Prognostic Significance of NLR and PLR in COVID-19: A Multi-Cohort Validation Study.

INTRODUCTION: Recent studies have highlighted the prognostic value of easily accessible inflammatory markers, neutrophil-to-lymphocyte ratio (NLR), and platelet-to-lymphocyte ratio (PLR) for predicting severe outcomes in patients affected by Coronavirus disease 2019 (COVID-19). Our study validates NLR and PLR cut-off values from a prior cohort at IRCCS Policlinico San Matteo (OSM) of Pavia, Italy, across two new cohorts from different hospitals. This aims to enhance the generalizability of these prognostic indicators. METHODS: In this retrospective cohort study, conducted at Milan's Ospedale Luigi Sacco (OLS) and IRCCS Ospedale Maggiore Policlinico (OMP) hospitals, we assess the predictive capacity of NLR and PLR for three main outcomes-non-invasive ventilation (NIV) or continuous positive airway pressure (CPAP) usage, invasive ventilation (IV), and death-in patients with COVID-19 at admission. For each outcome, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were computed separately for male and female cohorts. Distinct NLR and PLR cut-off values were used for men (7.00, 7.29, 7.00 for NLR; 239.22, 248.00, 250.39 for PLR) and women (6.36, 7.00, 6.28 for NLR; 233.00, 246.45, 241.54 for PLR), retrieved from the first cohort at OSM. RESULTS: A total of 3599 patients were included in our study, 1842 from OLS and 1757 from OMP. OLS and OMP sensitivity values for both NLR and PLR (NLR: 24-67%, PLR: 40-64%) were inferior to specificity values (NLR: 64-76%, PLR: 55-72%). Additionally, PPVs generally remained lower (< 63%), while NPVs consistently surpassed 68% for PLR and 72% for NLR. Finally, both PLR and NLR exhibited consistently higher NPVs for more severe outcomes (> 82%) compared to NPVs for CPAP/NIV. CONCLUSIONS: Consistent findings across diverse patient populations validate the reliability and applicability of NLR and PLR cut-off values. High NPVs emphasize their role in identifying individuals less likely to experience severe outcomes. These markers not only aid in risk stratification but also guide resource allocation in emergencies or limited-resource situations.

Molecular epidemiology of canine parvovirus type 2 in Sicily, southern Italy: A geographical island, an epidemiological continuum.

Since it emerged as a major dog pathogen, canine parvovirus type 2 (CPV-2) has featured a remarkable genetic and phenotypic heterogeneity, whose biological, epidemiological, and clinical impact is still debated. The continuous monitoring of this pathogen is thus of pivotal importance. In the present study, the molecular epidemiology of CPV-2 in Sicily, southern Italy, has been updated by analysing 215 nearly complete sequences of the capsid protein VP2, obtained from rectal swabs/faeces or tissue samples collected between 2019 and 2022 from 346 dogs with suspected infectious gastrointestinal disease. The presence of the original CPV-2 type (4%) and CPV-2a (9%), CPV-2b (18%), or CPV-2c (69%) variants was documented. Over the years, we observed a decrease in the frequency of CPV-2a/-2b and a rapid increase of CPV-2c frequency, with a progressive replacement of the European lineage of CPV-2c by the Asian lineage. The observed scenario, besides confirming epidemiological relevance of CPV-2, highlights the occurrence of antigenic variant shifts over time, with a trend toward the replacement of CPV-2a, CPV-2b, and the European lineage of CPV-2c by the emerging Asian CPV-2c lineage. The comparison with other Italian and international sequences suggests the occurrence of viral exchange with other Italian regions and different countries, although the directionality of such viral flows could not be often established with confidence. In several instances, potential CPV-2 introductions led to epidemiological dead ends. However, major, long-lasting clades were also identified, supporting successful infection establishment, local spreading, and evolution. These results, besides demonstrating the need for implementing more effective control measures to prevent viral introductions and minimize circulation, stress the relevance of routine monitoring activities as the only tool to effectively understand CPV-2 epidemiology and evolution, and develop adequate countermeasures.

Differential diagnosis of fever and rash cases negative for measles and rubella to complement surveillance activities.

In the quest to eliminate measles virus (MV) and rubella virus (Ruv), every suspected case must be properly identified and diagnosed. Since 2017, in Milan (Italy), a total of 978 measles and rubella suspected cases (fever and rash) were investigated and 310 were not laboratory confirmed (discarded cases). To improve surveillance activities, we investigated the presence in discarded cases of 8 other viral pathogens commonly associated with rash: human herpesvirus 6 (HHV-6) and 7 (HHV-7), parvovirus B19 (B19V), enterovirus (EV), Epstein-Barr virus (EBV), human adenovirus (HAdV), cytomegalovirus (HCMV), and SARS-CoV-2. Differential diagnosis was carried out on 289 discarded cases by multiplex real-time PCR assays. At least one pathogen was detected in 188 cases (65.1%) with HHV-7 being the most frequently detected virus. No difference in the number of detected infections overtime was observed and infections were identified in all age groups. As expected, most HHV-6, EV, HAdV, and HCMV-positive cases were found in children aged 0-4 years and HHV-7 was most frequent in the 15-39 age group. In light of the World Health Organization measles elimination goal, the introduction of laboratory methods for differential diagnosis is required for the final classification of clinically compatible cases. The used screening panel allowed us to increase the percentage of virus-positive cases to 87.5%, allowing us to clarify viral involvement and epidemiology, improve diagnosis, and strengthen surveillance activities. As all investigated pathogens were detected, this diagnostic panel was a suitable tool to complement MV and RuV surveillance activities.

The role of immune suppression in COVID-19 hospitalization: clinical and epidemiological trends over three years of SARS-CoV-2 epidemic.

Specific immune suppression types have been associated with a greater risk of severe COVID-19 disease and death. We analyzed data from patients >17 years that were hospitalized for COVID-19 at the "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" in Milan (Lombardy, Northern Italy). The study included 1727 SARS-CoV-2-positive patients (1,131 males, median age of 65 years) hospitalized between February 2020 and November 2022. Of these, 321 (18.6%, CI: 16.8-20.4%) had at least one condition defining immune suppression. Immune suppressed subjects were more likely to have other co-morbidities (80.4% vs. 69.8%, p < 0.001) and be vaccinated (37% vs. 12.7%, p < 0.001). We evaluated the contribution of immune suppression to hospitalization during the various stages of the epidemic and investigated whether immune suppression contributed to severe outcomes and death, also considering the vaccination status of the patients. The proportion of immune suppressed patients among all hospitalizations (initially stable at <20%) started to increase around December 2021, and remained high (30-50%). This change coincided with an increase in the proportions of older patients and patients with co-morbidities and with a decrease in the proportion of patients with severe outcomes. Vaccinated patients showed a lower proportion of severe outcomes; among non-vaccinated patients, severe outcomes were more common in immune suppressed individuals. Immune suppression was a significant predictor of severe outcomes, after adjusting for age, sex, co-morbidities, period of hospitalization, and vaccination status (OR: 1.64; 95% CI: 1.23-2.19), while vaccination was a protective factor (OR: 0.31; 95% IC: 0.20-0.47). However, after November 2021, differences in disease outcomes between vaccinated and non-vaccinated groups (for both immune suppressed and immune competent subjects) disappeared. Since December 2021, the spread of the less virulent Omicron variant and an overall higher level of induced and/or natural immunity likely contributed to the observed shift in hospitalized patient characteristics. Nonetheless, vaccination against SARS-CoV-2, likely in combination with naturally acquired immunity, effectively reduced severe outcomes in both immune competent (73.9% vs. 48.2%, p < 0.001) and immune suppressed (66.4% vs. 35.2%, p < 0.001) patients, confirming previous observations about the value of the vaccine in preventing serious disease.

Not Asian Anymore: Reconstruction of the History, Evolution, and Dispersal of the "Asian" Lineage of CPV-2c.

Variability has been one of the hallmarks of canine parvovirus type 2 (CPV-2) since its discovery, and several lineages and antigenic variants have emerged. Among these, a group of viruses commonly called Asian CPV-2c has recently been reported with increasing frequency in different regions. Currently, its global epidemiology and evolution are essentially unknown. The present work deals with this information gap by evaluating, via sequence, phylodynamic, and phylogeographic analyses, all the complete coding sequences of strains classified as Asian CPV-2c based on a combination of amino acid markers and phylogenetic analysis. After its estimated origin around 2008, this lineage circulated undetected in Asia until approximately 2012, when an expansion in viral population size and geographical distribution occurred, involving Africa, Europe, and North America. Asia was predicted to be the main nucleus of viral dispersal, leading to multiple introduction events in other continents/countries, where infection establishment, persistence, and rapid evolution occurred. Although the dog is the main host, other non-canine species were also involved, demonstrating the host plasticity of this lineage. Finally, although most of the strains showed an amino acid motif considered characteristic of this lineage, several exceptions were observed, potentially due to convergent evolution or reversion phenomena.

Serological investigation of SARS-CoV-2 infection in patients with suspect measles, 2017-2022.

BACKGROUND: Several studies suggested that SARS-CoV-2 was already spreading worldwide during the last months of 2019 before the first outbreak was detected in Wuhan, China. Lombardy (Northern Italy) was the first European region with sustained SARS-CoV-2 transmission and recent investigations detected SARS-CoV-2-RNA-positive patients in Lombardy since late 2019. METHODS: We tested for anti-SARS-CoV-2 IgG all serum samples available in our laboratory (N = 235, collected between March 2017 and March 2022) that we received within the framework of measles/rubella surveillance from measles and rubella virus-negative patients. RESULTS: Thirteen of 235 samples (5.5%) were IgG-positive. The positivity rate increased starting in 2019 and was significantly different from the expected false positive rate from 2019 onwards. Additionally, in 2019 the percentage of IgG-positive patients was significantly lower among SARS-CoV-2 RNA-negative patients (3/92) compared to SARS-CoV-2 RNA-positive patients (2/7, p = 0.04). The highest percentage of IgG positivity in the pre-pandemic period was recorded during the second half of 2019. This coincided with an increase in negativity for measles and a widening of the peak of the number of measles discarded cases per 100,000 inhabitants, indicating a higher-than-normal number of measles-negative patients experiencing fever and rash. This also coincided with the first patient positive for SARS-CoV-2 RNA (September 12th, 2019); this patient was also positive for anti-SARS-CoV-2 IgG and IgM. CONCLUSIONS: Although the number of samples was low and one cannot conclusively establish that the virus started circulating in Lombardy around September 2019, our findings should stimulate similar research investigating the possibility of undetected SARS-CoV-2 pre-pandemic circulation.

Detection of human papillomavirus in fresh and dried urine through an automated system for cervical cancer screening in low- and middle-income countries.

The majority of cervical cancer cases and associated deaths occur in low- and middle-income countries (LMICs), where sociocultural barriers, poor access to prevention and care, and technical and practical difficulties hinder screening coverage improvement. Using urine specimens for human papillomaviruses (HPV) molecular screening through automated testing platforms can help to overcome these problems. We evaluated the high-risk (HR) HPV detection performance of the Xpert® HPV test on GeneXpert® System (Cepheid), on fresh and dried urine (Dried Urine Spot [DUS]) samples as compared to an in-house polymerase chain reaction (PCR) genotyping assay. Forty-five concentrated urine samples collected from women with known cytological and HPV infection status, determined through in-house PCR and genotyping assays, were tested "as is" and as DUS with the Xpert® HPV test. This system detected HR-HPV in 86.4% of fresh and in 77.3% of dried urine samples collected from HPV+ women, correctly identifying HR-HPV infection in 100% of women with low- and high-grade lesions. High concordance (91.4%, k = 0.82) was found between PCR test and Xpert® HPV Test from urine. Urine-based Xpert® HPV test seems to be a suitable screening test for detection of HR-HPV infections associated with low- and high-grade lesions requiring follow-up monitoring or treatment. This methodology, relying on noninvasively collected samples and on available rapid testing platforms, could facilitate large, at-scale screening programs, particularly in LMICs and rural areas, thus reducing adverse outcomes of HPV infection and facilitating achievement of the WHO cervical cancer elimination goal.

A large A(H3N2) influenza outbreak with a high attack rate in a drug user community in Italy, April 2022.

Despite the COVID-19 pandemic, influenza remains an important issue. Especially in community settings, influenza outbreaks can be difficult to control and can result in high attack rates. In April 2022, a large A(H3N2) influenza outbreak spread in the largest Italian drug-rehabilitation community. One hundred eighty-four individuals presented influenza-like symptoms (attack rate of 26.2%); 56% previously received the influenza vaccine. Sequence analyses highlighted a genetic drift from the vaccine strain, which may have caused the observed lack of protection.

Detection at high prevalence of newlavirus (protoparvovirus) in the carcasses of red foxes.

Wildlife conservation also relies on the study of animal virome. We identified the DNA of a novel fox protoparvovirus, newlavirus, with high (71%) prevalence in the carcasses of red foxes. On genome sequencing, high genetic diversity and possible recombination was observed, suggesting complex evolutionary dynamics in wildlife.

Distinct epidemiological profiles of porcine circovirus 3 and fox circovirus in Canadian foxes (Vulpes spp.).

Circoviruses (genus Circovirus, family Circoviridae) are ssDNA viruses that infect mammals, and they sometimes can transmit among different species. We investigated the distribution and diversity of porcine circovirus 3 (PCV-3, species Porcine circovirus 3) and fox circovirus (species Canine circovirus 1) in different populations of foxes (Vulpes spp.) inhabiting the Canadian province of Newfoundland and Labrador to compare their epidemiological profiles. Of the 210 samples tested in this study 9 were positive for PCV-3 and 99 were positive for fox circovirus. Eight foxes were PCV-3-positive (8/128, 6.3%) and the virus was only found in the most human-populated areas. The PCV-3 positivity rate was significantly higher in stool (7/180, 8.8%) than in spleen (2/120, 1.7%: p < 0.05). Phylogenetic analyses showed that sequences from different animals were unrelated to each other. Fox circovirus was identified in 66 animals (51.6%) and positivity rates were the highest in the least human-populated areas. There were no significant differences between positivity rates in stool (32/80, 40.0%), spleen (59/120, 49.2%), or lymph nodes (8/10, 80.0%). Among 54 positive animals for which both spleen and stool samples were available, 25 (46.3%) had detectable virus in both samples. All fox circovirus sequences recovered in this study formed a monophyletic clade, and no geographic segregation of study strains was observed. The high prevalence and high genetic diversity observed for fox circovirus implies that the virus has been circulating in this population for a long time. PCV-3 cases were consistent with sporadic infections from multiple sources, possibly related to scavenging behavior and consumption of meat by-products and human waste, while fox circovirus was endemic, indicating that foxes are likely the maintenance host for this virus. To the best of our knowledge this is the first study demonstrating the presence of fox circovirus in North America and to show that PCV-3 can be detected in foxes. Future studies should evaluate the pathogenic potential of these viruses for wildlife.

A novel calicivirus discovered in trumpeter swans (Cygnus buccinator) expands the richness of known avian caliciviruses.

Caliciviruses are ssRNA viruses that can infect a wide range of hosts, including birds. While several avian caliciviruses have been discovered, their taxonomy and host distribution are largely unknown. We molecularly characterized a novel calicivirus (trumpeter swan calicivirus: TruSCV) in trumpeter swans over-wintering in south-west British Columbia, Canada. The positivity rate was 20.3% (14/69) and there were no significant differences in infection rates between males (5/34, 14.7%) and females (9/35, 25.7%) or among considered age groups (juveniles: 4/14, 28.6%; sub-adults: 1/9, 11.1%; adults: 9/46, 19.6%). Twelve infected swans died of lead poisoning, one because of starvation, and one from physical injuries. TruSCV complete genome possessed the typical organization and protein motifs of caliciviruses and a type 2 IRES and its closest relative was a virus circulating in Australian ducks. Phylogenetic analyses showed the existence of 34 different but monophyletic avian caliciviruses. These viruses, while having conserved genomic organization and protein motifs, possess different IRES types and group in several divergent clades, with only two of them corresponding to currently defined genera, highlighting the need for epidemiological investigations and systematic analyses to better define their taxonomy. Follow-up studies are needed to elucidate the diversity, distribution, and pathogenic potential of TruSCV.

Identification and Molecular Characterization of a Divergent Asian-like Canine Parvovirus Type 2b (CPV-2b) Strain in Southern Italy.

Canine parvovirus type 2 (CPV-2) is an infectious agent relevant to domestic and wild carnivorans. Recent studies documented the introduction and spread of CPV-2c strains of Asian origin in the Italian canine population. We investigated tissue samples from a puppy collected during necropsy for the presence of viral enteropathogens and all samples tested positive only for CPV-2. The full coding sequence of a CPV-2b (VP2 426Asp) strain was obtained. This virus was related to CPV-2c strains of Asian origin and unrelated to European CPV-2b strains. The sequence had genetic signatures typical of Asian strains (NS1: 60Val, 545Val, 630Pro; VP2: 5Gly, 267Tyr, 324Ile) and mutations rarely reported in Asian CPV-2b strains (NS1: 588N; VP2: 370Arg). Phylogenetic analyses placed this strain in well-supported clades, including Asian CPV-2c-like strains, but always as a basal, single-sequence long branch. No recombination was observed for this strain, and we speculate that it could have originated from an Asian CPV-2c-like strain that acquired the 426Asp mutation. This study reports the first evidence of an Asian-like CPV-2b strain in Italy, confirming the occurrence of continuous changes in the global CPV-2 spread. Since positive convergent mutations complicate data interpretation, a combination of phylogenetic and mutation pattern analyses is crucial in studying the origin and evolution of CPV-2 strains.

Breakthrough Infections: A Challenge towards Measles Elimination?

Measles is one of the most contagious diseases known to man. Despite the existence of a safe and effective live attenuated vaccine, measles can appear in vaccinated individuals. Paradoxically, breakthrough cases increase as vaccination coverage in the general population rises. In measles endemic areas, breakthrough cases represent less than 10% of total infections, while in areas with high vaccination coverage these are over 10% of the total. Two different vaccination failures have been described: primary vaccination failure, which consists in the complete absence of humoral response and occurs in around 5% of vaccinated individuals; and secondary vaccination failure is due to waning immunity or incomplete immunity and occurs in 2-10% of vaccinees. Vaccination failures are generally associated with lower viral loads and milder disease (modified measles) since vaccination limits the risk of complicated disease. Vaccination failure seems to occur between six and twenty-six years after the last vaccine dose administration. This review summarizes the literature about clinical, serological, epidemiological, and molecular characteristics of measles breakthrough cases and their contribution to virus transmission. In view of the measles elimination goal, the assessment of the potential decline in antibody protection and the targeted implementation of catch-up vaccination are essential.

Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy.

As a reference laboratory for measles and rubella surveillance in Lombardy, we evaluated the association between SARS-CoV-2 infection and measles-like syndromes, providing preliminary evidence for undetected early circulation of SARS-CoV-2. Overall, 435 samples from 156 cases were investigated. RNA from oropharyngeal swabs (N = 148) and urine (N = 141) was screened with four hemi-nested PCRs and molecular evidence for SARS-CoV-2 infection was found in 13 subjects. Two of the positive patients were from the pandemic period (2/12, 16.7%, March 2020-March 2021) and 11 were from the pre-pandemic period (11/44, 25%, August 2019-February 2020). Sera (N = 146) were tested for anti-SARS-CoV-2 IgG, IgM, and IgA antibodies. Five of the RNA-positive individuals also had detectable anti-SARS-CoV-2 antibodies. No strong evidence of infection was found in samples collected between August 2018 and July 2019 from 100 patients. The earliest sample with evidence of SARS-CoV-2 RNA was from September 12, 2019, and the positive patient was also positive for anti-SARS-CoV-2 antibodies (IgG and IgM). Mutations typical of B.1 strains previously reported to have emerged in January 2020 (C3037T, C14408T, and A23403G), were identified in samples collected as early as October 2019 in Lombardy. One of these mutations (C14408T) was also identified among sequences downloaded from public databases that were obtained by others from samples collected in Brazil in November 2019. We conclude that a SARS-CoV-2 progenitor capable of producing a measles-like syndrome may have emerged in late June-late July 2019 and that viruses with mutations characterizing B.1 strain may have been spreading globally before the first Wuhan outbreak. Our findings should be complemented by high-throughput sequencing to obtain additional sequence information. We highlight the importance of retrospective surveillance studies in understanding the early dynamics of COVID-19 spread and we encourage other groups to perform retrospective investigations to seek confirmatory proofs of early SARS-CoV-2 circulation.

A Novel Iridovirus Discovered in Deep-Sea Carnivorous Sponges.

Carnivorous sponges (family Cladorhizidae) use small invertebrates as their main source of nutrients. We discovered a novel iridovirus (carnivorous sponge-associated iridovirus, CaSpA-IV) in Chondrocladia grandis and Cladorhiza oxeata specimens collected in the Arctic and Atlantic oceans at depths of 537-852 m. The sequenced viral genome (~190,000 bp) comprised 185 predicted ORFs, including those encoding 26 iridoviral core proteins, and phylogenetic analyses showed that CaSpA-IV is a close relative to members of the genus Decapodiridovirus and highly identical to a partially sequenced virus pathogenic to decapod shrimps. CaSpA-IV was found in various anatomical regions of six C. grandis (sphere, stem, root) from the Gulf of Maine and Baffin Bay and of two C. oxeata (sphere, secondary axis) from Baffin Bay. Partial MCP sequencing revealed a divergent virus (CaSpA-IV-2) in one C. oxeata. The analysis of a 10 nt long tandem repeat showed a number of repeats consistent across sub-sections of the same sponges but different between animals, suggesting the presence of different strains. As the genetic material of crustaceans, particularly from the zooplanktonic copepod order Calanoida, was identified in the investigated samples, further studies are required to elucidate whether CaSpA-IV infects the carnivorous sponges, their crustacean prey, or both.

A new perspective on the evolution and diversity of the genus Amdoparvovirus (family Parvoviridae) through genetic characterization, structural homology modeling, and phylogenetics.

Amdoparvoviruses (genus Amdoparvovirus, family Parvoviridae) are primarily viruses of carnivorans, but recent studies have indicated that their host range might also extend to rodents and chiropterans. While their classification is based on the full sequence of the major nonstructural protein (NS1), several studies investigating amdoparvoviral diversity have been focused on partial sequences, leading to difficulties in accurately determining species demarcations and leaving several viruses unclassified. In this study, while reporting the complete genomic sequence of a novel amdoparvovirus identified in an American mink (British Columbia amdoparvovirus, BCAV), we studied the phylogenetic relationships of all amdoparvovirus-related sequences and provide a comprehensive reevaluation of their diversity and evolution. After excluding recombinant sequences, phylogenetic and pairwise sequence identity analyses allowed us to define fourteen different viruses, including the five currently classified species, BCAV, and four additional viruses that fulfill the International Committee on Taxonomy of Viruses criteria to be classified as species. We show that the group of viruses historically known as Aleutian mink disease virus (species Carnivore amdoparvovirus 1) should be considered as a cluster of at least four separate viral species that have been co-circulating in mink farms, facilitating the occurrence of inter-species recombination. Genome organization, splicing donor and acceptor sites, and protein sequence motifs were surprisingly conserved within the genus. The sequence of the major capsid protein virus protein 2 (VP2) was significantly more conserved between and within species compared to NS1, a phenomenon possibly linked to antibody-dependent enhancement (ADE). Homology models suggest a remarkably high degree of conservation of the spikes located near the icosahedral threefold axis of the capsid, comprising the surface region associated with ADE. A surprisingly high number of divergent amino acid positions were found in the luminal threefold and twofold axes of the capsid, regions of hitherto unknown function. We emphasize the importance of complete genome analyses and, given the marked phylogenetic inconsistencies across the genome, advise to obtain the complete coding sequences of divergent strains. Further studies on amdoparvovirus biology and structure as well as epidemiological and virus discovery investigations are required to better characterize the ecology and evolution of this important group of viruses.

Distribution and diversity of dog parvoviruses in wild, free-roaming and domestic canids of Newfoundland and Labrador, Canada.

Some parvoviruses of carnivorans can infect multiple host species. Since many canine parvoviruses were only discovered recently, their host-range is still unexplored. We examined the host distribution and diversity of five dog parvoviruses in four canine populations from Newfoundland and Labrador, Canada, and investigated the potential for these viruses to cross the species barriers. Canine bocavirus 2 (CBoV-2) and the minute virus of canines were detected in stool from free-roaming dogs from Labrador (5/48 [10.4%] and 3/48 [6.3%], respectively) and two different CBoV-2 variants were identified. Canine bufavirus was identified in stool from free-roaming dogs (1/48, 2.1%) and foxes (3/80, 3.8%) from Labrador, but two different variants were observed in the two host species. The variant found in foxes was highly divergent from previously identified strains. Two cachavirus 1 variants, genetically similar to those circulating in other Canadian wildlife, were found in spleens from Newfoundland coyotes (3/87, 3.5%). Canine parvovirus type 2 (CPV-2) was found in stool from free-roaming dogs from Labrador (2/48, 4.2%) and in spleens from Newfoundland coyotes (3/87, 3.5%). Comparing CPV-2 sequences from these hosts to those retrieved from local symptomatic domestic dogs revealed the presence of a highly heterogeneous viral population as detected strains belonged to five different clades. The close relationship between CPV-2a strains from a dog and a coyote suggests the occurrence of viral transfer between wild and domestic canids. The identification of highly related strains with a similar molecular signature characteristic of older CPV-2 strains in free-roaming and domestic dogs suggests a probable common ancestry and that older CPV-2 strains, which have not been identified in dogs since the 1990s, persist in this part of Canada. Follow-up studies should evaluate samples from a larger number of animals and host species to extensively investigate the possible occurrence of cross-species transmission for recently discovered parvoviruses.

Characterization of Vaccine Breakthrough Cases during Measles Outbreaks in Milan and Surrounding Areas, Italy, 2017-2021.

Despite the existence of an effective live-attenuated vaccine, measles can appear in vaccinated individuals. We investigated breakthrough measles cases identified during our surveillance activities within the measles/rubella surveillance network (MoRoNet) in Milan and surrounding areas (Northern Italy). Between 2017 and 2021, we confirmed measles virus (genotypes B3 or D8) infections in 653 patients and 51 of these (7.8%) were vaccinees. Among vaccinated individuals whose serum was available, a secondary failure was evidenced in 69.4% (25/36) of cases while 11 patients (30.6%) were non-responders. Non-responders were more frequently hospitalized and had significantly lower Ct values in both respiratory and urine samples. Median age and time since the last immunization were similar in the two groups. Importantly, we identified onward transmissions from vaccine failure cases. Vaccinees were involved in 20 outbreaks, in 10 of them they were able to transmit the virus, and in 8 of them, they were the index case. Comparing viral hemagglutinin sequences from vaccinated and non-vaccinated subjects did not show a specific mutation pattern. These results suggest that vaccination failure was likely due to the poor immune response of single individuals and highlights the importance of identifying breakthrough cases and characterizing their clinical and virologic profiles.

Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence?

Two years after the start of the COVID-19 pandemic, key questions about the emergence of its aetiological agent (SARS-CoV-2) remain a matter of considerable debate. Identifying when SARS-CoV-2 began spreading among people is one of those questions. Although the current canonically accepted timeline hypothesises viral emergence in Wuhan, China, in November or December 2019, a growing body of diverse studies provides evidence that the virus may have been spreading worldwide weeks, or even months, prior to that time. However, the hypothesis of earlier SARS-CoV-2 circulation is often dismissed with prejudicial scepticism and experimental studies pointing to early origins are frequently and speculatively attributed to false-positive tests. In this paper, we critically review current evidence that SARS-CoV-2 had been circulating prior to December of 2019, and emphasise how, despite some scientific limitations, this hypothesis should no longer be ignored and considered sufficient to warrant further larger-scale studies to determine its veracity.