Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru

Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean

Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.

Frequency of SARS-CoV-2 variants identified by real-time PCR in the AUNA healthcare network, Peru

Introduction

In Peru, on 11 February 2023, the Ministry of Health registered 4 million patients infected with COVID-19 and around 219,260 deaths. In 2020, the SARS-CoV-2 virus was acquiring mutations that impacted the properties of transmissibility, infectivity, and immune evasion, leading to new lineages. In the present study, the frequency of COVID-19 variants was determined during 2021 and 2022 in patients treated in the AUNA healthcare network.

Methods

The methodology used to detect mutations and identify variants was the Allplex™ SARS-CoV-2 Variants Assay I, II, and VII kit RT-PCR. The frequency of variants was presented by epidemiological weeks.

Results

In total, 544 positive samples were evaluated, where the Delta, Omicron, and Gamma variants were identified. The Delta variant was found in 242 (44.5%) patients between epidemiological weeks 39 and 52 in 2021. In the case of Gamma, it was observed in 8 (1.5%) patients at weeks 39, 41, 43, 45, and 46 of 2021. The Omicron variant was the most frequent with 289 (53.1%) patients during weeks 49 to 52 of 2021 and 1 to 22 of 2022. During weeks 1 through 22 of 2022, it was possible to discriminate between BA. 1 (n = 32) and BA.2 (n = 82).

Conclusion

The rapid identification of COVID-19 variants through the RT-PCR methodology contributes to timely epidemiological surveillance, as well as appropriate patient management.

Designing Organic and Hybrid Surfaces and Devices with Initiated Chemical Vapor Deposition (iCVD)

The initiated chemical vapor deposition (iCVD) technique is an all-dry method for designing organic and hybrid polymers. Unlike methods utilizing liquids or line-of-sight arrival, iCVD provides conformal surface modification over intricate geometries. Uniform, high-purity, and pinhole-free iCVD films can be grown with thicknesses ranging from >15 µm to <5 nm. The mild conditions permit damage-free growth directly onto flexible substrates, 2D materials, and liquids. Novel iCVD polymer morphologies include nanostructured surfaces, nanoporosity, and shaped particles. The well-established fundamentals of iCVD facilitate the systematic design and optimization of polymers and copolymers. The functional groups provide fine-tuning of surface energy, surface charge, and responsive behavior. Further reactions of the functional groups in the polymers can yield either surface modification, compositional gradients through the layer thickness, or complete chemical conversion of the bulk film. The iCVD polymers are integrated into multilayer device structures as desired for applications in sensing, electronics, optics, electrochemical energy storage, and biotechnology. For these devices, hybrids offer higher values of refractive index and dielectric constant. Multivinyl monomers typically produce ultrasmooth and pinhole-free and mechanically deformable layers and robust interfaces which are especially promising for electronic skins and wearable optoelectronics.