SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

Giovanetti, Marta; Cella, Eleonora; Benedetti, Francesca; Magalis, Brittany Rife; Fonseca, Vagner; Fabris, Silvia; Campisi, Giovanni; Ciccozzi, Alessandra; Angeletti, Silvia; Borsetti, Alessândra; Tambone, Vittoradolfo; Sagnelli, Caterina; Pascarella, Stefano; Riva, Alberto; Ceccarelli, Giancarlo; Marcello, Alessandro; Azarian, Taj; Wilkinson, Eduan; Oliveira, Túlio de; Alcântara, Luiz Carlos Júnior; Cauda, Roberto; Caruso, Arnaldo; Dean, Natalie E.; Browne, Cameron J.; Lourenço, José; Salemi, Marco; Zella, Davide; Ciccozzi, Massimo

doi:10.1038/s42003-021-02025-0

Cited by 25 publications

(19 citation statements)

References 42 publications

(29 reference statements)

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“…Similarly, Cameroon is still experiencing a growth of cases, while in other countries, such as Kenya and Nigeria, the situation is more stable. Italy was the first European country to be hit by the SARS-CoV-2 pandemic wave in February 2020, it experienced a second wave in the autumn, and is currently undergoing a third wave [24] . While vaccine rollout is in progress worldwide, its distribution is uneven, with marked differences in the pace of inoculation.…”

Section: Discussionmentioning

confidence: 99%

Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa

Baba¹,

Bitew²,

Fokam³

et al. 2021

EClinicalMedicine

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Background Management and control of the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus SARS-CoV-2 is critically dependent on quick and reliable identification of the virus in clinical specimens. Detection of viral RNA by a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a simple, reliable and cost-effective assay, deployable in resource-limited settings (RLS). Our objective was to evaluate the intrinsic and extrinsic performances of RT-LAMP in RLS. Methods This is a multicenter prospective observational study of diagnostic accuracy, conducted from October 2020 to February 2021 in four African Countries: Cameroon, Ethiopia, Kenya and Nigeria; and in Italy. We enroled 1657 individuals who were either COVID-19 suspect cases, or asymptomatic and presented for screening. RNA extracted from pharyngeal swabs was tested in parallel by a colorimetric RT-LAMP and by a standard real time polymerase chain reaction (RT-PCR). Findings The sensitivity and specificity of index RT LAMP compared to standard RT-PCR on 1657 prospective specimens from infected individuals was determined. For a subset of 1292 specimens, which underwent exactly the same procedures in different countries, we obtained very high specificity (98%) and positive predictive value (PPV = 99%), while the sensitivity was 87%, with a negative predictive value NPV = 70%, Stratification of RT-PCR data showed superior sensitivity achieved with an RT-PCR cycle threshold (Ct) below 35 (97%), which decreased to 60% above 35. Interpretation In this field trial, RT-LAMP appears to be a reliable assay, comparable to RT-PCR, particularly with medium-high viral loads (Ct < 35). Hence, RT-LAMP can be deployed in RLS for timely management and prevention of COVID-19, without compromising the quality of output.

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Section: Discussionmentioning

confidence: 99%

Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa

Baba¹,

Bitew²,

Fokam³

et al. 2021

EClinicalMedicine

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“…The effective population size represents the number of diverse genomes capable of producing progeny virions and indirectly reflects the number of infected individuals in the context of the epidemic (68,69). The Bayesian Skygrid model is an improved coalescent-based model with higher accuracy in recovering population size trajectories than Bayesian Skyline and Skyride models (70).…”

Section: Discussionmentioning

confidence: 99%

Molecular Phylogenesis and Spatiotemporal Spread of SARS-CoV-2 in Southeast Asia

Zhu

Shen

Zeng³

et al. 2021

Front. Public Health

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Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region.Materials and Methods: A total of 1491 complete SARS-CoV-2 genome sequences from 10 Southeast Asian countries were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) database on November 17, 2020. The evolutionary relationships were assessed using maximum likelihood (ML) and time-scaled Bayesian phylogenetic analyses, and the phylogenetic clustering was tested using principal component analysis (PCA). The spatial patterns of SARS-CoV-2 spread within Southeast Asia were inferred using the Bayesian stochastic search variable selection (BSSVS) model. The effective population size (Ne) trajectory was inferred using the Bayesian Skygrid model.Results: Four major clades (including one potentially endemic) were identified based on the maximum clade credibility (MCC) tree. Similar clustering was yielded by PCA; the first three PCs explained 46.9% of the total genomic variations among the samples. The time to the most recent common ancestor (tMRCA) and the evolutionary rate of SARS-CoV-2 circulating in Southeast Asia were estimated to be November 28, 2019 (September 7, 2019 to January 4, 2020) and 1.446 × 10−3 (1.292 × 10−3 to 1.613 × 10−3) substitutions per site per year, respectively. Singapore and Thailand were the two most probable root positions, with posterior probabilities of 0.549 and 0.413, respectively. There were high-support transmission links (Bayes factors exceeding 1,000) in Singapore, Malaysia, and Indonesia; Malaysia involved the highest number (7) of inferred transmission links within the region. A twice-accelerated viral population expansion, followed by a temporary setback, was inferred during the early stages of the pandemic in Southeast Asia.Conclusions: With available genomic data, we illustrate the phylogeography and phylodynamics of SARS-CoV-2 circulating in Southeast Asia. Continuous genomic surveillance and enhanced strategic collaboration should be listed as priorities to curb the pandemic, especially for regional communities dominated by developing countries.

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“…In addition, a study conducted in the East of England over a 5-week time period utilized genomic surveillance data to refute linked transmission between patients and health-care workers as a mechanism to monitor and target infection control measures 22 . In a similar study conducted in Italy, Giovanetti and colleagues were able to ascertain the dynamic shifts in SARS-CoV-2 transmission in response to the public health interventions by combining viral genetic and epidemiological data analyses 53 . Lastly, by coupling genetic variant data with mathematical modelling approaches researchers are able to pinpoint phylogenetic relationships between subpopulations more precisely, as well as identify sporadic clusters acting as hidden viral reservoirs throughout the pandemic 54 .…”

Section: Discussionmentioning

confidence: 99%

Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown

Munis

Andersson

Mobbs

et al. 2021

Sci Rep

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Epidemiological efforts to model the spread of SARS-CoV-2, the virus that causes COVID-19, are crucial to understanding and containing current and future outbreaks and to inform public health responses. Mutations that occur in viral genomes can alter virulence during outbreaks by increasing infection rates and helping the virus evade the host immune system. To understand the changes in viral genomic diversity and molecular epidemiology in Oxford during the first wave of infections in the United Kingdom, we analyzed 563 clinical SARS-CoV-2 samples via whole-genome sequencing using Nanopore MinION sequencing. Large-scale surveillance efforts during viral epidemics are likely to be confounded by the number of independent introductions of the viral strains into a region. To avoid such issues and better understand the selection-based changes occurring in the SARS-CoV-2 genome, we utilized local isolates collected during the UK’s first national lockdown whereby personal interactions, international and national travel were considerably restricted and controlled. We were able to track the short-term evolution of the virus, detect the emergence of several mutations of concern or interest, and capture the viral diversity of the region. Overall, these results demonstrate genomic pathogen surveillance efforts have considerable utility in controlling the local spread of the virus.

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SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

Cited by 25 publications

References 42 publications

Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa

Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa

Molecular Phylogenesis and Spatiotemporal Spread of SARS-CoV-2 in Southeast Asia

Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown

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