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

ABSTRACT: We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers and hospitalizations. Yet we present evidence of sustained viral spread among sporadic clusters acting as "hidden reservoirs" during summer 2020. Mathematical modelling shows that increased mobility among residents eventually catalyzed the coalescence of such clusters, thus driving up the number of infections and initiating a new epidemic wave. Our results suggest that the efficacy of public health interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.

SUBMITTER: Giovanetti M

PROVIDER: S-EPMC8060392 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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

Giovanetti Marta M Cella Eleonora E Benedetti Francesca F Rife Magalis Brittany B Fonseca Vagner V Fabris Silvia S Campisi Giovanni G Ciccozzi Alessandra A Angeletti Silvia S Borsetti Alessandra A Tambone Vittoradolfo V Sagnelli Caterina C Pascarella Stefano S Riva Alberto A Ceccarelli Giancarlo G Marcello Alessandro A Azarian Taj T Wilkinson Eduan E de Oliveira Tulio T Alcantara Luiz Carlos Junior LCJ Cauda Roberto R Caruso Arnaldo A Dean Natalie E NE Browne Cameron C Lourenco Jose J Salemi Marco M Zella Davide D Ciccozzi Massimo M

Communications biology 20210421 1

We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers an ...[more]

PMID: 33883675

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Project description:BackgroundApplied epidemiological models are used in predicting future trends of diseases, for the basic understanding of disease and health dynamics, and to improve the measurement of health indicators. Mapping the research outputs of epidemiological modelling studies concerned with transmission dynamics of infectious diseases and public health interventions in Africa will help to identify the areas with substantial levels of research activities, areas with gaps, and research output trends.MethodsA scoping review of applied epidemiological models of infectious disease studies that involved first or last authors affiliated to African institutions was conducted. Eligible studies were those concerned with the transmission dynamics of infectious diseases and public health interventions. The review was consistent with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) extension for scoping reviews. Four electronic databases were searched for peer-reviewed publications up to the end of April 2020.ResultsOf the 5927 publications identified, 181 met the inclusion criteria. The review identified 143 publications with first authors having an African institutional affiliation (AIA), while 81 had both first and last authors with an AIA. The publication authors were found to be predominantly affiliated with institutions based in South Africa and Kenya. Furthermore, human immunodeficiency virus, malaria, tuberculosis, and Ebola virus disease were found to be the most researched infectious diseases. There has been a gradual increase in research productivity across Africa especially in the last ten years, with several collaborative efforts spread both within and beyond Africa.ConclusionsResearch productivity in applied epidemiological modelling studies of infectious diseases may have increased, but there remains an under-representation of African researchers as leading authors. The study findings indicate a need for the development of research capacity through supporting existing institutions in Africa and promoting research funding that will address local health priorities.

Project description:Little is known about the transmission dynamics of Acinetobacter baumannii in hospitals, despite such information being critical for designing effective infection control measures. In the absence of comprehensive epidemiological data, mathematical modelling is an attractive approach to understanding transmission process. The statistical challenge in estimating transmission parameters from infection data arises from the fact that most patients are colonised asymptomatically and therefore the transmission process is not fully observed. Hidden Markov models (HMMs) can overcome this problem. We developed a continuous-time structured HMM to characterise the transmission dynamics, and to quantify the relative importance of different acquisition sources of A. baumannii in intensive care units (ICUs) in three hospitals in Melbourne, Australia. The hidden states were the total number of patients colonised with A. baumannii (both detected and undetected). The model input was monthly incidence data of the number of detected colonised patients (observations). A Bayesian framework with Markov chain Monte Carlo algorithm was used for parameter estimations. We estimated that 96-98% of acquisition in Hospital 1 and 3 was due to cross-transmission between patients; whereas most colonisation in Hospital 2 was due to other sources (sporadic acquisition). On average, it takes 20 and 31 days for each susceptible individual in Hospital 1 and Hospital 3 to become colonised as a result of cross-transmission, respectively; whereas it takes 17 days to observe one new colonisation from sporadic acquisition in Hospital 2. The basic reproduction ratio (R0) for Hospital 1, 2 and 3 was 1.5, 0.02 and 1.6, respectively. Our study is the first to characterise the transmission dynamics of A. baumannii using mathematical modelling. We showed that HMMs can be applied to sparse hospital infection data to estimate transmission parameters despite unobserved events and imperfect detection of the organism. Our results highlight the need to optimise infection control in ICUs.

Project description:Leprosy is a chronic infectious disease caused by Mycobacterium leprae (M. leprae) and the more recently discovered Mycobacterium lepromatosis (M. lepromatosis). The two leprosy bacilli cause similar pathologic conditions. They primarily target the skin and the peripheral nervous system. Currently it is considered a Neglected Tropical Disease, being endemic in specific locations within countries of the Americas, Asia, and Africa, while in Europe it is only rarely reported. The reason for a spatial inequality in the prevalence of leprosy in so-called endemic pockets within a country is still largely unexplained. A systematic review was conducted targeting leprosy transmission research data, using PubMed and Scopus as sources. Publications between January 1, 1945 and July 1, 2019 were included. The transmission pathways of M. leprae are not fully understood. Solid evidence exists of an increased risk for individuals living in close contact with leprosy patients, most likely through infectious aerosols, created by coughing and sneezing, but possibly also through direct contact. However, this systematic review underscores that human-to-human transmission is not the only way leprosy can be acquired. The transmission of this disease is probably much more complicated than was thought before. In the Americas, the nine-banded armadillo (Dasypus novemcinctus) has been established as another natural host and reservoir of M. leprae. Anthroponotic and zoonotic transmission have both been proposed as modes of contracting the disease, based on data showing identical M. leprae strains shared between humans and armadillos. More recently, in red squirrels (Sciurus vulgaris) with leprosy-like lesions in the British Isles M. leprae and M. lepromatosis DNA was detected. This finding was unexpected, because leprosy is considered a disease of humans (with the exception of the armadillo), and because it was thought that leprosy (and M. leprae) had disappeared from the United Kingdom. Furthermore, animals can be affected by other leprosy-like diseases, caused by pathogens phylogenetically closely related to M. leprae. These mycobacteria have been proposed to be grouped as a M. leprae-complex. We argue that insights from the transmission and reservoirs of members of the M. leprae-complex might be relevant for leprosy research. A better understanding of possible animal or environmental reservoirs is needed, because transmission from such reservoirs may partly explain the steady global incidence of leprosy despite effective and widespread multidrug therapy. A reduction in transmission cannot be expected to be accomplished by actions or interventions from the human healthcare domain alone, as the mechanisms involved are complex. Therefore, to increase our understanding of the intricate picture of leprosy transmission, we propose a One Health transdisciplinary research approach.

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

Publications

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

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