The importance of genomic analysis in cracking the coronavirus pandemic

Zella, Davide; Giovanetti, Marta; Cocco, Eleonora; Borsetti, Alessândra; Ciotti, Marco; Ceccarelli, Giancarlo; d’Ettorre, Gabriella; Pezzuto, Aldo; Tambone, Vittoradolfo; Campanozzi, Laura Leondina; Magheri, Marco; Unali, Francesco; Bianchi, Martina; Benedetti, Francesca; Pascarella, Stefano; Angeletti, Silvia; Ciccozzi, Massimo

doi:10.1080/14737159.2021.1917998

Cited by 17 publications

(13 citation statements)

References 121 publications

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“…SARS CoV-2 has spread worldwide during the previous year resulting in over 140 million cases and over 3 million deaths (WHO dashboard https://covid19.who.int) 1 . In late fall 2020, variant viruses were identified that exhibited altered infection, transmission and disease characteristics 2 reviewed in [3][4][5][6] . These variants may reflect immune response escape mutants as well as mutants adapting to replication and transmission in normal or immunocompromised human populations 7 8,9 , reviewed in 10,11 .…”

Section: Introductionmentioning

confidence: 99%

Protection of human ACE2 transgenic Syrian hamsters from SARS CoV-2 variants by human polyclonal IgG from hyper-immunized transchromosomic bovines

Gilliland

Liu

et al. 2021

Preprint

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Pandemic SARS CoV-2 has been undergoing rapid evolution during spread throughout the world resulting in the emergence of many Spike protein variants, some of which appear to either evade antibody neutralization, transmit more efficiently, or potentially exhibit increased virulence. This raises significant concerns regarding the long-term efficacy of protection elicited after primary infection and/or from vaccines derived from single virus Spike (S) genotypes, as well as the efficacy of anti-S monoclonal antibody based therapeutics. Here, we used fully human polyclonal human IgG (SAB-185), derived from hyperimmunization of transchromosomic bovines with DNA plasmids encoding the SARS-CoV-2 Wa-1 strain S protein or purified ectodomain of S protein, to examine the neutralizing capacity of SAB-185 in vitro and the protective efficacy of passive SAB-185 antibody (Ab) transfer in vivo. The Ab preparation was tested for neutralization against five variant SARS-CoV-2 strains: Munich (Spike D614G), UK (B.1.1.7), Brazil (P.1) and SA (B.1.3.5) variants, and a variant isolated from a chronically infected immunocompromised patient (Spike del144-146). For the in vivo studies, we used a new human ACE2 (hACE2) transgenic Syrian hamster model that exhibits lethality after SARS-Cov-2 challenge and the Munich, UK, SA and del144-146 variants. SAB-185 neutralized each of the SARS-CoV-2 strains equivalently on Vero E6 cells, however, a control convalescent human serum sample was less effective at neutralizing the SA variant. In the hamster model, prophylactic SAB-185 treatment protected the hamsters from fatal disease and minimized clinical signs of infection. These results suggest that SAB-185 may be an effective treatment for patients infected with SARS CoV-2 variants.

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Section: Introductionmentioning

confidence: 99%

Protection of human ACE2 transgenic Syrian hamsters from SARS CoV-2 variants by human polyclonal IgG from hyper-immunized transchromosomic bovines

Gilliland

Liu

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…Vaccines against coronavirus type viruses being developed and deployed may only result in short-term, i.e., 3–6-month immunity [ 93 ], and thus are not a panacea for success but are expected to curb morbidity and mortality. It is recommended that a vaccine not be administered in patients that have been infected with SARS-CoV-2 within the last 6 months because of the existence of natural immunity.…”

Section: Resultsmentioning

confidence: 99%

Guidelines for Reopening a Nation in a SARS-CoV-2 Pandemic: A Path Forward

Baker

Greiner

2021

Medicina

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Action, not fear, is the path forward in the coronavirus infectious disease 2019 (COVID-19) pandemic. Since early 2020, the world’s nations have faced conundrums over severe acute respiratory syndrome corona virus type 2 (SARS-CoV-2) infections resulting in COVID-19 resulting in national closures, and thus, a clear understandable plan that nations can implement is required to reopen. The healthcare benefits of reopening a nation more likely than not exceed the benefits of continued pandemic-related closure. Pandemic-related closures have resulted in countless delayed or avoided urgent care evaluations. Furthermore, routine care of acute and chronic illnesses, including evaluations, diagnoses, and treatments, has also been delayed. Isolation, loss of income, and fear have resulted in mental health conditions or exacerbated existing conditions. The magnitude of untoward ramifications is unknown and may ultimately represent an inestimable degree of danger and morbidity, and even death. Purpose. The pandemic of SARS-CoV-2 has created an atmosphere of fear of COVID-19 that has directly and indirectly injured the world’s population. Since this has resulted in increasing morbidity and mortality, creating economic chaos, and near systemic collapse of educational systems with no well described plan forward, it is the purpose of this study to provide guidelines that provide a path forward to safely open a nation. Physicians often equipped by their education, training, and experiences across disciplines are uniquely positioned to comprehend, coordinate, and teach other physicians, business owners, and municipal and government leaders from guidelines. As such, physicians may take the lead in a path forward to reopening a nation, including opening businesses, educational facilities, and religious establishments, while minimizing the risk of SARS-CoV-2 infection. Method. Reviews of the literature among the disciplines of environmental air, sanitation, social interaction, medical testing, vaccination, protection, and disease prevention and safety allowed for the conceptualization and eventual genesis of identifiable interventions which either reduce the viral load in the environment or inactivate the virus from replication. Each of the guidelines was selected based on the principle that it involved the elimination or inactivation of the viral particle. With a reduction in viral load or inactivation of replication, the implementation of these guidelines is expected to allow for reopening a nation with an increased level of safety. Results. The guidelines identified, including air exchange (ventilation), air filtration, personal protective filtering devices (masks), hand hygiene, social distancing, screening and testing, vaccines, high-risk patient protection, medical management, and adjunctive therapies, are described and referenced. Conclusions. In that the pandemic is primarily a public health issue, the path forward is best coordinated by local, regional, and national physicians. Many physicians with a breadth of experiences are uniquely positioned to coordinate the implementation of these interdisciplinary guidelines. Using these guidelines as a planned, coordinated action, not fear, is a path forward. Nations have a decision to make: closuring versus opening.

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“…The recent emergence and successful spread of SARS-CoV-2 variants of concern (VOCs) have triggered alarm ( 1 ). Definitive identification of these variants requires whole-genome sequencing (WGS) to identify the constellation of variant-specific mutations ( 2 ). In the search for a higher throughput, lower costs, and faster availability of data, alternative reverse transcription-PCR (RT-PCR)-based approaches have been proposed to prescreen these variants.…”

Section: Observationmentioning

confidence: 99%

Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern

et al. 2021

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Reverse transcription-PCRs (RT-PCRs) targeting SARS-CoV-2 variant of concern (VOC) mutations have been developed to simplify their tracking. We evaluated an assay targeting E484K/N501Y to identify B.1.351/P1. Whole-genome sequencing (WGS) confirmed only 72 (59.02%) of 122 consecutive RT-PCR P.1/B.1.351 candidates. Prescreening RT-PCRs must target a wider set of mutations, updated from WGS data from emerging variants.

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The importance of genomic analysis in cracking the coronavirus pandemic

Cited by 17 publications

References 121 publications

Protection of human ACE2 transgenic Syrian hamsters from SARS CoV-2 variants by human polyclonal IgG from hyper-immunized transchromosomic bovines

Protection of human ACE2 transgenic Syrian hamsters from SARS CoV-2 variants by human polyclonal IgG from hyper-immunized transchromosomic bovines

Guidelines for Reopening a Nation in a SARS-CoV-2 Pandemic: A Path Forward

Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern

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