Global epidemiology of Zika and Chikungunya virus human infections

Zika virus was discovered in 1947. The first reported case of Zika fever was in a sentinel rhesus monkey in Uganda in 1947, while the first human cases were reported in Nigeria in 1954. Since the first evidence of human infection, Zika was active in several countries in Africa and Asia, as sporadic cases and serological evidence of Zika human infections have been demonstrated in several reports. The outbreak of Zika in Yap Island in 2007 is considered the first emergency of this infection. Since then Zika has spread worldwide with a large ongoing epidemic in South and Central America. A huge concern nowadays is about the relationship between Zika infection and microcephaly and about the sexual transmission of the virus. The first identified outbreak of Chikungunya human infection, with an incidence estimated at 23%, was reported from July 1952 to March 1953 in the Southern Province of the current Tanzania. Since then Chikungunya circulated mainly in continental Africa with limited outbreaks. The virus started to spread east bound involving most of the areas surroundings the Indian Ocean. In 2004/2005 a large outbreak developed in La Reunion a French territory in the Indian Ocean: from this point Chikungunya spread to India and from there, due a viraemic traveller returning from Kerala, to Italy where in the summer of 2007 the first outbreak with local viral transmission in a temperate climate zone occurred. In the following years Chikungunya moved to the Caribbean and South America. Recently also the USA experienced the spread of this virus and a limited outbreak based again on local spreading occurred in the French Department of Var, in August 2017

Molecular Approach for the Laboratory Diagnosis of Periprosthetic Joint Infections

The incidence of total joint arthroplasty is increasing over time since the last decade and expected to be more than 4 million by 2030. As a consequence, the detection of infections associated with surgical interventions is increasing and prosthetic joint infections are representing both a clinically and economically challenging problem. Many pathogens, from bacteria to fungi, elicit the immune system response and produce a polymeric matrix, the biofilm, that serves as their protection. In the last years, the implementation of diagnostic methodologies reduced the error rate and the turn-around time: polymerase chain reaction, targeted or broad-spectrum, and next-generation sequencing have been introduced and they represent a robust approach nowadays that frees laboratories from the unique approach based on culture-based techniques

Viral Population Heterogeneity and Fluctuating Mutational Pattern during a Persistent SARS‐CoV‐2 Infection in an Immunocompromised Patient

Literature offers plenty of cases of immunocompromised patients, who develop chronic and severe SARS‐CoV‐2 infections. The aim of this study is to provide further insight into SARS-CoV‐2 evolutionary dynamic taking into exam a subject suffering from follicular lymphoma, who developed a persistent infection for over 7 months. Eight nasopharyngeal swabs were obtained, and were analyses by qRT‐PCR for diagnostic purposes. All of them were considered eligible (Ct < 30) for NGS sequencing. Sequence analysis showed that all sequences matched the B.1.617.2 AY.122 lineage, but they differed by few mutations identifying three genetically similar subpopulations, which evolved during the course of infection, demonstrating that prolonged replication is paralleled with intra‐host virus evolution. These evidences support the hypothesis that SARS‐CoV‐2 adaptive capacities are able to shape a heterogeneous viral population in the context of immunocompromised patients. Spill‐over of viral variants with enhanced transmissibility or immune escape capacities from these subjects is plausible

SARS-CoV-2 coinfection in immunocompromised host leads to the generation of recombinant strain

Objectives: Recombination related to coinfection is a huge driving force in determining the virus genetic variability, particularly in conditions of partial immune control, leading to prolonged infection. Here, we characterized a distinctive mutational pattern, highly suggestive of Delta-Omicron double infection, in a lymphoma patient. Methods: The specimen was characterized through a combined approach, analyzing the results of deep sequencing in primary sample, viral culture, and plaque assay. Results: Bioinformatic analysis on the sequences deriving from the primary sample supports the hypothesis of a double viral population within the host. Plaque assay on viral culture led to the isolation of a recombinant strain deriving from Delta and Omicron lineages, named XS, which virtually replaced its parent lineages within a single viral propagation. Conclusion: It is impossible to establish whether the recombination event happened within the host or in vitro; however, it is important to monitor co-infections, especially in the exceptional intrahost environment of patients who are immunocompromised, as strong driving forces of viral evolution

Omicron Sub-Lineage BA.5 and Recombinant XBB Evasion from Antibody Neutralisation in BNT162b2 Vaccine Recipients

The recent emergence of a number of new SARS-CoV-2 variants resulting from recombination between two distinct parental lineages or sub-lineages within the same lineage has sparked the debate regarding potential enhanced viral infectivity and immune escape. Among these, XBB, recombinant of BA.2.10 and BA.2.75, has caused major concern in some countries due to its rapid increase in prevalence. In this study, we tested XBB escape capacity from mRNA-vaccine-induced (BNT162b2) neutralising antibodies compared to B.1 ancestral lineage and another co-circulating variant (B.1.1.529 BA.5) by analysing sera collected 30 days after the second dose in 92 healthcare workers. Our data highlighted an enhanced and statistically significant immune escape ability of the XBB recombinant. Although these are preliminary results, this study highlights the importance of immune escape monitoring of new and forthcoming variants and of the reformulation of existing vaccines

Mutational induction in SARS-CoV-2 major lineages by experimental exposure to neutralising sera

Abstract The ongoing evolution of SARS-CoV-2 and the emergence of new viral variants bearing specific escape mutations responsible for immune evasion from antibody neutralisation has required a more accurate characterisation of the immune response as one of the evolutive forces behind viral adaptation to a largely immunised human population. In this work, culturing in the presence of neutralising sera vigorously promoted mutagenesis leading to the acquisition of known escape mutations on the spike as well as new presumptive escape mutations on structural proteins whose role as target of the neutralizing antibody response might have been thus far widely neglected. From this perspective, this study, in addition to tracing the past evolution of the species back to interactions with neutralising antibody immune response, also offers a glimpse into future evolutive scenarios

Evaluation of STANDARDTM M10 SARS-CoV-2, a Novel Cartridge-Based Real-Time PCR Assay for the Rapid Identification of Severe Acute Respiratory Syndrome Coronavirus 2

Since the beginning of the pandemic, SARS-CoV-2 has caused problems for all of world’s population, not only in terms of deaths but also in terms of overloading healthcare facilities in all countries. Diagnosis is one of the key aspects of controlling the spread of SARS-CoV-2, and among the current molecular techniques, real-time PCR is considered as the gold standard. The availability of tests that allow for the rapid and accurate identification of SARS-CoV-2 is therefore of considerable importance. Moreover, if these tests allow for even minimal intervention by the operator, any risk of contamination is reduced. In this study, the performances of the new STANDARDTM M10 SARS-CoV-2 (SD Biosensor Inc., Suwon, Korea) rapid molecular test, which incorporates the above-mentioned features, were characterized. The clinical and analytical performances measured by testing different variants circulating in Italy of STANDARDTM M10 SARS-CoV-2 were compared to the test already on the market and recognized as the gold standard: Xpert Xpress SARS-CoV-2 (Cepheid, Sunnyvale, CA, USA). The results obtained between the two tests are largely comparable, suggesting that STANDARDTM M10 SARS-CoV-2 can be used with excellent results in the fight against the global spread of SARS-CoV-2

Genomic and Temporal Analysis of Deletions Correlated to qRT-PCR Dropout in N Gene in Alpha, Delta and Omicron Variants

Since the first SARS-CoV-2 outbreak, mutations such as single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) have changed and characterized the viral genome sequence, structure and protein folding leading to the onset of new variants. The presence of those alterations challenges not only the clinical field but also the diagnostic demand due to failures in gene detection or incompleteness of polymerase chain reaction (PCR) results. In particular, the analysis of understudied genes such as N and the investigation through whole-genome next generation sequencing (WG-NGS) of regions more prone to mutate can help in the identification of new or reacquired mutations, with the aim of designing robust and long-lasting primers. In 48 samples of SARS-CoV-2 (including Alpha, Delta and Omicron variants), a lack of N gene amplification was observed in the genomes analyzed through WG-NGS. Three gene regions were detected hosting the highest number of SNPs and INDELs. In several cases, the latter can interfere deeply with both the sensitivity of diagnostic methodologies and the final protein folding. The monitoring over time of the viral evolution and the reacquisition among different variants of the same mutations or different alterations within the same genomic positions can be relevant to avoid unnecessary consumption of resources

Trend of microbiologically-confirmed tuberculosis in a low-incidence setting with high immigration rates

BACKGROUND: The metropolitan area of Bologna, a city in Northern Italy (Emilia Romagna region), is considered a low incidence setting for TB, but has a high rate of foreign immigration (13.5% official resident immigrants relative to the whole population in 2011). The aim of this study was to describe the epidemiological trend of TB, focusing on differences between Italian and foreign-born cases. METHODS: We examined all bacteriologically confirmed TB cases identified in the Microbiology Unit of Bologna University Hospital from January 2008 and December 2011. We compared demographic, clinical and microbiological data for Italian vs. foreign-born TB cases. RESULTS: Out of 255 TB cases identified during the study period, 168 (65.9%) were represented by foreign-born cases. The proportion of immigrants with TB progressively increased over the study period (from 60.8% in 2008 to 67.5% in 2011). Although foreign-born cases were significantly younger than Italian cases (mean age 32.3 ± 14.4 years vs 61.9 ± 21.5 years), the mean age among the latter decreased from 71.2 in 2008 to 54.6 years in 2011 (p = 0.036). Concerning TB localization, 65.9% (n = 168) had pulmonary TB (P-TB) and 34.1% (n = 87) extra-pulmonary TB (EP-TB). In this study, 35.6% of Italian-born P-TB cases were smear positive, versus 51.4% of foreign-born P-TB cases. The highest proportion of high-grade positive microscopy P-TB was among subjects between 25–34 years old (36.9%; p = 0.004). Mono-resistance to isoniazid (mono-H) was found among 9.2% and 10.1% of Italian and foreign-born cases, respectively. Among Italian cases, resistance to H and any other first line drug (poly-H) and Multidrug resistant TB (MDR-TB) were 4.6% and 1.2%, respectively. In foreign-born cases poly-H (12.8%) and MDR-TB (6.9%) significantly increased over the time (p = 0.003 and p = 0.007, respectively). The proportion of MDR-TB was significantly higher among immigrants from Eastern Europe (10.9%) compared to Italian-born patients (p = 0.043). All (n = 9) MTB strains resistant to four or five first line drugs and Extensively drug resistant (XDR-TB) strains were from foreign-born cases. CONCLUSIONS: TB epidemiology in a low incidence setting is strongly influenced by immigration rates. Ethnicity, mean age, and incidence of MDR-TB among foreign-born cases reflect immigration trends in Northern Italy