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1.
PLoS One ; 17(6): e0270301, 2022.
Article in English | MEDLINE | ID: covidwho-1902642

ABSTRACT

The preliminary assessments of the impact of the COVID-19 pandemic have recently rekindled worries about the feasibility of the Sustainable Development Goals (SDGs). Notwithstanding the concern voiced by key academic and political actors, the actual evidence on the current gaps and distance from the goals is still very much unknown. This study estimates the global evolution curves for each health-related SDGs indicator in the World Health Organization's SDGs platform. These curves synthesize the transnational trends at play in the evolution of each health-related topic, offering an average global counterfactual to compare with the actual information for each country. The empirical investigation focuses on the American continent, highlighting the health gaps before the COVID-19 outbreak in 33 countries of the region. The study also extrapolates these trends to predict the evolution of the health-related SDGs in each of these countries over the next decade using as the baseline scenario the International Monetary Fund's economic forecasts. The results show a widening gap in the region, associated with the differential economic capacity of these countries. Some bottlenecks are shared by most countries in the continent, especially in the themes of violence and infectious diseases. The latter is likely to improve faster than other health themes in the next decade, whereas improvements in the theme non-communicable diseases can be more challenging. The findings provide much needed comparative evidence to guide the countries in the region to set priorities and concentrate efforts to accelerate progress in the health-related SDGs.


Subject(s)
COVID-19 , Sustainable Development , Americas/epidemiology , COVID-19/epidemiology , Global Health , Humans , Pandemics
3.
PLoS One ; 16(12): e0260899, 2021.
Article in English | MEDLINE | ID: covidwho-1546972

ABSTRACT

The COVID-19 is one of the worst pandemics in modern history. We applied principal component analysis (PCA) to the daily time series of the COVID-19 death cases and confirmed cases for the top 25 countries from April of 2020 to February of 2021. We calculated the eigenvalues and eigenvectors of the cross-correlation matrix of the changes in daily accumulated data over monthly time windows. The largest eigenvalue describes the overall evolution dynamics of the COVID-19 and indicates that evolution was faster in April of 2020 than in any other period. By using the first two PC coefficients, we can identify the group dynamics of the COVID-19 evolution. We observed groups under critical states in the loading plot and found that American and European countries are represented by strong clusters in the loading plot. The first PC plays an important role and the correlations (C1) between the normalized logarithmic changes in deaths or confirmed cases and the first PCs may be used as indicators of different phases of the COVID-19. By varying C1 over time, we identified different phases of the COVID-19 in the analyzed countries over the target time period.


Subject(s)
COVID-19/epidemiology , Americas/epidemiology , COVID-19/mortality , Europe/epidemiology , Global Health/statistics & numerical data , Humans , Principal Component Analysis
4.
Infect Genet Evol ; 97: 105164, 2022 01.
Article in English | MEDLINE | ID: covidwho-1536954

ABSTRACT

The widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuously impacts our economic and public health. The potential of emerging variants to increase transmissibility and evade vaccine-induced immunity lets us put more effort to research on viral mutations and explore the pathogenic haplotypes. In this study, we characterized the haplotype and sub-haplotype diversity of SARS-CoV-2 global variants in January-March and the areas with low and high COVID19 vaccination rates in May 2021 by analyzing viral proteome of complete genome sequences published. Phylogenetic tree analysis of the proteomes of SARS-CoV-2 variants with Neighbor-Joining and Maximum Parsimony methods indicated that haplotype 2 variant with nsp12 P323L and Spike D614G was dominant (98.81%), including new sub-haplotypes 2A_1 to 2A_3, 2B_1 to 2B_3, and 2C_1 to 2C_2 emerged post-one-year COVID-19 outbreak. In addition, the profiling of sub-haplotypes indicated that sub-haplotype 2A_1 with the mutations at N501Y, A570D, D614G, P681H, T716I, S982A, and D118H in Spike was over 58% in May 2021 in the high partly vaccinated rate group (US, Canada, and Germany). Meanwhile, the new haplotype 2C_3 bearing the mutations at EFR156-158del, T19R, A222V, L452R, T478K, and D614G in Spike occupied over 54.8% in May 2021 in the low partly vaccinated rate group (India, Malaysia, Taiwan, and Vietnam). Sub-haplotypes 2A_1 and 2C_3 had a meaningful alternation of ACE2-specific recognition site, neutralization epitopes, and furin cleavage site in SARS-CoV-2 Spike protein. The results discovered the haplotype diversity and new sub-haplotypes of SARS-CoV-2 variants post one-year pandemic in January-March 2021, showing the profiles of sub-haplotypes in the groups with low and high partly vaccinated rates in May 2021. The study reports the emergence of new SARS-CoV-2 sub-haplotypes during ongoing pandemic and vaccination in early 2021, which might help inform the response to vaccination strategies.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/epidemiology , COVID-19/prevention & control , Mutation , SARS-CoV-2/pathogenicity , Spike Glycoprotein, Coronavirus/genetics , Americas/epidemiology , Amino Acid Substitution , Asia/epidemiology , COVID-19/immunology , COVID-19/transmission , Epidemiological Monitoring , Europe/epidemiology , Gene Expression , Genome, Viral , Haplotypes , Humans , Immune Evasion , Models, Molecular , Phylogeny , Protein Interaction Domains and Motifs , SARS-CoV-2/classification , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/metabolism , Vaccination Coverage/statistics & numerical data
5.
Nat Commun ; 12(1): 6223, 2021 10 28.
Article in English | MEDLINE | ID: covidwho-1510592

ABSTRACT

In 2016 the World Health Organization set the goal of eliminating hepatitis B globally by 2030. Horizontal transmission has been greatly reduced in most countries by scaling up coverage of the infant HBV vaccine series, and vertical transmission is therefore becoming increasingly dominant. Here we show that scaling up timely hepatitis B birth dose vaccination to 90% of new-borns in 110 low- and middle-income countries by 2030 could prevent 710,000 (580,000 to 890,000) deaths in the 2020 to 2030 birth cohorts compared to status quo, with the greatest benefits in Africa. Maintaining this could lead to elimination by 2030 in the Americas, but not before 2059 in Africa. Drops in coverage due to disruptions in 2020 may lead to 15,000 additional deaths, mostly in South-East Asia and the Western Pacific. Delays in planned scale-up could lead to an additional 580,000 deaths globally in the 2020 to 2030 birth cohorts.


Subject(s)
Hepatitis B Vaccines/administration & dosage , Hepatitis B/prevention & control , Africa/epidemiology , Americas/epidemiology , Asia, Southeastern/epidemiology , Disease Eradication/statistics & numerical data , Female , Hepatitis B/epidemiology , Hepatitis B/mortality , Hepatitis B/virology , Hepatitis Viruses/genetics , Hepatitis Viruses/immunology , Humans , Infant , Infant, Newborn , Male , Vaccination , World Health Organization
6.
Virus Res ; 305: 198553, 2021 11.
Article in English | MEDLINE | ID: covidwho-1386720

ABSTRACT

COVID-19 is seriously threatening human health all over the world. A comprehensive understanding of the genetic mechanisms driving the rapid evolution of its pathogen (SARS-CoV-2) is the key to controlling this pandemic. In this study, by comparing the entire genome sequences of SARS-CoV-2 isolates from Asia, Europe and America, and analyzing their phylogenetic histories, we found a lineage derived from a recombination event that likely occurred before March 2020. More importantly, the recombinant offspring has become the dominant strain responsible for more than one-third of the global cases in the pandemic. These results indicated that the recombination might have played a key role in the pandemic of the virus.


Subject(s)
COVID-19/epidemiology , Evolution, Molecular , Genome, Viral , Homologous Recombination , Mosaicism , SARS-CoV-2/genetics , Americas/epidemiology , Asia/epidemiology , Base Sequence , COVID-19/history , COVID-19/transmission , COVID-19/virology , Europe/epidemiology , Genomics/methods , History, 21st Century , Humans , Mutation , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/pathogenicity
7.
HLA ; 96(3): 277-298, 2020 09.
Article in English | MEDLINE | ID: covidwho-1388402

ABSTRACT

We report detailed peptide-binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV-1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide-binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV-1. Among the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA-A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV-1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions. In particular, Indigenous peoples of America show both higher frequencies of strongest and lower frequencies of weakest HLA binders. As many HLA proteins are found to be strong binders of peptides derived from distinct viral families, and are hence promiscuous (or generalist), we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to past pathogenic infections. Our findings are highly relevant for both evolutionary genetics and the development of vaccine therapies. However they should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables.


Subject(s)
Coronavirus Infections/epidemiology , HIV Infections/epidemiology , HLA Antigens/chemistry , Influenza, Human/epidemiology , Pandemics , Peptides/chemistry , Pneumonia, Viral/epidemiology , Severe Acute Respiratory Syndrome/epidemiology , Viral Proteins/chemistry , Africa/epidemiology , Americas/epidemiology , Amino Acid Sequence , Asia/epidemiology , Australia/epidemiology , Betacoronavirus/genetics , Betacoronavirus/immunology , COVID-19 , Computational Biology , Coronavirus Infections/immunology , Coronavirus Infections/virology , Europe/epidemiology , HIV Infections/immunology , HIV Infections/virology , HIV-1/genetics , HIV-1/immunology , HLA Antigens/classification , HLA Antigens/genetics , HLA Antigens/immunology , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/immunology , Influenza A Virus, H7N9 Subtype/genetics , Influenza A Virus, H7N9 Subtype/immunology , Influenza, Human/immunology , Influenza, Human/virology , Kinetics , Middle East Respiratory Syndrome Coronavirus/genetics , Middle East Respiratory Syndrome Coronavirus/immunology , Peptides/genetics , Peptides/immunology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Protein Binding , SARS Virus/genetics , SARS Virus/immunology , SARS-CoV-2 , Severe Acute Respiratory Syndrome/immunology , Severe Acute Respiratory Syndrome/virology , Viral Proteins/genetics , Viral Proteins/immunology
8.
Viruses ; 13(7)2021 06 25.
Article in English | MEDLINE | ID: covidwho-1289020

ABSTRACT

The SARS-CoV-2 coronavirus is the focus of attention as it has caused more than three million human deaths globally. This and other coronaviruses, such as MERS-CoV, have been suggested to be related to coronaviruses that are hosted in bats. This work shows, through a bibliographic review, the frequency of detection of coronavirus in bats species of the Americas. The presence of coronavirus in bats has been examined in 25 investigations in 11 countries of the Americas between 2007 and 2020. Coronaviruses have been explored in 9371 individuals from 160 species of bats, and 187 coronavirus sequences have been deposited in GenBank distributed in 43 species of bats. While 91% of the coronaviruses sequences identified infect a single species of bat, the remainder show a change of host, dominating the intragenera change. So far, only Mex-CoV-6 is related to MERS-CoV, a coronavirus pathogenic for humans, so further coronavirus research effort in yet unexplored bat species is warranted.


Subject(s)
Chiroptera/virology , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Coronavirus/classification , Coronavirus/genetics , Americas/epidemiology , Animals , COVID-19/epidemiology , Coronavirus/isolation & purification , Coronavirus Infections/virology , Humans , Middle East Respiratory Syndrome Coronavirus/genetics , Middle East Respiratory Syndrome Coronavirus/isolation & purification , Phylogeny , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification
9.
Trop Med Int Health ; 26(7): 716-719, 2021 07.
Article in English | MEDLINE | ID: covidwho-1195800

ABSTRACT

The SARS-CoV-2 infection, which causes the COVID-19 disease, has impacted every nation on the globe, albeit disproportionately. African countries have seen lower infection and mortality rates than most countries in the Americas Europe and Asia. In this commentary, we explore some of the factors purported to be responsible for the low COVID-19 infection and case fatality rates in Africa: low testing rate, poor documentation of cause of death, younger age population, good vitamin D status as a result of exposure to sunlight, cross-immunity from other viruses including coronaviruses, and lessons learnt from other infectious diseases such as HIV and Ebola. With the advent of a new variant of COVID-19 and inadequate roll-out of vaccines, an innovative and efficient response is needed to ramp up testing, contact tracing and accurate reporting of infection rates and cause of death in order to mitigate the spread of the infection.


Subject(s)
COVID-19/mortality , Africa/epidemiology , Americas/epidemiology , Asia/epidemiology , COVID-19/prevention & control , COVID-19 Testing/statistics & numerical data , COVID-19 Vaccines/administration & dosage , Cause of Death , Europe/epidemiology , Humans , SARS-CoV-2
10.
Hum Antibodies ; 29(1): 27-40, 2021.
Article in English | MEDLINE | ID: covidwho-1170066

ABSTRACT

A novel Coronavirus (SARS-CoV-2) causing a cluster of respiratory infections (Coronavirus Disease 2019, COVID-19) first discovered in Wuhan, China, is responsible for a new illness that has been found to affect the lungs and airways of patients with associated symptoms of fever, cough and shortness of breath. In the light of few cases recorded so far in West Africa there is tendency for complacency. The region needs to make strategic plans based on available evidence to enable them effectively deal with this rapidly evolving pandemic. At this very moment countries like China, Italy, France, Spain, Iran, UK and many others are witnessing sustained and intensive community transmission of this virus and increasing numbers of severe disease and death particularly among elderly patients with other comorbidities. The reality of the seriousness of this pandemic is alarming. Government of member states of ECOWAS need to prepare themselves by building capacity as well as implement evidenced-based steps to mitigate this rapidly evolving pandemic by testing persons presenting with symptoms (fever, cough and shortness of breath), isolating and treating those found positive, tracing and quarantining contacts, implementing social distancing as well as optimizing human and material endowment to allow healthcare workers offer safe quality clinical care for affected patients to prevent secondary infection among healthcare workers.


Subject(s)
COVID-19/epidemiology , COVID-19/prevention & control , Civil Defense/organization & administration , Pandemics , SARS-CoV-2/pathogenicity , Africa, Western/epidemiology , Age Factors , Americas/epidemiology , Asia/epidemiology , COVID-19/diagnosis , COVID-19/transmission , Europe/epidemiology , Global Health/statistics & numerical data , Humans , Incidence , Personal Protective Equipment/supply & distribution , Physical Distancing , Quarantine/methods , Quarantine/organization & administration
11.
Infect Dis Poverty ; 10(1): 30, 2021 Mar 17.
Article in English | MEDLINE | ID: covidwho-1140516

ABSTRACT

The ongoing coronavirus disease 2019 (COVID-19) pandemic has put a strain on health systems globally. Although Africa is the least affected region to date, it has the weakest health systems and an exponential rise in cases as has been observed in other regions, is bound to overwhelm its health systems. Early detection and isolation of suspected and confirmed COVID-19 cases are pivotal to the prevention and control of the pandemic. The World Health Organization (WHO) recommends that all laboratory-confirmed cases should be isolated and treated in a health care facility; however, where this is not possible due to the health system capacity, patients can be isolated in re-purposed facilities or at home. An already very apparent future challenge for Africa is facility-based isolation of COVID-19 cases, given the already limited health infrastructure and health workforce, and the risk of nosocomial transmission. Use of repurposed facilities requires additional resources, including health workers. Home isolation, on the other hand, would be a challenge given the poor housing, overcrowding, inadequate access to water and sanitation, and stigma related to infectious disease that is prevalent in many African societies. Conflict settings on the continent pose an additional challenge to the prevention and control of COVID-19 with the resultant population displacements in overcrowded camps where access to social services is limited. These unique cultural, social, economic and developmental differences on the continent, call for a tailored approach to COVID-19 case management strategies. This article proposes three broad case management strategies based on the transmission scenarios defined by WHO, and the criteria and package of care for each option, for consideration by policy makers and governments in African countries. Moving forward, African countries should generate local evidence to guide the development of realistic home-grown strategies, protocol and equipment for the management of COVID-19 cases on the continent .


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Case Management , SARS-CoV-2 , Africa/epidemiology , Americas/epidemiology , Asia/epidemiology , COVID-19/diagnosis , COVID-19/therapy , Delivery of Health Care , Disease Management , Europe/epidemiology , Health Care Surveys , Humans
12.
Infect Genet Evol ; 91: 104800, 2021 07.
Article in English | MEDLINE | ID: covidwho-1116814

ABSTRACT

The pandemic spread of Coronavirus Disease 2019 (COVID-19) is still ongoing since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is identified as the etiologic pathogen late December 2019. After over six-month spread of COVID-19, SARS-CoV-2 causes critical threats to global public health and economy. The investigations on evolution and genotyping on genetic variations are of great importance, therefore, the present study characterized the molecular variation of SARS-CoV-2 by analyzing 4230 complete genome sequences from the worldwide samples collected during the first 6-month pandemic. Phylogenetic tree analysis with Neighbor-Joining and Maximum-Parsimony methods indicated that the haplotypes of SARS-CoV-2 genome sequences were classified into four clades with the unique nucleotide and amino acid changes: T27879C (ORF8 L84S) in clade 1 (25.34%), A23138G (spike D614G) in clade 2 (63.54%), G10818T (nsp6 L37F), C14540T (nsp12 T442I), and G25879T (ORF3a V251F) in clade 3 (2.58%), and miscellaneous changes in clade 4 (8.54%). Interestingly, subclade 2B with the amino acid changes at nsp2 T85I, Spike D614G, and ORF3a Q57H was firstly reported on March 4, 2020 in United States of America, becoming the most frequent sub-haplogroup in the world (36.21%) and America (45.81%). Subclade 1C with the amino acid changes at nsp13 P504L and ORF8 L84S was becoming the second most frequent sub-haplogroup in the world (19.91%) and America (26.29%). Subclade 2A with the amino acid changes in Spike D614G and Nucleocapsid R203K and G204R was highly prevalent in Asia (18.82%) and Europe (29.72%). The study highlights the notable clades and sub-clades with unique mutations, revealing the genetic and geographical relevant post the six-month outbreak of COVID-19. This study thoroughly observed the genetic feature of SARS-CoV-2 haplotyping, providing an epidemiological trend of COVID-19.


Subject(s)
COVID-19/epidemiology , Genetic Variation , Genome, Viral , Nucleocapsid Proteins/genetics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Americas/epidemiology , Amino Acid Substitution , Asia/epidemiology , COVID-19/transmission , COVID-19/virology , Europe/epidemiology , Evolution, Molecular , Gene Expression Regulation, Viral , Haplotypes , Humans , Mutation Rate , Open Reading Frames , Phylogeny , SARS-CoV-2/classification , Selection, Genetic
13.
JSLS ; 24(4)2020.
Article in English | MEDLINE | ID: covidwho-1090243

ABSTRACT

OBJECTIVE: To evaluate the use of social media platforms by medical students, surgical trainees, and practicing surgeons for surgical education during the Covid-19 pandemic. METHODS: An online, 15-question survey was developed and posted on Facebook and WhatsApp closed surgeon groups. RESULTS: The online survey was completed by 219 participants from South America (87%), North America (7%), Europe (5%), Central America, and Asia. Respondents included medical students (6.4%), surgical residents/fellows (24.2%), and practicing surgeons (69.4%). The most common age group was 35-44 years. When asked which social media platforms they preferred, the video sharing site YouTube (33.3%), the messaging app WhatsApp (21%), and "other" (including videoconferencing sites) (22.3%) were most popular. Respondents reported using social media for surgical education either daily (38.4%) or weekly (45.2%), for an average of 1-5 hours/week. Most (85%) opined that surgical conferences that were cancelled during the pandemic should be made available online, with live discussions. CONCLUSION: Social media use for surgical education during Covid-19 appears to be increasing and evolving.


Subject(s)
COVID-19 , Education, Distance/methods , Education, Medical/methods , General Surgery/education , Social Media/trends , Adolescent , Adult , Aged , Americas/epidemiology , Asia/epidemiology , COVID-19/epidemiology , COVID-19/prevention & control , Cross-Sectional Studies , Education, Distance/statistics & numerical data , Education, Medical/trends , Europe/epidemiology , Female , General Surgery/trends , Global Health , Humans , Male , Middle Aged , Pandemics , Surveys and Questionnaires , Young Adult
14.
J Infect Dev Ctries ; 15(1): 9-21, 2021 01 31.
Article in English | MEDLINE | ID: covidwho-1079739

ABSTRACT

INTRODUCTION: On the eleventh of March 2020, the World Health Organization (WHO) declared the novel coronavirus disease 2019 (COVID-19) a pandemic by the number of cases and deaths worldwide: more than 91.1 million confirmed cases and approx. 1.9 million deaths globally, as of date. The aims of this systematic review were to identify and to evaluate the reports associated on Knowledge, Attitude and Practices (KAP) towards COVID-19 pandemic in America. METHODOLOGY: The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were adopted for searching reports published from December 2019 to September 2020, regarding "COVID-19 KAP" across six electronic databases. Inclusion and exclusion criteria were taken up to select the articles and focus to the topic. RESULTS: Thirteen scientific papers were finally eligible and included in this systematic review. The surveys were directed to common citizens, healthcare workers and patients with chronic conditions. General public acquired information about COVID-19 mainly through social media; several misconceptions due to falsehoods circulating on-line were identified. The pandemic COVID-19 has severely affected the physical and emotional health of many people in America. Nevertheless, many American citizens do not recognize or have poor knowledge about COVID-19 risks. CONCLUSIONS: This systematic review brings information for governments and scientific community that may be useful in the development of official awareness and prevention campaigns aiming mainly at marginated groups of the society.


Subject(s)
COVID-19/epidemiology , COVID-19/psychology , Health Knowledge, Attitudes, Practice , Americas/epidemiology , Health Personnel , Humans , Meta-Analysis as Topic , Surveys and Questionnaires
15.
Epidemiol Prev ; 44(5-6 Suppl 2): 60-68, 2020.
Article in English | MEDLINE | ID: covidwho-1068125

ABSTRACT

OBJECTIVES: to describe and compare the effectiveness of national and local lockdowns in controlling the spread of COVID-19. METHODS: a rapid review of published and grey literature on COVID-19 pandemic was conducted following predefined eligibility criteria by searching electronic databases, repositories of pre-print articles, websites and databases of international health, and research related institutions and organisations. RESULTS: of 584 initially identified records up to 5 July 2020, 19 articles met the inclusion criteria and were included in the review. Most of the studies (No. 11) used the reproduction  number (Rt) as a measure of effect and in all of them areduction of the estimated value at post-intervention period was found. The implementation of lockdown in 11 European countries was associated with an average 82% reduction of Rt, ranging from a  posterior Rt of 0.44 (95%CI 0.26-0.61) for Norway to a posterior Rt of 0.82 (95%CI 0.73- 0.93) for  Belgium. Changes in infection rates and transmission rates were estimated in 8 studies. Daily changes in infection rates ranged from -0.6% (Sweden) to -11.3% (Hubei and Guangdong provinces). Additionally, other studies reported a change in the trend of hospitalizations (Italy, Spain) and positive effects on the  doubling time of cases (Hubei, China) after lockdown. CONCLUSIONS: results of this rapid review suggest a positive effect of the containment measures on the spread of COVID-19 pandemic, with a major effect in  countries where lockdown started early and was more restrictive. Rigorous research is warranted to evaluate which approach is the most effective in each stage of the epidemic and in specific social contexts, in particular addressing if these approaches should be implemented on the whole population or target specific risk groups.


Subject(s)
COVID-19/prevention & control , Communicable Disease Control/methods , Pandemics/prevention & control , Physical Distancing , Quarantine , SARS-CoV-2 , Americas/epidemiology , Australia/epidemiology , COVID-19/epidemiology , COVID-19/transmission , China/epidemiology , Communicable Disease Control/statistics & numerical data , Europe/epidemiology , Forecasting , Health Policy , Humans , Iran/epidemiology , Italy/epidemiology , Program Evaluation , Quarantine/statistics & numerical data
16.
BMJ Open ; 11(2): e042034, 2021 02 03.
Article in English | MEDLINE | ID: covidwho-1063074

ABSTRACT

OBJECTIVE: We aimed to identify the country-level determinants of the severity of the first wave of the COVID-19 pandemic. DESIGN: Ecological study of publicly available data. Countries reporting >25 COVID-19 related deaths until 8 June 2020 were included. The outcome was log mean mortality rate from COVID-19, an estimate of the country-level daily increase in reported deaths during the ascending phase of the epidemic curve. Potential determinants assessed were most recently published demographic parameters (population and population density, percentage population living in urban areas, population >65 years, average body mass index and smoking prevalence); economic parameters (gross domestic product per capita); environmental parameters (pollution levels and mean temperature (January-May); comorbidities (prevalence of diabetes, hypertension and cancer); health system parameters (WHO Health Index and hospital beds per 10 000 population); international arrivals; the stringency index, as a measure of country-level response to COVID-19; BCG vaccination coverage; UV radiation exposure; and testing capacity. Multivariable linear regression was used to analyse the data. PRIMARY OUTCOME: Country-level mean mortality rate: the mean slope of the COVID-19 mortality curve during its ascending phase. PARTICIPANTS: Thirty-seven countries were included: Algeria, Argentina, Austria, Belgium, Brazil, Canada, Chile, Colombia, the Dominican Republic, Ecuador, Egypt, Finland, France, Germany, Hungary, India, Indonesia, Ireland, Italy, Japan, Mexico, the Netherlands, Peru, the Philippines, Poland, Portugal, Romania, the Russian Federation, Saudi Arabia, South Africa, Spain, Sweden, Switzerland, Turkey, Ukraine, the UK and the USA. RESULTS: Of all country-level determinants included in the multivariable model, total number of international arrivals (beta 0.033 (95% CI 0.012 to 0.054)) and BCG vaccination coverage (-0.018 (95% CI -0.034 to -0.002)), were significantly associated with the natural logarithm of the mean death rate. CONCLUSIONS: International travel was directly associated with the mortality slope and thus potentially the spread of COVID-19. Very early restrictions on international travel should be considered to control COVID-19 outbreaks and prevent related deaths.


Subject(s)
COVID-19/mortality , Pandemics/statistics & numerical data , Adult , Africa/epidemiology , Age Factors , Aged , Air Pollution/statistics & numerical data , Americas/epidemiology , Asia/epidemiology , Body Mass Index , COVID-19/epidemiology , Diabetes Mellitus/epidemiology , Europe/epidemiology , Female , Humans , Hypertension/epidemiology , Male , Middle Aged , Neoplasms/epidemiology , Population Density , SARS-CoV-2 , Smoking/epidemiology , Social Determinants of Health/statistics & numerical data , Temperature , Travel , Young Adult
19.
Infect Genet Evol ; 88: 104708, 2021 03.
Article in English | MEDLINE | ID: covidwho-1039486

ABSTRACT

The pandemic due to novel coronavirus, SARS-CoV-2 is a serious global concern now. More than thousand new COVID-19 infections are getting reported daily for this virus across the globe. Thus, the medical research communities are trying to find the remedy to restrict the spreading of this virus, while the vaccine development work is still under research in parallel. In such critical situation, not only the medical research community, but also the scientists in different fields like microbiology, pharmacy, bioinformatics and data science are also sharing effort to accelerate the process of vaccine development, virus prediction, forecasting the transmissible probability and reproduction cases of virus for social awareness. With the similar context, in this article, we have studied sequence variability of the virus primarily focusing on three aspects: (a) sequence variability among SARS-CoV-1, MERS-CoV and SARS-CoV-2 in human host, which are in the same coronavirus family, (b) sequence variability of SARS-CoV-2 in human host for 54 different countries and (c) sequence variability between coronavirus family and country specific SARS-CoV-2 sequences in human host. For this purpose, as a case study, we have performed topological analysis of 2391 global genomic sequences of SARS-CoV-2 in association with SARS-CoV-1 and MERS-CoV using an integrated semi-alignment based computational technique. The results of the semi-alignment based technique are experimentally and statistically found similar to alignment based technique and computationally faster. Moreover, the outcome of this analysis can help to identify the nations with homogeneous SARS-CoV-2 sequences, so that same vaccine can be applied to their heterogeneous human population.


Subject(s)
COVID-19/epidemiology , Coronavirus Infections/epidemiology , Genetic Variation , Genome, Viral , Pandemics , SARS-CoV-2/genetics , Severe Acute Respiratory Syndrome/epidemiology , Africa/epidemiology , Americas/epidemiology , Asia/epidemiology , Australia/epidemiology , Base Sequence , COVID-19/transmission , COVID-19/virology , Computational Biology/methods , Coronavirus Infections/transmission , Coronavirus Infections/virology , Europe/epidemiology , Host-Pathogen Interactions/genetics , Humans , Middle East Respiratory Syndrome Coronavirus/genetics , Middle East Respiratory Syndrome Coronavirus/pathogenicity , SARS Virus/genetics , SARS Virus/pathogenicity , SARS-CoV-2/pathogenicity , Sequence Alignment , Severe Acute Respiratory Syndrome/transmission , Severe Acute Respiratory Syndrome/virology
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