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1.
Int J Infect Dis ; 122: 444-448, 2022 Jun 18.
Article in English | MEDLINE | ID: covidwho-1895084

ABSTRACT

OBJECTIVES: Intra-host SARS-CoV-2 evolution during chronic infection in immunocompromised hosts has been suggested as being the possible trigger of the emergence of new variants. METHODS: Using a deep sequencing approach, we investigated the SARS-CoV-2 intra-host genetic evolution in a patient with HIV over a period of 109 days. RESULTS: Sequencing of nasopharyngeal swabs at three time points demonstrated dynamic changes in the viral population, with the emergence of 26 amino acid mutations and two deletions, 57% of them in the Spike protein. Such a combination of mutations has never been observed in other SARS-CoV-2 lineages detected so far. CONCLUSION: Our data confirm that persistent infection in certain immunocompromised individuals for a long time may favor the dangerous emergence of new SARS-CoV-2 variants with immune evasion properties.

2.
SSRN;
Preprint in English | SSRN | ID: ppcovidwho-326281

ABSTRACT

Background: The omicron variant has spread globally at unprecedented speed due to a combination of epidemiological and virological factors that still need to be fully unraveled. Although boosting of immunity in vaccinated populations has proven to increase the antibody recognition for this variant, we still ignore the impact that this intervention has on protection from infection and disease. Methods: Relying on a live virus neutralization assay and a commercial chemiluminescence immunoassay targeting antibodies against the receptor binding domain (RBD) of the parental Spike protein, we tested the efficacy of homologous and heterologous booster vaccinations in inducing antibodies against SARS-CoV-2 parental, delta, beta and omicron variants by history of SARS-CoV-2 infection and age of population. Booster vaccination was performed with the BNT126b2 vaccine, while individuals who underwent heterologous booster vaccination were primed with the ChAdOx1 nCov-19 vaccine. Moreover, we studied the impact that prior immunity has on vaccination, in mildly infected individuals who received 2-3 doses of the BNT1262b vaccine at different times after infection. Children previously infected with delta were evaluated 3·5 months after infection. To translate neutralization data into estimates of protection, we relied on published predictive models and inferred variant-specific thresholds of protection for both assays and assessed the accuracy of the commercial assay at identifying highly protected individuals. Findings: We confirm that boosting significantly restores the ability of antibodies to recognize omicron and other variants, and that the homologous protocol with the BNT126b2 vaccine achieves higher and more broadly reactive neutralizing antibody titers, than those observed among individuals who crossed-over vaccines. On the other hand, mild prior infection with the parental virus and subsequent homologous vaccination with BNT126b2 induces high antibody levels, but with moderate breadth of response, while children aged 5-11 show negligible neutralizing antibodies against the omicron variant few months from infection. Neutralizing and binding antibodies correlate across all variants and allow the identification of variant-specific anti-RBD thresholds for 90% protection efficacy. Interpretation: Boosting with the BNT126b2 vaccine is an immediate and effective measure to increase the protection against omicron, in naïve, as well as in previously infected individuals. Identification through serological commercial assays of thresholds of protection against the omicron and delta variants is a crucial step towards large-scale serosurveys to finely assess infection risk both at population and individual level.

3.
Microorganisms ; 9(11)2021 Oct 20.
Article in English | MEDLINE | ID: covidwho-1534189

ABSTRACT

The increasing involvement of wild waterfowl in H5 Highly Pathogenic Avian Influenza Virus (HPAIV) circulation continues to pose a threat to animal and public health worldwide. In winter 2020-2021, two field surveillance activities were carried out on a weekly basis, through virological and serological analyses, in 823 hunted and 521 trapped migratory aquatic birds in northeast Italy. Sixty Eurasian teals were recaptured several times, which allowed us to follow the progression of the HPAI H5 infection in naturally infected wild waterfowl. Oropharyngeal, cloacal, and feather swabs (OS, CS and FS) were collected from each duck and tested by real time rRT-PCR Type A influenza. The identified viruses were characterized and pathotyped by sequencing. Several viruses belonging to three different HPAI H5 subtypes were detected: H5N8, H5N5, and H5N1. High prevalence of infection with HPAI H5 clade 2.3.4.4b during November-December 2020 (up to 27.1%) was observed in captured Eurasian teals, while infection rates in hunted dabbling ducks, mainly Eurasian wigeons, showed the highest prevalence of infection in November 2020 (8.9%) and January 2021 (10.2%). All HPAI positive birds were also clinically healthy when recaptured weeks apart. The OS and FS showed the highest detection efficiency of HPAIV. Our results highlight that HPAI passive surveillance should be complemented by a targeted active surveillance to more efficiently detect novel HPAI viruses.

5.
Microorganisms ; 9(8)2021 Aug 14.
Article in English | MEDLINE | ID: covidwho-1355014

ABSTRACT

SARS-CoV-2 infection was monitored in 1898 health care workers (HCWs) after receiving full vaccination with BNT162b2. Untill 30 June 2021, 10 HCWs tested positive for SARS-CoV-2 using real time RT-PCR, resulting in a 4-month cumulative incidence of 0.005%. The infection was mildly symptomatic in six (60%) and asymptomatic in four (40%) individuals. Among the infected HCWs, eight consenting individuals provided paired NPS and saliva during the course of infection, for the purpose of the analysis performed in the present study. Genomic and subgenomic viral RNAs were investigated using real-time RT-PCR in both biological specimens. The temporal profile of viral load was measured using ddPCR. Viral mutations were also analysed. Subgenomic viral RNA was detected in 8/8 (100%) NPS and in 6/8 (75%) saliva specimens at the baseline. The expression of subgenomic RNA was observed for up to 7 days in 3/8 (38%) symptomatic cases. Moreover, concordance was observed between NPS and saliva in the detection of viral mutations, and both N501Y and 69/70del (associated with the B.1.1.7 variant) were detected in the majority 6/8 (75%) of subjects, while the K417T mutation (associated with the P.1-type variants) was detected in 2/8 (25%) individuals. Overall, our findings report a low frequency of infected HCWs after full vaccination. It is, therefore, important to monitor the vaccinees in order to identify asymptomatic infected individuals. Saliva can be a surrogate for SARS-CoV-2 surveillance, particularly in social settings such as hospitals.

6.
Eur J Epidemiol ; 36(7): 685-707, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1326830

ABSTRACT

Coronavirus disease (COVID-19) is a respiratory disease affecting many people and able to be transmitted through direct and perhaps indirect contact. Direct contact transmission, mediated by aerosols or droplets, is widely demonstrated, whereas indirect transmission is only supported by collateral evidence such as virus persistence on inanimate surfaces and data from other similar viruses. The present systematic review aims to estimate SARS-CoV-2 prevalence on inanimate surfaces, identifying risk levels according to surface characteristics. Data were obtained from studies in published papers collected from two databases (PubMed and Embase) with the last search on 1 September 2020. Included studies had to be papers in English, had to deal with coronavirus and had to consider inanimate surfaces in real settings. Studies were coded according to our assessment of the risk that the investigated surfaces could be contaminated by SARS-CoV-2. A meta-analysis and a metaregression were carried out to quantify virus RNA prevalence and to identify important factors driving differences among studies. Thirty-nine out of forty retrieved paper reported studies carried out in healthcare settings on the prevalence of virus RNA, five studies carry out also analyses through cell culture and six tested the viability of isolated viruses. Overall prevalences of SARS-CoV-2 RNA on high-, medium- and low-risk surfaces were 0.22 (CI95 [0.152-0.296]), 0.04 (CI95 [0.007-0.090]), and 0.00 (CI95 [0.00-0.019]), respectively. The duration surfaces were exposed to virus sources (patients) was the main factor explaining differences in prevalence.


Subject(s)
COVID-19 , Equipment Contamination , Fomites/virology , RNA, Viral/isolation & purification , SARS-CoV-2/isolation & purification , Humans , Microbial Viability , Prevalence
7.
Pediatrics ; 148(3)2021 09.
Article in English | MEDLINE | ID: covidwho-1280670

ABSTRACT

BACKGROUND: Recent evidence suggests that neutralizing antibodies (nAbs) to severe acute respiratory syndrome coronavirus 2 may persist over time; however, knowledge regarding pediatric subjects is limited. METHODS: A single-center, prospective observational study was conducted on 57 family clusters of coronavirus disease 2019, including children of neonatal and pediatric age attending the University Hospital of Padua (Italy). For each patient, blood samples were collected for both the quantification of nAbs through a plaque reduction neutralizing test and the detection of antinucleocapsid-spike protein immunoglobulin G and/or immunoglobulin M. RESULTS: We analyzed 283 blood samples collected from 152 confirmed coronavirus disease 2019 cases (82 parents and 70 children or older siblings of median age of 8 years, interquartile range: 4-13), presenting asymptomatic or with mildly symptomatic disease. Despite the decrease of immunoglobulin G over time, nAbs were found to persist up to 7 to 8 months in children, whereas adults recorded a modest declining trend. Interestingly, children aged <6 years, and, in particular, those aged <3 years, developed higher long-lasting levels of nAbs compared with older siblings and/or adults. CONCLUSIONS: Mild and asymptomatic severe acute respiratory syndrome coronavirus 2 infections in family clusters elicited higher nAbs among children.


Subject(s)
Antibodies, Neutralizing/blood , Antibodies, Viral/blood , COVID-19/blood , SARS-CoV-2/immunology , Adolescent , Adult , Age Factors , COVID-19/immunology , COVID-19 Serological Testing , Child , Child, Preschool , Cluster Analysis , Data Collection , Humans , Immunoglobulin G/blood , Immunoglobulin M/blood , Infant , Infant, Newborn , Italy , Neutralization Tests , Prospective Studies , Symptom Assessment , Time Factors
8.
Animals (Basel) ; 11(6)2021 Jun 01.
Article in English | MEDLINE | ID: covidwho-1256417

ABSTRACT

Despite the reported increase in SARS-CoV-2-infected pets, the description of the clinical features from natural infection and the medical follow up in symptomatic pets is still not sufficiently documented. This study reports the case of an indoor cat that displayed respiratory signs and a gastrointestinal syndrome, following the COVID-19 diagnosis of his owners. Thoracic radiographies were suggestive of bronchial pneumonia, while blood tests were indicative of a mild inflammatory process. Nasal and oropharyngeal swabs tested positive through RT-qPCR assays targeting SARS-CoV-2 genes 14 days after his owners tested positive for the virus. Nasal swabs persisted to be RT-qPCR positive after 31 days. Serology confirmed the presence of antibodies through ELISA, electrochemiluminescence analysis and plaque reduction neutralization test, recording a high antibody titre after 31 days. The cat improved after medical treatment and clinically recovered. This study suggests that exposure to SARS-CoV-2 could lead to a natural infection with bronchial pneumonia in cats along with a possible prolonged persistence of SARS-CoV-2 RNA in the upper airways, albeit at a low level. The cat developed neutralizing antibodies, reaching a high titre after 31 days. Further descriptions of SARS-CoV-2 naturally infected pets, their medical management and diagnostic findings would be useful to enhance knowledge about COVID-19 in susceptible animals.

9.
Infection ; 49(6): 1341-1345, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1174038

ABSTRACT

PURPOSE: We report on the first identified cluster of the B.1.1.7 variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in the northeast of Italy. METHODS: The cluster was recognized in January 2021 with an epidemiological started from the hospitalization of a 68-year-old man suffering from coronavirus disease 2019 (COVID-19) related pneumonia and we surprisingly found three families involved in the same cluster. RESULTS: We retrospectively rebuilt the pathway of infection and performed a virological analysis. CONCLUSION: This allow us to make clear the very high attack rate and the great infective capacity of this B.1.1.7 variant of SARS-CoV-2.


Subject(s)
COVID-19 , SARS-CoV-2 , Aged , Humans , Italy/epidemiology , Male , Retrospective Studies
10.
Sci Total Environ ; 778: 146191, 2021 Jul 15.
Article in English | MEDLINE | ID: covidwho-1117651

ABSTRACT

The current pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led people to implement preventive measures, including surface disinfection and use of alcohol-based hand gel, in order to avoid viral transmission via fomites. However, the role of surface transmission is still debated. The present systematic review aims to summarize all the evidence on surface survival of coronaviruses infecting humans. The analysis of 18 studies showed the longest coronavirus survival time is 28 days at room temperature (RT) on different surfaces: polymer banknotes, vinyl, steel, glass, and paper banknotes. Concerning SARS-CoV-2 human infection from contaminated surfaces, dangerous viral load on surfaces for up to 21 days was determined on polymer banknotes, steel, glass and paper banknotes. For viruses other than SARS-CoV-2, the longest period of survival was 14 days, recorded on glass. Environmental conditions can affect virus survival, and indeed, low temperatures and low humidity support prolonged survival of viruses on contaminated surfaces independently of surface type. Furthermore, it has been shown that exposure to sunlight significantly reduces the risk of surface transmission. Although studies are increasingly investigating the topic of coronavirus survival, it is difficult to compare them, given the methodology differences. For this reason, it is advisable to define a reference working protocol for virus survival trials, but, as an immediate measure, there is also a need for further investigations of coronavirus survival on surfaces.


Subject(s)
COVID-19 , Fomites , Humans , Humidity , Pandemics , SARS-CoV-2
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