An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India

Yadav, Pragya; Nyayanit, Dimpal A; Majumdar, Triparna; Patil, Savita; Kaur, Harmanmeet; Gupta, Nivedita; Shete, Anita M.; Pandit, Priyanka; Kumar, Abhinendra; Aggarwal, Neeraj; Narayan, Jitendra; Vijay, Neetu; Kalawat, Usha; Sugunan, A P; Munivenkatappa, Ashok; Sharma, Tara; Devi, S. Bilasini; Majumdar, Tapan; Jaryal, Subhash Chand; Bakshi, Rupinder; Joshi, Yash B.; Sahay, Rima R.; Shastri, JS; Singh, Mini P.; Kumar, Manoj; Rawat, Vinita; Dutta, Shanta; Yadav, Sarita; Krishnasamy, Kaveri; Raut, Sharmila; Biswas, Debasis; Borkakoty, Biswajyoti; Verma, Santwana; Rani, Sudha; Deval, Hirawati; Patel, Disha; Turuk, Jyotirmayee; Malhotra, Bharti; Fomda, Bashir Ahmad; Nag, Vijaylakshmi; Jain, Amita; Bhargava, Anudita; Potdar, Varsha; Cherian, Sarah; Abraham, Priya; Gopal, Anjani; Panda, Samiran; Bhargava, Balram

doi:10.3390/v13050925

Cited by 29 publications

(38 citation statements)

References 25 publications

(22 reference statements)

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“…During the second wave, we observed milder cases, less expectoration, less fever, fewer co‐morbidities, and the impact on transplant activities was less pronounced during the second wave, possibly due to the less virulent mutant strain. 29 We have documented an important decrease in the use of hydroxychloroquine and tocilizumab, which were often prescribed during the first wave, while dexamethasone and remdesivir prescriptions increased in the second wave. A recent study from Madrid reported six blood tests (neutrophil‐to‐lymphocyte ratio, C‐reactive protein, LDH, IL‐6, urea and d‐dimer) as predictors of severe COVID‐19 in both waves.…”

Section: Discussionmentioning

confidence: 98%

Consequences of the first and secondCOVID‐19 wave on kidney transplant recipients at a large Indian transplant centre

et al. 2021

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Background There is a scarcity of data comparing the consequences of first and second COVID‐19 waves on kidney transplant recipients (KTRs) in India. Methods We conducted a single‐centre retrospective study of 259 KTRs with COVID‐19 to compare first wave (March 15–December 31 2020, n = 157) and second wave (April 1–May 31 2021, n = 102). Results KTRs during second wave were younger (43 vs. 40 years; p ‐value .04) and also included paediatric patients (0 vs. 5.9%; p ‐value .003). Symptoms were milder during the second wave (45 vs. 62.7%; p ‐value .007); COVID‐19 positive patients had less frequent cough (32 vs. 13.8%; p ‐value .001), fever was less frequent (58 vs. 37%; p ‐value .001), and we observed fewer co‐morbidities (11 vs. 20.6%; p ‐value .04). The percentages of neutrophils (77 vs. 83%; p ‐value .001) and serum ferritin (439 vs. 688; p ‐value .0006) were higher during second wave, while lymphocyte counts were reduced (20 vs. 14%; p ‐value .0001). Hydroxychloroquine (11 vs. 0%; p ‐value .0001) and tocilizumab (7 vs. 0%; p ‐value .004) were more frequently prescribed during first wave, while utilization of dexamethasone (6 vs. 27%; p ‐value .0001) and remdesivir (47 vs. 65%; p ‐value .03) increased during the second wave. Mucormycosis (1.3 vs. 10%; p ‐value .01) and ICU admissions (20 vs. 37.2%; p ‐value .002) were more frequent during second wave. The 28‐day mortality rate (9.6 vs. 10%; p ‐value 1) was not different. Conclusions There has been a different clinical spectrum of COVID‐19 amongst KTR with similar mortality between the two waves at a large Indian transplant centre.

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Section: Discussionmentioning

confidence: 98%

Consequences of the first and secondCOVID‐19 wave on kidney transplant recipients at a large Indian transplant centre

et al. 2021

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“…In addition, in India during the period from November 2020 to May 2021, there were other lineages, such as B.1, B.1.1, B.1.36, B.1.351, B.1.618 and B.1.1.216, that were not common in the state of Maharashtra. Our earlier studies [ 9 , 20 ] that were based on genome sequences from India from January to August/September 2020 had demonstrated that the dominant lineages were B.1.113, B.1.1.32, B.1.1.8, B.1.80, B.4 and B.6. This reflects the diversity of lineages in the country and also the switches in the dominant lineages.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India

et al. 2021

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As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being used to investigate its transmission and evolution. Against the backdrop of the global emergence of “variants of concern” (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches were undertaken to identify possible new variants and gauge the fitness of the current circulating strains. Phylogenetic analysis revealed that newly identified lineages B.1.617.1 and B.1.617.2 were predominantly circulating. The signature mutations possessed by these strains were L452R, T478K, E484Q, D614G and P681R in the spike protein, including within the receptor-binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R, T478K and E484Q revealed that these may possibly result in increased ACE2 binding while P681R in the furin cleavage site could increase the rate of S1-S2 cleavage, resulting in better transmissibility. The two RBD mutations, L452R and E484Q, indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Further in vitro/in vivo studies would help confirm the phenotypic changes of the mutant strains. Overall, the study revealed that the newly emerged variants were responsible for the second wave of COVID-19 in Maharashtra. Lineage B.1.617.2 has been designated as a VOC delta and B.1.617.1 as a variant of interest kappa, and they are being widely reported in the rest of the country as well as globally. Continuous monitoring of these and emerging variants in India is essential.

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“…The spread beyond East Asia was accompanied by the appearance of the more infectious G614 virus mutation, and over the next weeks and months this strain became dominant over the original D614 strain in most parts of the world. 11,14,15 The D614 virus remained dominant beyond May of 2020 in only few regions: most of China, Singapore, Malaysia, the South of India and the Delhi region (https://www.gisaid.org/; https://cov.lanl.gov/apps/covid-19/map/) 14,[16][17][18][19][20][21][22][23][24][25] The co-existence of the D614 and G614 viruses made it impossible, in most regions, to discern whether differences in the prevalence of anosmia were due to differences among the host populations (frequency of variants of the entry proteins ACE2 or TMPRSS2 and thus ethnic differences), or were due to differences in the infectivity and cell entry efficiencies of the coronavirus. In East Asia, nearly all studies were conducted when the D614 virus was dominant.…”

Section: The Spread and Increasing Dominance Of The G614 Virus Over The D614 Virusmentioning

confidence: 99%

“…Dominance of D614 vs G614 virus was determined by reviewing studies that mapped the temporospatial changes within different regions of the Indian subcontinent. 17,19,25,28,[33][34][35] For our systematic review and search strategy, we adhered to the PRISMA guidelines 41 (Fig. 2).…”

Section: Systematic Review and Meta-analysis Of South Asian Studiesmentioning

confidence: 99%

The D614G virus mutation enhances anosmia in COVID-19 patients: Evidence from a systematic review and meta-analysis of studies from South Asia

Bartheld

Hagen

Butowt

2021

Preprint

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The prevalence of chemosensory dysfunction in patients with COVID-19 varies greatly between populations. It is unclear whether such differences are due to factors at the level of the human host, or at the level of the coronavirus, or both. At the host level, the entry proteins which allow virus binding and entry have variants with distinct properties, and the frequency of such variants differs between ethnicities. At the level of the virus, the D614G mutation enhances virus entry to the host cell. Since the two virus strains (D614 and G614) co-existed in the first six months of the pandemic in most populations, it has been difficult to distinguish between contributions of the virus and contributions of the host for anosmia. To answer this question, we conducted a systematic review and meta-analysis of studies in South Asian populations when either the D614 or the G614 virus was dominant. We show that populations infected predominantly with the G614 virus had a much higher prevalence of anosmia (pooled prevalence of 31.8%) compared with the same ethnic populations infected mostly with the D614 virus strain (pooled anosmia prevalence of 5.3%). We conclude that the D614G mutation is a major contributing factor that increases the prevalence of anosmia in COVID-19, and that this enhanced effect on olfaction constitutes a previously unrecognized phenotype of the D614G mutation. The new virus strains that have additional mutations on the background of the D614G mutation can be expected to cause a similarly increased prevalence of chemosensory dysfunctions.

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An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India

Cited by 29 publications

References 25 publications

Consequences of the first and secondCOVID‐19 wave on kidney transplant recipients at a large Indian transplant centre

Consequences of the first and secondCOVID‐19 wave on kidney transplant recipients at a large Indian transplant centre

SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India

The D614G virus mutation enhances anosmia in COVID-19 patients: Evidence from a systematic review and meta-analysis of studies from South Asia

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