-2 infection, and whole genome sequences (WGS) of seven virus isolates from the first reported cases in India, with various international travel histories. Comorbidities such as ... ...

Abstract	We report clinical profile of hundred and nine patients with SARS CoV-2 infection, and whole genome sequences (WGS) of seven virus isolates from the first reported cases in India, with various international travel histories. Comorbidities such as diabetes, hypertension, and cardiovascular disease were frequently associated with severity of the disease. WBC and neutrophil counts showed an increase, while lymphocyte counts decreased in patients with severe infection suggesting a possible neutrophil mediated organ damage, while immune activity may be diminished with decrease in lymphocytes leading to disease severity. Increase in SGOT, SGPT and blood urea suggests the functional deficiencies of liver, heart, and kidney in patients who succumbed to the disease when compared to the group of recovered patients. The WGS analysis showed that these isolates were classified into two clades: I/A3i, and A2a (four according to GISAID: O, L, GR, and GH). Further, WGS phylogeny and travel history together indicate possible transmission from Middle East and Europe. Three S protein variants: Wuhan reference, D614G, and Y28H were identified predicted to possess different binding affinities to host ACE2.
MeSH term(s)	Adult ; Aged ; Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/metabolism ; COVID-19/immunology ; COVID-19/pathology ; COVID-19/virology ; Female ; Genome, Viral ; Humans ; India ; Male ; Middle Aged ; Phylogeny ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Whole Genome Sequencing
Chemical Substances	RNA, Viral ; Spike Glycoprotein, Coronavirus ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-02-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0246173
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Clinical and whole genome characterization of SARS-CoV-2 in India.

Radhakrishna Muttineni / Nagamani Kammili / Thrilok Chander Bingi / Raja Rao M / Kalyani Putty / Pankaj Singh Dholaniya / Ravi Kumar Puli / Sunitha Pakalapati / Saritha S / Shekar K / Mallikarjuna Reddy Doodipala / Amit A Upadhyay / Steven E Bosinger / Rama R Amara / Anand K Kondapi

PLoS ONE, Vol 16, Iss 2, p e

2021 Volume 0246173

Abstract	We report clinical profile of hundred and nine patients with SARS CoV-2 infection, and whole genome sequences (WGS) of seven virus isolates from the first reported cases in India, with various international travel histories. Comorbidities such as diabetes, hypertension, and cardiovascular disease were frequently associated with severity of the disease. WBC and neutrophil counts showed an increase, while lymphocyte counts decreased in patients with severe infection suggesting a possible neutrophil mediated organ damage, while immune activity may be diminished with decrease in lymphocytes leading to disease severity. Increase in SGOT, SGPT and blood urea suggests the functional deficiencies of liver, heart, and kidney in patients who succumbed to the disease when compared to the group of recovered patients. The WGS analysis showed that these isolates were classified into two clades: I/A3i, and A2a (four according to GISAID: O, L, GR, and GH). Further, WGS phylogeny and travel history together indicate possible transmission from Middle East and Europe. Three S protein variants: Wuhan reference, D614G, and Y28H were identified predicted to possess different binding affinities to host ACE2.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Factors associated with conversion of long-term non-progressors to progressors: a prospective study of HIV perinatally infected paediatric survivors.

Radhakrishna, Muttineni / Durga, Kharidehal / Rao, Ravilla Kondal / Reddy, Doodipala Mallikarjuna / Kondapi, Anand Kumar

The Indian journal of medical research

2013 Volume 138, Issue 3, Page(s) 322–328

Abstract: Background & objectives: Survival pattern among children infected with the human immune deficiency virus (HIV) follows a bimodel distribution. Some children survive beyond 9 years age and are known as long term survivors (LTS) while others had a more ... ...

Abstract	Background & objectives: Survival pattern among children infected with the human immune deficiency virus (HIV) follows a bimodel distribution. Some children survive beyond 9 years age and are known as long term survivors (LTS) while others had a more rapid course to death during the first few years of life. In the LTS group of children, two sub-populations have emerged, the long term non-progressors (LTNP) who have remained asymptomatic over a period of years and those who have survived despite clinical and laboratory evidence of disease progression, the long term progressors (LTP). The aim of the present study was to determine the factors influencing the conversion of LTNPs to LTPs in a group of perinatally HIV infected children who were followed up for five years. Methods: A total of 26 HIV seropositive paediatric patients were monitored from 2006 to 2011 with CD4 cell counts, onset of clinical manifestations, body weight, biochemical, haematological and immunological parameters. Statistical analyses, both qualitative and quantitative, were used to determine the degree of conversion of non-progressors to progressors. Results: All 26 (13 female and 13 male) perinatally HIV infected children, born during 1991-1996 were healthy until 2006. But by 2011, 18 were placed in progressors group with antiretroviral therapy (ART), while six remained in non progressors group and two died. As per the Kaplan-Meier survival analysis, AIDS free median survival period (years) in LTP group (CD4 count) of the cohort was 10 ± 0.66 (<200; P=<0.05); 11 ± 0.61 (200-350, P=<0.05), 12 ± 0.18 (>350, P=<0.05). Intercurrent and opportunistic infections (OIs) were observed in LTPs only. The incidence of OI in LTPs was higher when compared to general paediatric population. Interpretation & conclusions: Our findings show that CD4 counts and OIs play an important role in influencing the survival chances of perinatally HIV infected children.
MeSH term(s)	Adolescent ; Child ; Female ; HIV Infections/physiopathology ; HIV Long-Term Survivors ; Humans ; Infectious Disease Transmission, Vertical ; Male ; Prospective Studies
Language	English
Publishing date	2013-10-14
Publishing country	India
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390883-5
ISSN	0971-5916 ; 0019-5340
ISSN	0971-5916 ; 0019-5340
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: HIV sero-prevalance in general population of Warangal, A.P., South India.

Radhakrishna, Muttineni / Reddy, M Krishna / Krishna, D R

Journal of environmental biology

2007 Volume 28, Issue 4, Page(s) 865–867

Abstract: HIV/AIDS pandemic has devastated many countries reversing national development; HIV was not seen in Asia and India till 1980. Now India has become epicenter of AIDS pandemic. During April 2002 to March 2003 the HIV+ ve pregnant women and their husbands ... ...

Abstract	HIV/AIDS pandemic has devastated many countries reversing national development; HIV was not seen in Asia and India till 1980. Now India has become epicenter of AIDS pandemic. During April 2002 to March 2003 the HIV+ ve pregnant women and their husbands were encouraged to enroll in the prospective study with informed consent. The study results consist of most of the females who are in the age group between 16-25 years who were affected by HIV High infection is observed in people with lower socio-economic and education background. High infection rate is observed in house wives (26.7%), laborers (23%) and agricultural workers (12.1%) followed by toddy tapers (5%), drivers (5.96%) and others (6 47%). HIV +ve subjects at Mother To Child Transmission (MTCT) centers are surprisingly clinically very healthy. No disease manifestation was noticed.
MeSH term(s)	Female ; HIV Seroprevalence ; Humans ; India/epidemiology ; Male
Language	English
Publishing date	2007-10
Publishing country	India
Document type	Journal Article
ISSN	0254-8704
ISSN	0254-8704
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Factors associated with conversion of long-term non-progressors to progressors

Muttineni Radhakrishna / Kharidehal Durga / Ravilla Kondal Rao / Doodipala Mallikarjuna Reddy / Anand Kumar Kondapi

Indian Journal of Medical Research, Vol 138, Iss 3, Pp 322-

A prospective study of HIV perinatally infected paediatric survivors

2013 Volume 328

Abstract: Background & objectives : Survival pattern among children infected with the human immune deficiency virus (HIV) follows a bimodel distribution. Some children survive beyond 9 years age and are known as long term survivers (LTS) while others had a more ... ...

Abstract	Background & objectives : Survival pattern among children infected with the human immune deficiency virus (HIV) follows a bimodel distribution. Some children survive beyond 9 years age and are known as long term survivers (LTS) while others had a more rapid course to death during the first few years of life. In the LTS group of children, two sub-populations have emerged, the long term non-progressors (LTNP) who have remained asymptomatic over a period of years and those who have survived despite clinical and laboratory evidence of disease progression, the long term progressors (LTP). The aim of the present study was to determine the factors influencing the conversion of LTNPs to LTPs in a group of perinatally HIV infected children who were followed up for five years. Methods : A total of 26 HIV seropositive paediatric patients were monitored from 2006 to 2011 with CD4 cell counts, onset of clinical manifestations, body weight, biochemical, haematological and immunological parameters. Statistical analyses, both qualitative and quantitative, were used to determine the degree of conversion of non-progressors to progressors. Results : All 26 (13 female and 13 male) perinatally HIV infected children, born during1991-1996 were healthy until 2006. But by 2011, 18 were placed in progressors group with antiretroviral therapy (ART), while six remained in non progressors group and two died. As per the Kaplan-Meier survival analysis, AIDS free median survival period (years) in LTP group (CD4 count) of the cohort was 10΁0.66 (<200; P=<0.05); 11΁0.61 (200-350, P=<0.05), 12΁0.18 (>350, P=<0.05). Intercurrent and opportunistic infections (OIs) were observed in LTPs only. The incidence of OI in LTPs was higher when compared to general paediatric population. Interpretation & conclusions : Our findings show that CD4 counts and OIs play an important role in influencing the survival chances of perinatally HIV infected children.
Keywords	AIDS - HIV - LTNPs - LTP - paediatric - progressors ; Medicine ; R ; Medicine (General) ; R5-920
Subject code	360
Publishing date	2013-01-01T00:00:00Z
Publisher	Indian Council of Medical Research
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 variants and spike mutations involved in second wave of COVID-19 pandemic in India.

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Article: SARS‐CoV‐2 variants and spike mutations involved in second wave of COVID‐19 pandemic in India

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Article ; Online: Clinical and whole genome characterization of SARS-CoV-2 in India.

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Article ; Online: Clinical and whole genome characterization of SARS-CoV-2 in India.

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Article: Factors associated with conversion of long-term non-progressors to progressors: a prospective study of HIV perinatally infected paediatric survivors.

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Article: HIV sero-prevalance in general population of Warangal, A.P., South India.

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Article ; Online: Factors associated with conversion of long-term non-progressors to progressors

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