Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India

Raghwani, Jayna; Plessis, Louis du; McCrone, John; Hill, Sarah C.; Parag, Kris V; Thézé, Julien; Kumar, Dinesh; Puvar, Apurvasinh; Pandit, Ramesh; Pybus, Oliver G.; Fournié, Guillaume; Joshi, Madhvi; Joshi, Chaitanya

doi:10.3201/eid2804.212053

Cited by 9 publications

(12 citation statements)

References 25 publications

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“…Many studies have been conducted in genomic epidemiology to find the transmission dynamics of COVID-19 in different cities and lineages of the virus [ 74 , 75 , 76 , 77 ]. These studies can see how many different lineages are responsible for affecting each city or country and which lineages are more deadly, more transmissible, and faster.…”

Section: Results and Interpretationmentioning

confidence: 99%

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Modeling COVID-19 Transmission Dynamics: A Bibliometric Review

Goswami

Labib

2022

IJERPH

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A good amount of research has evolved just in three years in COVID-19 transmission, mortality, vaccination, and some socioeconomic studies. A few bibliometric reviews have already been performed in the literature, especially on the broad theme of COVID-19, without any particular area such as transmission, mortality, or vaccination. This paper fills this gap by conducting a bibliometric review on COVID-19 transmission as the first of its kind. The main aim of this study is to conduct a bibliometric review of the literature in the area of COVID-19 transmission dynamics. We have conducted bibliometric analysis using descriptive and network analysis methods to review the literature in this area using RStudio, Openrefine, VOSviewer, and Tableau. We reviewed 1103 articles published in 2020–2022. The result identified the top authors, top disciplines, research patterns, and hotspots and gave us clear directions for classifying research topics in this area. New research areas are rapidly emerging in this area, which needs constant observation by researchers to combat this global epidemic.

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Section: Results and Interpretationmentioning

confidence: 99%

“…A similar type of study was conducted in India, Gujrat. They found more than 100 lineages of the virus, and this was associated with international travel [ 75 ].…”

Section: Results and Interpretationmentioning

confidence: 99%

Modeling COVID-19 Transmission Dynamics: A Bibliometric Review

Goswami

Labib

2022

IJERPH

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“…Pathogen sequencing played a highly valuable role in the COVID-19 pandemic and remains a critical global and national capability. This is highlighted by studies of viral transmission that have yielded important insights into the modes of pathogen spread [1][2][3][4][5]. In addition, identification of emerging variants-of-concern guided public health and policy responses, [28] as well as informing assessments about the impact of emerging variants on the impact of therapeutics (such as monoclonal antibodies) and vaccines [7,29].…”

Section: Given Evidence Of Global Mixing and Limited Diversity Betwee...mentioning

confidence: 99%

“…Viral genomic sequencing has been pivotal in understanding and responding to SARS-CoV-2 viral evolution during the COVID-19 pandemic. Global sharing of data and comparison of samples has facilitated public health surveillance by tracking the emergence of variants globally, [1] demonstrating the impact of travel restrictions on viral dynamics across continents, [2] and of travel and quarantine on spread within countries, [3,4] as well as demonstrating transmission routes within hospitals [5]. As successive waves driven by new viral variants emerged, it became clear that rapidly detecting new lineages is critical both for understanding and predicting disease epidemiology as well as for guiding both public health measures and treatment of infection, including the use of neutralising antibodies [6,7].…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 sequencing with cloud-based analysis illustrates expedient co-ordinated surveillance of viral genomic epidemiology across six continents

Amoako,

Anh,

Brouard

et al. 2023

Preprint

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Viral sequencing has been critical in the COVID-19 pandemic response, but sequencing and bioinformatics capacity remain inconsistent. To examine the utility of a cloud-based sequencing analysis platform for SARS-CoV-2 sequencing, we conducted a cross-sectional study incorporating seven countries in July 2022. Sites submitted sequential SARS-CoV-2 sequences over two weeks to the Global Pathogen Analysis Service (GPAS). The GPAS bioinformatics cloud platform performs sequence assembly plus lineage and related sample identification. Users can share information with collaborators while retaining data ownership. Seven sites contributed sequencing reads from 5,346 clinical samples, of which 4,799/5,346 (89.8%) had a lineage identified. Omicron lineages dominated, with the vast majority being BA.5, BA.4 and BA.2, commensurate with contemporary genomic epidemiological observations. Phylogenetic analysis demonstrated low within-lineage diversity, and highly similar sequences present in globally disparate sites. A cloud-based analysis platform like GPAS addresses bioinformatics bottlenecks and facilitates collaboration in pathogen surveillance, enhancing epidemic and pandemic preparedness.

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“…The global persistence of H3N2 IAV results from a migrating metapopulation in which multiple different localities may seed seasonal epidemics in temperate regions in a given year. [9][10][11][12] Therefore, population density and regional connectivity are essential in maintaining the virus population. The rapid and extensive global circulation provides many opportunities for antigen selection of influenza viruses.…”

mentioning

confidence: 99%

Nonpharmaceutical interventions for COVID‐19 disrupt the dynamic balance between influenza A virus and human immunity

Liu

Mao

et al. 2022

Journal of Medical Virology

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During the COVID‐19 epidemic, nonpharmaceutical interventions (NPIs) blocked the transmission route of respiratory diseases. This study aimed to investigate the impact of NPIs on the influenza A virus (IAV) outbreak. The present study enrolled all children with respiratory tract infections who came to the Children's Hospital of Zhejiang University between January 2019 and July 2022. A direct immunofluorescence assay kit detected IAV. Virus isolation and Sanger sequencing were performed. From June to July 2022, in Hangzhou, China, the positive rate of IAV infection in children has increased rapidly, reaching 30.41%, and children over 3 years old are the main infected population, accounting for 75% of the total number of infected children. Influenza A (H3N2) viruses are representative strains during this period. In this outbreak, H3N2 was isolated from a cluster of its own and is highly homologous with A/South_Dakota/22/2022 (2021–2022 Northern Hemisphere). Between isolated influenza A (H3N2) viruses and A/South_Dakota/22/2022, the nucleotide homology of the HA gene ranged from 97.3% to 97.5%; the amino acid homology was 97%–97.2%, and the genetic distance of nucleotides ranged from 0.05 to 0.052. Compared with A/South_Dakota/22/2022, the isolated H3N2 showed S156H, N159Y, I160T, D186S, S198P, I48T, S53D, and K171N mutations. There was no variation in 13 key amino acid sites associated with neuraminidase inhibitor resistance in NA protein. Long‐term NPIs have significantly affected the evolution and transmission of the influenza virus and human immunity, breaking the dynamic balance between the IAV and human immunity.

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Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India

Cited by 9 publications

References 25 publications

Modeling COVID-19 Transmission Dynamics: A Bibliometric Review

Modeling COVID-19 Transmission Dynamics: A Bibliometric Review

SARS-CoV-2 sequencing with cloud-based analysis illustrates expedient co-ordinated surveillance of viral genomic epidemiology across six continents

Nonpharmaceutical interventions for COVID‐19 disrupt the dynamic balance between influenza A virus and human immunity

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