Near-Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Peru

Padilla‐Rojas, Carlos; Lope‐Pari, Priscila; Vega-Chozo, K.; Balbuena-Torres, Johanna; Cáceres, Omar; Bailon, Henri; Huaringa, Maribel; Rojas‐Serrano, Nancy

doi:10.1128/mra.00303-20

Cited by 8 publications

(7 citation statements)

References 5 publications

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“…It possibly indicates that the relative influence of intercontinental and international travel has been less important in driving the dispersal dynamics of the Uruguay outbreak compared to other, larger or more connected countries like Belgium. Data from other South-American countries besides Uruguay, Brazil, and Chile are scarce [31,[47][48][49][50]. The town of Rivera, situated on the border with Brazil, has been a main concern for the government and many outbreaks occurred along the border that were rapidly brought under control.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay

Elizondo¹,

Harkins

Mabvakure

et al. 2021

Emerging Microbes & Infections

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COVID-19 is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and declared by the World Health Organization a global public health emergency. Among the severe outbreaks across South America, Uruguay has become known for curtailing SARS-CoV-2 exceptionally well. To understand the SARS-CoV-2 introductions, local transmissions, and associations with genomic and clinical parameters in Uruguay, we sequenced the viral genomes of 44 outpatients and inpatients in a private healthcare system in its capital, Montevideo, from March to May 2020. We performed a phylogeographic analysis using sequences from our cohort and other studies that indicate a minimum of 23 independent introductions into Uruguay, resulting in five major transmission clusters. Our data suggest that most introductions resulting in chains of transmission originate from other South American countries, with the earliest seeding of the virus in late February 2020, weeks before the borders were closed to all non-citizens and a partial lockdown implemented. Genetic analyses suggest a dominance of S and G clades (G, GH, GR) that make up >90% of the viral strains in our study. In our cohort, lethal outcome of SARS-CoV-2 infection significantly correlated with arterial hypertension, kidney failure, and ICU admission (FDR < 0.01), but not with any mutation in a structural or non-structural protein, such as the spike D614G mutation. Our study contributes genetic, phylodynamic, and clinical correlation data about the exceptionally well-curbed SARS-CoV-2 outbreak in Uruguay, which furthers the understanding of disease patterns and regional aspects of the pandemic in Latin America.

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Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay

Elizondo¹,

Harkins

Mabvakure

et al. 2021

Emerging Microbes & Infections

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“…From December 2020, the emergence of viral variants of SARS‐CoV‐2 has been associated with higher transmissibility, immune escape, or increased pathogenicity. The variants of concern (VOC) and variants of interest (VOI), having different epidemiological and clinical characteristics, represent an important threat to the global containment of the pandemic 1,2 …”

Section: Introductionmentioning

confidence: 99%

Genomic analysis reveals a rapid spread and predominance of lambda (C.37) SARS‐COV‐2 lineage in Peru despite circulation of variants of concern

Padilla‐Rojas

Jiménez-Vásquez

Hurtado

et al. 2021

Journal of Medical Virology

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The pandemic generated by SARS‐Cov‐2 has caused a large number of cases and deaths in the world, but South America has been one of the continents that were most hard hit. The appearance of new variants causes concern because of the possibility that they may evade the protection generated by vaccination campaigns, their greater capacity to be transmitted, or their higher virulence. We analyzed the circulating variants in Peru after improving our Genomic Surveillance program. The results indicate a steep increase of the lambda lineage (C.37) until becoming predominant between January and April 2021, despite the cocirculation of other variants of concern or interest. Lambda lineage deserves close monitoring and could probably become a variant of concern in the near future.

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“…The cultures were observed daily for 10 days through the inverted microscope. Lung virus isolation was confirmed by RT-PCR, as described previously 66 . The IFA was performed using a polyclonal antibody against SARS-CoV-2 from convalescent patients of COVID-19 disease, and anti-human IgG peroxidase conjugate (Sigma).…”

Section: Viral Viability: Culture and Immunofluorescence Assay (Ifa)mentioning

confidence: 99%

Development and pre-clinical evaluation of Newcastle disease virus-vectored SARS-CoV-2 intranasal vaccine candidate

Fernández-Díaz¹,

Calderón²,

Rojas-Neyra³

et al. 2021

Preprint

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The COVID-19 pandemic has claimed the lives of millions of people worldwide and threatens to become an endemic problem, therefore the need for as many types of vaccines as possible is of high importance. Because of the millions of doses required, it is desirable that vaccines are not only safe and effective, but also easy to administer, store, and inexpensive to produce. Newcastle Disease Virus (NDV) is responsible for a respiratory disease in chickens. It has no pathogenic homologue in humans. NDV is recognized as an oncolytic virus, and its use in humans for oncological treatment is being evaluated. In the present work, we have developed two types of NDV-vectored candidate vaccines, which carry the surface-exposed RBD and S1 antigens of SARS-CoV-2, respectively. These vaccine candidates were produced in specific-pathogen-free embryonating chicken eggs, and purified from allantoic fluid before lyophilization. These vaccines were administered intranasally to three different animal models: mice, rats and hamsters, and evaluated for safety, toxicity, immunogenicity, stability and efficacy. Efficacy was evaluated in a challenge assay against active SARS-CoV-2 virus in the Golden Syrian hamster model. The NDV-vectored vaccine based on the S1 antigen was shown to be safe and highly immunogenic, with the ability to neutralize SARS-CoV-2 in-vitro, even with an extreme dilution of 1/640. Our results reveal that this vaccine candidate protects the lungs of the animals, preventing cellular damage in this tissue. In addition, this vaccine reduces the viral load in the lungs, suggesting that it may significantly reduce the likelihood of transmission. Being lyophilized, this vaccine candidate is very stable and can be stored for several months at 4-8°C. In conclusion, our NDV-based vaccine candidate has shown a very favorable performance in the pre-clinical study, serving as evidence for a future evaluation in a Phase-I human clinical trial. This candidate represents a promising tool in the fight against COVID-19.

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Near-Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Peru

Abstract: A near-complete genome sequence was obtained for a novel coronavirus (SARS-CoV-2) strain obtained from an oropharyngeal swab from a Peruvian patient with coronavirus syndrome (COVID-19) who had contact with an individual who had returned to Peru from travel to Italy.

Cited by 8 publications

References 5 publications

SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay

SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay

Genomic analysis reveals a rapid spread and predominance of lambda (C.37) SARS‐COV‐2 lineage in Peru despite circulation of variants of concern

Development and pre-clinical evaluation of Newcastle disease virus-vectored SARS-CoV-2 intranasal vaccine candidate

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