What's Next for Flu? Out-of-Season Circulation of Influenza Viruses in Southern Italy, August 2022.

The COVID-19 pandemic has modified the seasonal pattern of respiratory infections. The objective of the present study is to characterize the out-of-season circulation of influenza viruses and an influenza outbreak that occurred in southern Italy in August 2022. Nasopharyngeal swabs collected from patients with influenza-like illnesses (ILI) were tested for the presence of influenza and other respiratory viruses. Epidemiological investigations on 85 patients involved in an influenza outbreak were performed. Sequencing and phylogenetic analysis of hemagglutinin genes was undertaken on samples positive for influenza A. In August 2022, in the Apulia region (Italy), influenza A infection was diagnosed in 19 patients, 18 infected with A/H3N2 and one with A/H1N1pdm09 virus. Seven influenza-positive patients were hospitalized with ILI. A further 17 symptomatic subjects, associated with an influenza outbreak, were also tested; 11 were positive for influenza A/H3N2 virus. Phylogenetic analysis of 12 of the A/H3N2 sequences showed that they all belonged to subclade 3C.2a1b.2a.2. The A/H1N1pdm09 strain belonged to subclade 6B.1A.5a.2. The out-of-season circulation of the influenza virus during the summer months could be linked to changing dynamics in the post-COVID-19 era, as well as to the impact of climate change. Year-round surveillance of respiratory viruses is needed to monitor this phenomenon and to provide effective prevention strategies.

Characteristics of the First 284 Patients Infected with the SARS-CoV-2 Omicron BA.2 Subvariant at a Single Center in the Apulia Region of Italy, January-March 2022.

Since its initial detection, the SARS-CoV-2 Omicron sublineage BA.2 has been spreading rapidly worldwide. The aims of this study were to describe the first 284 patients infected with the Omicron BA.2 variant of concern (VOC) in the Apulia region of southern Italy and to assess the differences in the demographic and clinical characteristics of patients infected with the SARS-CoV-2 BA.1 and BA.2 variants. The demographic characteristics of patients, as well as information about symptoms, vaccinations and hospitalizations for COVID-19, were collected. A subset of samples from patients infected with the BA.2 variant was subjected to whole-genome sequencing. The characteristics of the first 284 patients infected with Omicron BA.2 and the first 175 patients infected with Omicron BA.1 were compared. The proportion of patients infected with the BA.2 variant rapidly increased, from 0.5% during the third week of 2022 to 29.6% during the tenth week of 2022. Ten isolates (out of 34 BA.2 isolates) contain the substitutional mutation, H78K in ORF3a, and four isolates include two mutations, A2909V in ORF1a and L140F in ORDF3a. Compared with patients infected with BA.1, those infected with BA.2 were more likely to be symptomatic and booster-vaccinated, and showed a shorter time from the last dose of vaccine to infection. The high transmissibility and immune-evasive properties of Omicron BA.2, which will become the leading SARS-CoV-2 VOC, suggest that short-term public health measures should not be discontinued in Italy.

The Challenge of Using an Antigen Test as a Screening Tool for SARS-CoV-2 Infection in an Emergency Department: Experience of a Tertiary Care Hospital in Southern Italy.

BACKGROUND: In emergency hospital settings, rapid diagnosis and isolation of SARS-CoV-2 patients are required. The aim of the study was to evaluate the performance of an antigen chemiluminescence enzymatic immunoassay (CLEIA) and compare it with that of Real-time Reverse transcription-Polymerase Chain Reaction (RT-qPCR), the gold standard assay, to assess its suitability as a rapid diagnostic method for managing patients in the emergency department (ED). METHODS: Consecutive patients with no previous history of SARS-CoV-2 infection attending the ED of the Policlinico Hospital of Bari between 23rd October and 4th November 2020 were enrolled. Clinical and demographic data were collected for all patients. Nasopharyngeal swabs collected on admission were subjected both to molecular (RT-qPCR) and antigen (CLEIA) tests for SARS-CoV-2. The performance of the CLEIA antigen test was analyzed using R Studio software and Microsoft Excel. Receiver operating characteristics were also performed. RESULTS: A total of 911 patients were enrolled, of whom 469 (51.5%) were male. Of the whole cohort, 23.7% tested positive for SARS-CoV-2 by RT-qPCR and 24.5% by CLEIA. The overall concordance rate was 96.8%. The sensitivity, specificity, positive predictive value, and negative predictive value of the antigen test were 94.9% (95% CI, 91.9-97.0), 97.4% (95% CI, 96.5-98.1), 91.9% (95% CI, 89.0-94.0), and 98.4% (95% CI, 97.4-99.1), respectively. The area under the curve (AUC) was 0.99. The kappa coefficient was 0.91. The overall positive and negative likelihood ratios were 37 (95% CI 23-58) and 0.05 (95% CI, 0.03-0.09), respectively. CONCLUSIONS: Data analysis demonstrated that the antigen test showed very good accuracy for discriminating SARS-CoV-2-infected patients from negative participants. The CLEIA is suitable for rapid clinical diagnosis of patients in hospital settings, particularly in EDs with a high prevalence of symptomatic patients and where a rapid turnaround time is critical. Timely and accurate testing for SARS-CoV-2 plays a crucial role in limiting the spread of the virus.

An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021.

The SARS-CoV-2 P.1 variant of concern (VOC) was first identified in Brazil and is now spreading in European countries. It is characterized by the E484K mutation in the receptor-binding domain, which could contribute to the evasion from neutralizing antibodies. In Italy, this variant was first identified in January 2021. Here, we report an autochthonous outbreak of SARS-CoV-2 P.1 variant infections in southern Italy in subjects who had not travelled to endemic areas or outside the Apulia region. The outbreak involved seven subjects, three of whom had received a COVID-19 vaccine (one had received two doses and two had received one dose). Four patients had a mild clinical presentation. Laboratory investigations of nasopharyngeal swabs revealed that all strains were S-gene target failure-negative and molecular tests revealed they were the P.1 variant. Whole-genome sequencing confirmed that five subjects were infected with closely related strains classified as the P.1 lineage. The circulation of VOCs highlights the importance of strictly monitoring the spread of SARS-CoV-2 variants through genomic surveillance and of investigating local outbreaks. Furthermore, public health measures including social distancing, screening, and quarantine for travelers are key tools to slow down the viral transmission and to contain and mitigate the impact of VOC diffusion, and rapid scaling-up of vaccination is crucial to avoid a possible new epidemic wave.

Symptomatic SARS-CoV-2 Reinfection in a Healthy Healthcare Worker in Italy Confirmed by Whole-Genome Sequencing.

This study describes a case of SARS-CoV-2 reinfection confirmed by whole-genome sequencing in a healthy physician who had been working in a COVID-19 hospital in Italy since the beginning of the pandemic. Nasopharyngeal swabs were obtained from the patient at each presentation as part of routine surveillance. Nucleic acid amplification testing was performed on the two samples to confirm SARS-CoV-2 infection, and serological tests were used to detect SARS-CoV-2 IgG antibodies. Comparative genome analysis with whole-genome sequencing was performed on nasopharyngeal swabs collected during the two episodes of COVID-19. The first COVID-19 episode was in March 2020, and the second was in January 2021. Both SARS-CoV-2 infections presented with mild symptoms, and seroconversion for SARS-CoV-2 IgG was documented. Genomic analysis showed that the viral genome from the first infection belonged to the lineage B.1.1.74, while that from the second infection to the lineage B.1.177. Epidemiological, clinical, serological, and genomic analyses confirmed that the second episode of SARS-CoV-2 infection in the healthcare worker met the qualifications for "best evidence" for reinfection. Further studies are urgently needed to assess the frequency of such a worrisome occurrence, particularly in the light of the recent diffusion of SARS-CoV-2 variants of concern.