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1.
Virus Research ; : 198785, 2022.
Article in English | ScienceDirect | ID: covidwho-1799663

ABSTRACT

Brazil ranks as third in terms of total number of reported SARS-CoV-2 cases globally. The COVID-19 epidemic in Brazil was characterised by the co-circulation of multiple variants as a consequence of multiple independent introduction events occurring through time. Here, we describe the SARS-CoV-2 variants that are currently circulating and co-circulating in the country, with the aim to highlight which variants have driven the different epidemic waves. For this purpose, we retrieved metadata information of Coronavirus sequences collected in Brazil and available at the GISAID database. SARS-CoV-2 lineages have been identified along with eleven variants, labelled as VOCs (Alpha, Gamma, Beta, Delta and Omicron) VOIs (Lambda and Mu) VUMs (B.1.1.318) and FMVs (Zeta, Eta and B.1.1.519). Here we show that, in the Brazilian context, after 24 months of sustained transmission and evolution of SARS-CoV-2, local variants (among them the B.1.1.28 and B.1.1.33) were displaced by recently introduced VOCs firstly with the Gamma, followed by Delta and more recently Omicron. The rapid spread of some of those VOCs (such as Gamma and Omicron) was also mirror by a large increase in the number of cases and deaths in the country. This in turn reinforces that, due to the emergence of variants that appear to induce a substantial evasion against neutralizing antibody response, it is important to strengthen genomic effort within the country and how vaccination still remains a critical process to protect the vulnerable population, still at risk of infection and death.

2.
J Med Virol ; 94(6): 2479-2486, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1797827

ABSTRACT

The COVID-19 pandemic continues to have a threatening impact on a global scale, largely due to the emergence of newly SARS-CoV-2 variants. The Mu (PANGO lineage B.1.621), was first identified in Colombia in January 2021 and was classified as a variant of interest (VOI) in August 2021, due to a constellation of mutations that likely-mediate an unexpectedly enhanced immune resistance to inactivated vaccine-elicited antibodies. Despite recent studies suggesting that the Mu variant appears to have less infectivity than the Delta variant, here we examined the structural effect of the Mu spike protein mutations and predicted the potential impact on infectivity of the Mu variant compared with the Delta and Delta plus spike protein.

4.
J Med Virol ; 94(4): 1689-1692, 2022 04.
Article in English | MEDLINE | ID: covidwho-1718387

ABSTRACT

The appearance of emerging variants of SARS-CoV-2 carrying mutations into the spike protein has recently raised concern with respect to tracking their transmission and mitigating the impact in the evolving pandemic across countries. AY.4.2, a recently detected Delta variant sublineage, is considered a new variant under investigation (VUI) as it carries specific genetic signatures present in the spike protein, called Y145H and A222V. Here, using genomic epidemiology, we provide the first preliminary insight regarding the circulation of this emerging VUI in Italy.


Subject(s)
COVID-19/epidemiology , Genome, Viral/genetics , SARS-CoV-2/genetics , Adolescent , Adult , Aged , COVID-19/virology , Child , Female , Genomics , Humans , Italy/epidemiology , Male , Middle Aged , Molecular Epidemiology , Mutation , Phylogeny , RNA, Viral/genetics , SARS-CoV-2/isolation & purification , Young Adult
5.
J Med Virol ; 2021 Oct 16.
Article in English | MEDLINE | ID: covidwho-1718361

ABSTRACT

Despite the SARS-CoV-2 pandemic not yet being under control, post-Covid-19 syndrome is already a challenging topic: long-term multiorgan sequelae, although increasingly described, have not yet been systematized. As post-Covid-19 syndrome can significantly impact both the working capacity and the relationship life of surviving patients, we performed a systematic review of the evidence published over the last year and currently available in medical literature search databases (MEDLINE/Pubmed) and searching clinical trial registries, to evaluate the available evidence among workers. From 31 publications that initially matched inclusion criteria, 13 studies have been considered suitable for relevance and age of subjects. A wide range of patients (16%-87%) have post-Covid syndrome; pneumological and neuropsychological symptoms were the most common disorders reported. The most frequent organic sequel found in post-Covid patients was pulmonary fibrosis. The number of symptoms during acute SARS-CoV-2 infection, severity of the disease, and high serum levels of d-dimer were related to high risk of post-Covid syndrome. In conclusion, post-Covid-19 syndrome can significantly impact the health conditions of surviving patients. Rehabilitation and follow-up in multidisciplinary rehabilitation programs should be considered for working-age patients.

8.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-318541

ABSTRACT

Background: Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the first coronavirus disease 2019 (COVID-19) outbreak in China and has become a public health emergency of international concern. SARS-CoV-2 outbreak has been declared a pandemic by WHO on March 11 th , 2020 and the same month several Countries put in place different lockdown restrictions and testing strategies in order to contain the spread of the virus. Methods: : The calculation of the Case Fatality Rate of SARS-CoV-2 in the Countries selected was made by using the data available at https://github.com/owid/covi-19-data/tree/master/public/data . Case fatality rate was calculated as the ratio between the death cases due to COVID-19, over the total number of SARS-CoV-2 reported cases 14 days before. Standard Case Fatality Rate values were normalized by the Country-specific ρ factor, i.e. the number of PCR tests/1 million inhabitants over the number of reported cases/1 million inhabitants. Case-fatality rates between Countries were compared using proportion test. Post-hoc analysis in the case of more than two groups was performed using pairwise comparison of proportions and p-value was adjusted using Holm method.We also analyzed 487 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 from January 2020 to April 2020 in Italy, Spain, Germany, France, Sweden, UK and USA. SARS-CoV-2 reference genome was obtained from the GenBank database (NC_045512.2). Genomes alignment was performed using Muscle and Jalview software. We, then, calculated the Case Fatality Rate of SARS-CoV-2 in the Countries selected. Results: : In this study we analyse how different lockdown strategies and PCR testing capability adopted by Italy, France, Germany, Spain, Sweden, UK and USA have influenced the Case Fatality Rate and the viral mutations spread. We calculated case fatality rates by dividing the death number of a specific day by the number of patients with confirmed COVID-19 infection observed 14 days before and normalized by a ρ factor which takes into account the diagnostic PCR testing capability of each Country and the number of positive cases detected. We notice the stabilization of a clear pattern of mutations at sites nt241, nt3037, nt14408 and nt23403. A novel nonsynonymous SARS-CoV-2 mutation in the spike protein (nt24368) has been found in genomes sequenced in Sweden, which enacted a soft lockdown strategy. Conclusions: : Strict lockdown strategies together with a wide diagnostic PCR testing of the population were correlated with a relevant decline of the case fatality rate in different Countries. The emergence of specific patterns of mutations concomitant with the decline in case fatality rate needs further confirmation and their biological significance remains unclear.

9.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-318540

ABSTRACT

Background: SARS-CoV-2 is a RNA coronavirus responsible for the pandemic of the Severe Acute Respiratory Syndrome (COVID-19). RNA viruses are characterized by a high mutation rate, up to a million times higher than that of their hosts. Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA Polymerase (RdRp). Mutation rate drives viral evolution and genome variability, thereby enabling viruses to escape host immunity and to develop drug resistance. Methods. We analyzed 220 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 worldwide from December 2019 to mid-March 2020. SARS-CoV-2 reference genome was obtained from the GenBank database. Genomes alignment was performed using Clustal Omega. Mann-Whitney and Fisher-Exact tests were used to assess statistical significance.Results. We characterized 8 novel recurrent mutations of SARS-CoV-2, located at positions 1397, 2891, 14408, 17746, 17857, 18060, 23403 and 28881. Mutations in 2891, 3036, 14408, 23403 and 28881 positions are predominantly observed in Europe, whereas those located at positions 17746, 17857 and 18060 are exclusively present in North America. We noticed that the 14408 mutation, emerged for the first time in Europe in mid-February 2020, is present in the SARS-CoV-2 RdRp gene sequence. Viruses with RdRp mutation have a median of 3 point mutations [range: 2-5], otherwise they have a median of 1 mutation [range: 0-3] (p value < 0.001). Conclusions. These findings suggest that the virus is evolving and European, North American and Asian strains might coexist, each of them characterized by a different mutation pattern. The contribution of the mutated RdRp to this phenomenon needs to be investigated. To date, several drugs targeting RdRp enzymes are being employed for SARS-CoV-2 infection treatment. Some of them have a predicted binding moiety in a SARS-CoV-2 RdRp hydrophobic cleft, which is adjacent to the 14408 mutation we identified. Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. It is also important to recognize whether the presence of some mutations might correlate with different SARS-CoV-2 mortality rates.

10.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-306875

ABSTRACT

The Coronavirus disease (COVID-19) is a new viral infection caused by severe acute respiratory coronavirus 2 (SARS-CoV-2) that was initially reported in city of Wuhan, China and afterwards spread globally. Genomic analyses revealed that SARS-CoV-2 is phylogenetically related to severe acute respiratory syndrome-like (SARS-like) Pangolin and Bat coronavirus specific isolates. In this study we focused on two proteins of Sars-CoV-2 surface: Envelope protein and Membrane protein. Sequences from Sars-CoV-2 isolates and other closely related virus were collected from the GenBank through TBlastN searches. The retrieved sequences were multiply aligned with MAFFT. The Envelope protein is identical to the counterparts from Pangolin CoV MP798 isolate and Bat CoV isolates CoVZXC21, CoVZC45 and RaTG13. However, a substitution at position 69 where an Arg replace for Glu, and a deletion in position 70 corresponding to Gly or Cys in other Envelope proteins were found. The Membrane glycoprotein appears more variable with respect to the SARS CoV proteins than the Envelope: a heterogeneity at the N-terminal position, exposed to the virus surface, was found between Pangolin CoV MP798 isolate and Bat CoV isolates CoVZXC21, CoVZC45 and RaTG13. Mutations observed on Envelope protein are drastic and may have significant implications for conformational properties and possibly for protein-protein interactions. Mutations on Membrane protein may also be relevant because this protein cooperates with the Spike during the cell attachment and entry. Therefore, these mutations may influence interaction with host cells. The mutations that have been detected in these comparative studies may reflect functional peculiarities of the Sars-CoV-2 virus and may help explaining the epizootic origin the COVID-19 epidemic.

11.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-306874

ABSTRACT

The Sars-CoV-2 is the causative agent of the current coronavirus disease pandemic. To effectively fight this pathogen, it is important to understand its evolution and the mechanism of adaptation to the host. A software workflow has been utilized to scan 26,016 Sars-CoV-2 genomes available in GISAID databank to analyse the distribution and frequency of mutations in the corresponding proteomes. A filtering procedure has been applied to remove data inconsistencies and redundancies. The number of observed mutations appears proportional to protein sequence length except for ORF3a, Nucleocapsid and Nsp2 that seem to accept more mutations than expected. The most pervasive mutations of the three proteins have been reported and the most variable and conservative regions mapped onto the respective sequences. The results suggest that these proteins may have a role in the adaptation of virus to new hosts and influence its pathogenicity and replication. These considerations prompt the experimental study and characterization of the three proteins.

12.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-306652

ABSTRACT

Background: The new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first detected in Wuhan (China) in December of 2019 is responsible for the current global pandemic.Phylogenetic analysis revealed that it is similar to other betacoronaviruses, such as SARS-CoV and Middle-Eastern Respiratory Syndrome, MERS-CoV. Its genome is ∼30 kb in length and contains two large overlapping polyproteins, ORF1a and ORF1ab that encode for several structural and non-structural proteins. The non-structural protein 1 (nsp1) is arguably the most important pathogenic determinant, and previous studies on SARS-CoV indicate that it is both involved in viral replication and hampering the innate immune system response. Detailed experiments of site-specific mutagenesis and in vitro reconstitution studies determined that the mechanisms of action are mediated by i) the presence of specific amino acid residues of nsp1 and b) the interaction between the protein and the host’s small ribosomal unit. In fact, substitution of certain amino acids resulted in reduction of its negative effects. Methods: : A total of 17928 genome sequences were obtained from the GISAID database (December 2019 to July 2020) from patients infected by SARS-CoV-2 from different areas around the world. Genomes alignment was performed using MAFFT (REFF) and the nsp1 genomic regions were identified using BioEdit and verified using BLAST. Nsp1 protein of SARS-CoV-2 with and without deletion have been subsequently modelled using I-TASSER. Results: We identified SARS-CoV-2 genome sequences, from several Countries, carrying a previously unknown deletion of 9 nucleotides in position 686-694, corresponding to the AA position 241-243 (KSF). This deletion was found in different geographical areas. Structural prediction modelling suggests an effect on the C-terminal tail structure. Conclusions: Modelling analysis of a newly identified deletion of 3 amino acids (KSF) of SARS-CoV-2 nsp1 suggests that this deletion could affect the structure of the C-terminal region of the protein, important for regulation of viral replication and negative effect on host’s gene expression. In addition, substitution of the two amino acids (KS) from nsp1 of SARS-CoV was previously reported to revert loss of interferon-alpha expression. The deletion that we describe indicates that SARS-CoV-2 is undergoing profound genomic changes. It is important to: i) confirm the spreading of this particular viral strain, and potentially of strains with other deletions in the nsp1 protein, both in the population of asymptomatic and pauci-symptomatic subjects, and ii) correlate these changes in nsp1 with potential decreased viral pathogenicity.

13.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-306651

ABSTRACT

Background: With the aim of providing a dynamic evaluation of the effects of basic environmental parameters on COVID-19-related death rate, we assessed the correlation between average monthly high temperatures and population density, with death/rate (monthly number of deaths/1M people) for the months of March (start of the analysis and beginning of local epidemic in most of the Western World, except in Italy where it started in February) and April 2020 (continuation of the epidemic). Different geographical areas of the Northern Hemisphere in the United States and in Europe were selected in order to provide a wide range among the different parameters. The death rates were gathered from an available dataset. As a further control, we also included latitude, as a proxy for temperature. Methods: Utilizing a publicly available dataset, we retrieved data for the months of March and April 2020 for 25 areas in Europe and in the US. We computed the monthly number of deaths/1M people of confirmed COVID-19 cases and calculated the average monthly high temperatures and population density for all these areas. We determined the correlation between number of deaths/1M people and the average monthly high temperatures, the latitude and the population density. Results: We divided our analysis in two parts: analysis of the correlation among the different variables in the month of March and subsequent analysis in the month of April. The differences were then evaluated. In the month of March there was no statistical correlation between average monthly high temperatures of the considered geographical areas and number of deaths/1M people. However, a statistically significant inverse correlation became significant in the month of April between average monthly high temperatures (p=0.0043) and latitude (p=0.0253) with number of deaths/1M people. We also observed a statistically significant correlation between population density and number of deaths/1M people both in the month of March (p=0.0297) and in the month of April (p=0.0116), when three areas extremely populated (NYC, Los Angeles and Washington DC) were included in the calculation. Once these three areas were removed, the correlation was not statistically significant (p=0.1695 in the month of March, and p=0.7076 in the month of April). Conclusions: The number of COVID-19-related deaths/1M people was essentially the same during the month of March for all the geographical areas considered, indicating essentially that the infection was circulating quite uniformly except for Lombardy, Italy, where it started earlier. Lockdown measures were implemented between the end of March and beginning of April, except for Italy which started March 9 th . We observed a strong, statistically significant inverse correlation between average monthly high temperatures with the number of deaths/1M people. We confirmed the data by analyzing the correlation with the latitude, which can be considered a proxy for high temperature. Previous studies indicated a negative effect of high climate temperatures on Sars-COV-2 spreading. Our data indicate that social distancing measure are more successful in the presence of higher average monthly temperatures in reducing COVID-19-related death rate, and a high level of population density seems to negatively impact the effect of lockdown measures.

16.
Aging Clin Exp Res ; 34(2): 475-479, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1616315

ABSTRACT

We compare the expected all-cause mortality with the observed one for different age classes during the pandemic in Lombardy, which was the epicenter of the epidemic in Italy. The first case in Italy was found in Lombardy in early 2020, and the first wave was mainly centered in Lombardy. The other three waves, in Autumn 2020, March 2021 and Summer 2021 are also characterized by a high number of cases in absolute terms. A generalized linear mixed model is introduced to model weekly mortality from 2011 to 2019, taking into account seasonal patterns and year-specific trends. Based on the 2019 year-specific conditional best linear unbiased predictions, a significant excess of mortality is estimated in 2020, leading to approximately 35000 more deaths than expected, mainly arising during the first wave. In 2021, instead, the excess mortality is not significantly different from zero, for the 85+ and 15-64 age classes, and significant reductions with respect to the 2020 estimated excess mortality are estimated for other age classes.


Subject(s)
COVID-19 , Humans , Italy/epidemiology , Linear Models , Mortality , Pandemics , SARS-CoV-2
17.
Front Public Health ; 9: 735601, 2021.
Article in English | MEDLINE | ID: covidwho-1581127

ABSTRACT

Despite the "migrants and COVID-19" topic has been neglected since felt marginal concerning other aspects of the SARS-CoV-2 pandemic, it represents a relevant public health issue in the European countries. This report describes COVID-19 containment strategies adopted in a large Italian reception center hosting recently arrived asylum-seeker migrants. Risk assessment and prevention measures adopted were described. Geo-spatial epidemiological analysis of the outbreak was reported. Significant gaps in the knowledge of self-protection measures from contagious diseases and in the perception of the pandemic risk were observed in migrants; health promotion activities, targeted to remove cultural barriers and improve behaviors appropriate to individual protection, were able to fulfill this gap. In low-resource settings, especially in closed communities, the implementation of social distancing strategies, the systematic use of individual protection devices, and active syndromic surveillance are essential tools to limit the risk of outbreaks. In the event of an outbreak, it is relevant to rapidly activate containment procedures based on systematic screening, isolation, and quarantine, taking into consideration the limits of tracing contacts within a closed community. Not being able to trace certain contacts, the geo-spatial epidemiological analysis of cases distribution could be key in the management of the outbreak. Interestingly, positive cases identified in our facility were all clinically pauci-symptomatic or asymptomatic. Dedicated strategies are needed to minimize the chance of SARS-CoV-2 transmission in a limited space such as reception centers and a vulnerable population such as migrants.


Subject(s)
COVID-19 , Transients and Migrants , Developing Countries , Europe , Humans , SARS-CoV-2
18.
Int J Environ Res Public Health ; 19(1)2021 Dec 21.
Article in English | MEDLINE | ID: covidwho-1580863

ABSTRACT

The syndemic framework proposed by the 2021-2030 World Health Organization (WHO) action plan for patient safety and the introduction of enabling technologies in health services involve a more effective interpretation of the data to understand causation. Based on the Systemic Theory, this communication proposes the "Systemic Clinical Risk Management" (SCRM) to improve the Quality of Care and Patient Safety. This is a new Clinical Risk Management model capable of developing the ability to observe and synthesize different elements in ways that lead to in-depth interventions to achieve solutions aligned with the sustainable development of health services. In order to avoid uncontrolled decision-making related to the use of enabling technologies, we devised an internal Learning Algorithm Risk Management (LARM) level based on a Bayesian approach. Moreover, according to the ethics of Job Well Done, the SCRM, instead of giving an opinion on events that have already occurred, proposes a bioethical co-working because it suggests the best way to act from a scientific point of view.


Subject(s)
COVID-19 , Bayes Theorem , Humans , Pandemics/prevention & control , Risk Management , SARS-CoV-2 , Syndemic
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