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Recombination is the main contributor to RNA virus evolution, and SARS-CoV-2 during the pandemic produced several recombinants. The most recent SARS-CoV-2 recombinant is the lineage labeled XBB, also known as Gryphon, which arose from BJ.1 and BM. 1.1.1. Here we performed a genome-based survey aimed to compare the new recombinant with its parental lineages that never became dominant. Genetic analyses indicated that the recombinant XBB and its first descendant XBB.1 show an evolutionary condition typical of an evolutionary blind background with no further epidemiologically relevant descendant. Genetic variability and expansion capabilities are slightly higher than parental lineages. Bayesian Skyline Plot indicates that XBB reached its plateau around October 6, 2022 and after an initial rapid growth the viral population size did not further expand, and around November 10, 2022 its levels of genetic variability decreased. Simultaneously with the reduction of the XBB population size, an increase of the genetic variability of its first sub-lineage XBB.1 occurred, that in turn reached the plateau around November 9, 2022 showing a kind of vicariance with its direct progenitors. Structure analysis indicates that the affinity for ACE2 surface in XBB/XBB.1 RBDs is weaker than for BA.2 RBD. In conclusion, nowadays XBB and XBB.1 do not show evidence about a particular danger or high expansion capability. Genome-based monitoring must continue uninterrupted in order to individuate if further mutations can make XBB more dangerous or generate new subvariants with different expansion capability.

PubMed, Scopus, and ISI Web of Knowledge databases were searched to identify studies published up to December 2020 on the involvement of urinary and male genital systems in COVID-19. Sixteen studies involving a total of 575 patients (538 males and 37 females) were included in this systematic review. The COVID-19 phase was available for 479 patients: 426 in the acute and 53 in the recovery phase. De novo lower urinary tract symptoms (LUTS) were observed in 43 patients and deterioration of preexisting LUTS in 7. Bladder hemorrhage was observed in 3 patients and acute urinary retention in one. Regarding male genital system, scrotal discomfort was observed in 8 patients, swelling in 14, pain in 16, and erythema in one; low flow priapism was observed in 2 patients. Ultrasound examination identified acute orchitis in 10 patients, acute epididymitis in 7, and acute epididymo-orchitis in 16. A case-control study reported that patients with moderate COVID-19 show a significant reduction in sperm concertation, total number of sperms per ejaculate, progressive motility, and complete motility. Contrary to what known from the first studies on the subject, this review also including subsequent studies give evidence of an involvement of lower urinary tract and male genital system in COVID-19. This article is protected by copyright. All rights reserved.

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.

In December 2020, Italy experienced the first case of severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) B.1.1.7 lineage. In January 2021, we identified 21 cases of this variant in Corzano, defining the first outbreak of SARS‐CoV‐2 B.1.1.7 lineage in Italy. The high transmissibility of the B.1.1.7 variant represented an important benefit for the virus, which became rapidly dominant on the territory. Containment measures induced the epidemic curve onto a decreasing trajectory underlining the importance of appropriate control and surveillance for restraint of virus spread. Highlights The first Italian outbreak of SARS‐CoV‐2 B.1.1.7 lineage occurred in Lombardy in January 2021. The outbreak originated by a single introduction of the B.1.1.7 lineage. The genomic sequencing revealed, for the first time, the presence of the V551F mutation in the B.1.1.7 lineage in Italy. Surveillance, prompt sequencing and tracing efforts were fundamental to identify and to quickly contain the outbreak.

Early detection and prompt response are crucial measures to prevent and control outbreaks. Public health agencies, therefore, designed the Communicable Disease Surveillance System (CDSS) to obtain essential data instantaneously to be used for appropriate action. However, a periodic evaluation of CDSS is indispensable to ensure the functionality of the system. For this reason, this study aims to assess the performance of the core and support functions of the CDSS in the Kurdistan Region of Iraq. A descriptive cross-sectional study was used. From a total of 291 health facilities HFs (Primary health care centers and Hospitals) in the Kurdistan region of Iraq that have surveillance activities, 74 HFs were selected using a random stratified sampling approach. The World Health Organization (WHO) generic questionnaire has been used to interview the surveillance staff, together with direct collection of the data. Our analysis shows a lack of surveillance guiding manual in the HFs. Even at the district level, where a surveillance manual existed, case definitions, thresholds, and control measures were still missing. To note, more than 93% of HFs had organized and comprehensive patients registers for the collection of their clinical and secondary data. Also, all HFs had functioning laboratories. The majority of them (almost 93%) were equipped to collect, process, and store blood, stool, and urine specimens. About 72% of these laboratories were also able to transport timely the specimens to more specialized laboratories. At all levels, data reporting to the higher level exceeded the recommended minimum rate of 80%. The reporting system at the district level was based on emails, while in the periphery on hand-delivered in paper-based formats (50%), telephone (22%), and social media (22%). Furthermore, our analysis highlights the lack of data analysis: only 3.8% of Primary Health Care Centers conduct simple data analysis regularly, while hospitals do not do any sort of analysis. Also, only a few HFs investigated an outbreak, though using system routine sources to capture these public health events. Our findings show a lack in epidemic preparedness (3%), in feedback (53%), in standard guidelines, training, supervision, and resource allocations in HFs (0%). Taken together, our data show the importance of strengthening the CDSS in the Kurdistan region of Iraq, by reinforcing the surveillance system with continuous feedback, supervision, well-trained and motivated staff, technical support, and coordination between researchers and physicians.

While the number of detected Monkeypox infections are widely available, an understanding of the extent of undetected cases is urgently needed for an effective tackling of its spread. The aim of this study is to estimate the true number of Monkeypox (detected and undetected) infections in most affected countries. The question being asked is: How many cases have actually occurred? We propose a lower bound estimator for the true number of Monkeypox cases. The estimator is data-driven and can be easily computed from the cumulative distributions of weekly cases. We focused on the ratio of the total estimated cases to the observed cases on July 31, 2022: The proportion of undetected cases was relevant in all countries, with countries whose estimated true number of infections could be more than three times the observed one. We provided a practical contribution to the understanding of the current Monkeypox wave and reliable estimates on how many undetected cases are going around in several countries, where the epidemic spreads differently.

The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019‐nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many initial patients were exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019‐nCoV sequence. Results obtained from our analyses suggest that the 2019‐nCoV may appear to be a recombinant virus between the bat coronavirus and an origin‐unknown coronavirus. The recombination may occurred within the viral spike glycoprotein, which recognizes a cell surface receptor. Additionally, our findings suggest that 2019‐nCoV has most similar genetic information with bat coronovirus and most similar codon usage bias with snake. Taken together, our results suggest that homologous recombination may occur and contribute to the 2019‐nCoV cross‐species transmission., Research Highlights Taken together, our results suggest that homologous recombination may occur and contribute to the 2019‐nCoV cross‐species transmission.

The role of viruses in community acquired pneumonia (CAP) has been largely underestimated in the pre‐coronavirus disease 2019 age. However, during flu seasonal early identification of viral infection in CAP is crucial to guide treatment and in‐hospital management. Though recommended, the routine use of nasopharyngeal swab (NPS) to detect viral infection has been poorly scaled‐up, especially in the emergency department (ED). This study sought to assess the prevalence and associated clinical outcomes of viral infections in patients with CAP during peak flu season. In this retrospective, observational study adults presenting at the ED of our hospital (Rome, Italy) with CAP from January 15th to February 22th, 2019 were enrolled. Each patient was tested on admission with Influenza rapid test and real time multiplex assay. Seventy five consecutive patients were enrolled. 30.7% (n = 23) tested positive for viral infection. Of these, 52.1% (n = 12) were H1N1/FluA. 10 patients had multiple virus co‐infections. CAP with viral infection did not differ for any demographic, clinic and laboratory features by the exception of CCI and CURB‐65. All intra‐ED deaths and mechanical ventilations were recorded among CAP with viral infection. Testing only patients with CURB‐65 score ≥2, 10 out of 12 cases of H1N1/FluA would have been detected saving up to 40% tests. Viral infection occurred in one‐third of CAP during flu seasonal peak 2019. Since not otherwise distinguishable, NPS is so far the only reliable mean to identify CAP with viral infection. Testing only patients with moderate/severe CAP significantly minimize the number of tests., Highlights This study stresses the incidence of viral pneumonia during the flu season and underlies the role of viral infection screening at the ED regardless of the current COVID‐19 pandemic.

The worldwide spread of severe acute respiratory syndrome cor-onavirus 2 (SARS-CoV-2), the novel human pathogen, first detectedin China quickly became a global health emergency, culminating withthe World Health Organization publicly proclaiming the SARS-CoV-2 outbreak as a pandemic (11 March 2020). SARS-CoV-2 is an enveloped +single-stranded RNAvirus, belonging to the Betacoronavirus genus, which includes twoother RNA viruses that have caused recent important epidemics:SARS caused by SARS-CoV and the Middle East respiratory syndrome (MERS) caused by MERS-CoV. Viral fitness of RNA viruses is influenced by their very high fre-quency of mutation, which, in turn, can affect infection speed andevolution rate.However, the resulting genetic variability needs to bebalanced between the maintenance of genetic information integrity andsurvival within the host.68The viral genome mutagenic process isdepended on sever al factors, including viral enzymes responsible fornucleic acids replication, which may have few or no proofreading and/orpostreplicative nucleic acid repair capability. Several reports result show that SARSCoV2 is rapidly movingacross countries, and new mutation hotspots are emerging in differentparts of the genome.Such variability indeed has implications forcontrol of the pandemic and potential emergence of viral strains withdifferent characteristics, including increased or reduced infectivity and lethality.

Last December 2019, a new virus, named novel Coronavirus (COVID‐2019) causing many cases of severe pneumonia was reported in Wuhan, China. The virus knowledge is limited and especially about COVID‐2019 pathogenesis. The Open Reading Frame 1ab (ORF1ab) of COVID‐2019 has been analyzed to evidence the presence of mutation caused by selective pressure on the virus. For selective pressure analysis fast‐unconstrained Bayesian approximation (FUBAR) was used. Homology modelling has been performed by SwissModel and HHPred servers. The presence of transmembrane helical segments in Coronavirus ORF1ab non structural protein 2 (nsp2) and nsp3 was tested by TMHMM, MEMSAT, and MEMPACK tools. Three‐dimensional structures have been analyzed and displayed using PyMOL. FUBAR analysis revealed the presence of potential sites under positive selective pressure (P, Highlights Analysis of selective pressure on COVID‐19 ORF1ab has been analyzed.Aminoacid position 501, 723 and 1010 have changed than SARs virus and Bat‐SARS‐like coronaviirus.Stabilizing mutation at nsp2 protein could explain why COVID‐19 is more contagious than SARS.Destabilizing mutaion of nsp3 protein could explain the difference oberved between SARS and COVID‐19.

A novel Coronavirus, 2019-nCoV, has been identified as the causal pathogen of an ongoing epidemic, with the first cases reported in Wuhan, China, last December 2019, and has since spread to other countries worldwide, included Europe and very recently Italy. In this short report, phylogenetic reconstruction was used to better understand the transmission dynamics of the virus from its first introduction in China focusing on the more recent evidence of infection in a couple of Chinese tourists arrived in Italy on 23rd January 2020 and labeled as Coronavirus Italian cases. A maximum clade credibility tree has been built using a dataset of 54 genome sequences of 2019-nCoV plus two closely related bat strains (SARS-like CoV) available in GenBank. Bayesian time-scaled phylogenetic analysis was implemented in BEAST 1.10.4. The Bayesian phylogenetic reconstruction showed that 2019-2020 nCoV firstly introduced in Wuhan on 25 November 2019, started epidemic transmission reaching many countries worldwide, including Europe and Italy where the two strains isolated dated back 19 January 2020, the same that the Chinese tourists arrived in Italy. Strains isolated outside China were intermixed with strains isolated in China as evidence of likely imported cases in Rome, Italy, and Europe, as well. In conclusion, this report suggests that further spread of 2019-nCoV epidemic was supported by human mobility and that quarantine of suspected or diagnosed cases is useful to prevent further transmission. Viral genome phylogenetic analysis represents a useful tool for the evaluation of transmission dynamics and preventive action.

Hepatitis B virus (HBV) infection represents the most common cause of chronic liver diseases worldwide. Consequently, to the introduction of the universal HBV vaccination program, the prevalence of hepatitis B surface antigen was markedly reduced and less than 1% of the population of Western Europe and North America is chronically infected. To date, despite great advances in therapeutics, HBV chronic infection is considered an incurable disease. Ten hepatitis B virus genotypes (A-J) and several subgenotypes have been identified so far, based on intergroup divergences of 8% and 4%, respectively, in the complete viral genome. HBV-D genotype has been found throughout the world, with highest prevalence in the Mediterranean area. In the present review, several articles concerning HBV epidemiology, and phylogeny in Italy have been analyzed, mainly focusing on the changes occurred in the last decade.