A novel candidate hepatitis C virus genotype 4 subtype identified by next generation sequencing full-genome characterization in a patient from Saudi Arabia.

Background and aim: Hepatitis C virus (HCV) infection is a major global public health concern, being a leading cause of chronic liver diseases such as chronic hepatitis, cirrhosis, and hepatocellular carcinoma. The virus is classified into 8 genotypes and 93 subtypes, each displaying distinct geographic distributions. Genotype 4 is the most predominant in the Middle East and Eastern Mediterranean and is associated with high rates of hepatitis C infection worldwide. This study used next-generation sequencing to fully characterize the HCV genome and identify a novel subtype within genotype 4 isolated from a 64-year-old Saudi man diagnosed with hepatitis C. Methods: We analyzed the complete genome of the 141-HCV isolate using whole-genome sequencing. Results: Our phylogenetic reconstructions, based on the entire genome of HCV-4 strains, revealed that the 141-HCV isolate formed a distinct group within the genotype 4 classification, providing valuable new insights into the variability of HCV. Conclusion: This discovery of a previously unclassified HCV subtype within genotype 4 sheds light on the ongoing evolution and diversity of the virus. Such knowledge has significant implications for diagnostic and therapeutic approaches, as different subtypes may exhibit varying drug sensitivities and resistance profiles.

Lack of Evidence for a Role of ACE-2 Polymorphisms as a Bedside Clinical Prognostic Marker of COVID-19.

The novel SARS-CoV-2 coronavirus causes a severe respiratory syndrome referred to as coronavirus disease (COVID-19). The angiotensin-converting enzyme 2 (ACE-2) plays an important role as a cellular receptor for SARS-CoV-2 and is largely expressed in lungs, kidneys, heart and the gastrointestinal tract along with being shed in plasma. The ACE-2 gene and protein show a high level of genetic polymorphism, including simple nucleotide variation, transcriptional variation, post-transcriptional changes, and putative protein mutations that could interfere with the binding or entry of SARS-CoV-2 and affect tissue damage in lungs or other organs. Genetic polymorphisms can impact SARS-CoV-2 viral entry and COVID-19 severity. This single-center study evaluated the possible role of the main ACE-2 polymorphisms (rs143936283, rs2285666, rs41303171, rs35803318, and rs2106809) as potential prognostic markers in SARS-CoV-2-infected individuals. Frozen whole blood was used for DNA isolation and genomic DNA samples were sheared using the Covaris LE220 Focused-ultrasonicator for targeting a peak size of 410 bp. Whole-genome sequencing libraries were generated from fragmented DNA using the Illumina TruSeq DNA PCR-Free HT Library Preparation Kit and sequenced on an Illumina NovaSeq 6000. We did not identify any correlation between ACE-2 polymorphisms and COVID-19 prognosis, suggesting that the interpretation and clinical use of ACE-2 genetic polymorphisms in real-world clinical settings requires further experimental and clinical validation.

Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals.

The study aimed to characterize the genotype and subgenotypes of HBV circulating in Saudi Arabia, the presence of clinically relevant mutations possibly associated with resistance to antivirals or immune escape phenomena, and the possible impact of mutations in the structural characteristics of HBV polymerase. Plasma samples from 12 Saudi Arabian HBV-infected patients were analyzed using an in-house PCR method and direct sequencing. Saudi patients were infected with mainly subgenotype D1. A number of mutations in the RT gene (correlated to antiviral resistance) and within and outside the major hydrophilic region of the S gene (claimed to influence immunogenicity and be related to immune escape) were observed in almost all patients. Furthermore, the presence of mutations in the S region caused a change in the tertiary structure of the protein compared with the consensus region. Clinical manifestations of HBV infection may change dramatically as a result of viral and host factors: the study of mutations and protein-associated cofactors might define possible aspects relevant for the natural and therapeutic history of HBV infection.

Increased SARS-CoV-2 seroprevalence in healthy blood donors after the second pandemic wave in South-Eastern Italy: evidence for asymptomatic young donors as potential virus spreaders.

BACKGROUND: Italy experienced SARS-CoV-2 spread during the second wave and the southern regions were severely affected. In this prospective study, we assessed the changes in SARS-CoV-2 seroprevalence rates in non-vaccinated blood donors to evaluate the spread of SARS-CoV-2 among healthy individuals in our geographical area. METHODS: 8,183 healthy blood donors visiting the Transfusion Centre at the University Hospital "Riuniti" of Foggia (Italy) to donate blood from May 2020 to March 2021 were tested twice for anti-SARS-CoV-2 antibodies by Ortho Clinical Diagnostics VITROS® 3600 through anti-SARS-CoV-2 Total and IgG reagent kit. None of the subjects had diagnosed symptomatic COVID-19 infection, and none had received vaccination. RESULTS: Overall, 516 out of 8,183 had antibodies to SARS-CoV-2 (total and IgG antibodies) (6.3%, 95% CI: 0.03-0.15%), 387 were male and 129 female. There was a significant increase of seropositive donors from May 2020 to March 2021 (p < .001). The difference in seroprevalence was significantly associated with age but not sex (2-sided p < .05 for age; 2-sided p ≥ .05 for sex) in both groups. CONCLUSIONS: Our study showed a significant increase in SARS-CoV-2 seroprevalence in blood donors and suggests that asymptomatic individuals might contribute to the spread of SARS-CoV-2. These results may contribute to revised containment measures, priorities in vaccine campaigns and monitoring of seroprevalence in public places like Transfusion Centres. Serologic testing of blood donors may be relevant to monitor SARS-CoV-2 circulation in the general population.

Genetic Subtypes and Natural Resistance Mutations in HCV Genotype 4 Infected Saudi Arabian Patients.

This study aimed to characterize the HCV genetic subtypes variability and the presence of natural occurring resistance-associated substitutions (RASs) in Saudi Arabia patients. A total of 17 GT patients were analyzed. Sequence analysis of NS3, NS5A, and NS5B regions was performed by direct sequencing, and phylogenetic analyses were used to determine genetic subtypes, RAS, and polymorphisms. Nine patients were infected by GT 4a, two with GT 4o and three with GT 4d. Two patients were infected with apparent recombinant virus (4a/4o/4a in NS3/NS5A/NS5B), and one patient was infected with a previously unknown, unclassifiable, virus of GT 4. Natural RASs were found in six patients (35%), including three infected by GT 4a, two by GT 4a/GT 4o/GT 4a, and one patient infected by an unknown, unclassifiable, virus of GT 4. In particular, NS3-RAS V170I was demonstrated in three patients, while NS5A-RASs (L28M, L30R, L28M + M31L) were detected in the remaining three patients. All patients were treated with sofosbuvir plus daclatasvir; three patients were lost to follow-up, whereas 14 patients completed the treatment. A sustained virological response (SVR) was obtained in all but one patient carrying NS3-RAS V170I who later relapsed. GT 4a is the most common subtype in this small cohort of Saudi Arabia patients infected with hepatitis C infection. Natural RASs were observed in about one-third of patients, but only one of them showed a treatment failure.

Low Prevalence of Antibodies to SARS-CoV-2 and Undetectable Viral Load in Seropositive Blood Donors from South-Eastern Italy.

Recently, a significant cluster of pneumonia caused by a novel betacoronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) was described initially in China and then spread throughout the world. Like other coronaviridae, the viral transmission occurs mainly through droplets. In addition, the virus has been detected in different clinical specimens, suggesting a potential transmission by other routes, including blood transfusion. However, the potential risk of transmission of SARS-CoV-2 via blood products is still unclear. The aim of our study was to investigate the prevalence of antibodies against SARS-CoV-2 among blood donors from South-Eastern Italy. Moreover, in the seropositive donors, we searched for the presence of the virus in nasopharyngeal swabs and in plasma samples. Overall, 1,797 blood donors from the Apulia region were tested for anti-SARS-CoV-2 antibodies, using a commercially available assay. Only 18/1,797 donors (1.0%) tested positive for anti-SARS-CoV-2 antibodies; in none of them SARS-CoV-2 viral RNA was detected in nasopharyngeal swabs and in plasma samples. Our results indicate that most of the blood donors in Apulia remained uninfected during this wave of the pandemic; further, none had detectable virus both in nasopharyngeal swabs and in blood samples. The risk to carry and transmit the virus by healthy and asymptomatic blood donors is probably very low.

Resistance Associated Mutations in HCV Patients Failing DAA Treatment.

Currently, treatment of chronic hepatitis C is based on a combination of direct-acting antiviral agents (DAAs) which achieve HCV clearance in more than 95% of patients. Despite this high rate of cure, treatment failures can occur in about 3-5% of treated patients. Resistance associated substitutions (RAS) are commonly detected after virological failure, although their role in real-life DAA failures is still debated. This study aimed to evaluate in real-life DAA-failing patients the prevalence of clinically relevant RASs for the different DAA classes and to identify possible predictors. Fifty consecutive HCV-infected patients who experienced a virological failure to a DAA-containing regimen were included in the study. Direct sequencing of HCV regions involved in DAA resistance (NS3, NS5A and NS5B) was performed with Sanger-based homemade protocols. The presence of mutations in the NS3 and NS5A regions was statistically associated with regimens containing protease inhibitors (p<0.0032) and NS5A inhibitors (p<0.0006), respectively. On the contrary, for the NS5B region, the known mutations associated with the NS5B RNA polymerase inhibitors were detected in treated HCV patients, although there was no statistical significance (p>0.5). A significant correlation was found between the presence of RASs and advanced fibrosis/cirrhosis, but not with age, sex and viral load. Our study demonstrates a high frequency of RASs in patients with DAA failure, thus highlighting the usefulness of genotypic tests in this setting. The identification of RASs may guide the choice of the most appropriate drugs for HCV re-treatment.

Preliminary Data From the Study of Coagulative Profile of HIV Infected Individuals Suggest a Role For Point Mutations in the Gene in Protein S Deficiency in Individuals Undergoing Highly Antiretroviral Therapy.

BACKGROUND: HIV infection is a known prothrombotic condition but factors involved are still controversial. A role for antiretrovirals, especially protease inhibitors, was advocated. OBJECTIVES: The study aimed to analyze the levels of anticoagulant proteins in virally suppressed HIV-infected subjects treated with different anti-retroviral regimens. MATERIALS AND METHODS: Forty-four patients were included in the study. C and PS, D-Dimers and Fibrinogen levels were determined as well as APC-resistance. PROS1 gene was sequenced in a group of patient. RESULTS: Twelve of the 44 subjects (27%) showed reduced levels of PS, while lower levels of PC were found only in 2 patients (4,5%). No difference in the mean values of PC and PS was found stratifying the study population by antiretroviral regimen administrated (p>0.05).Three patients had higher levels of D-Dimer concentrations and in two of these patients, an association between higher D-Dimer values and lower levels of PS was observed; but however no correlation was found by statistical analysis.PROS1 gene analysis was performed in 26 of the 44 HIV-1 patients and the subjects with low levels of PS had mutation in the fifteen exon of PROS 1 gene. While among individuals with normal levels, this mutation was observed only in 8/18 (44%) of the cases (p=0,0072). CONCLUSION: The majority of patients with low PS levels also had mutations in the fifteen exon of PROS 1 gene. Genetic determinants, deserving further investigations, rather than antiretrovirals might cause PS deficiency in HIV-1 positive patients.

QuantiFERON-TB Gold In-Tube test (QFT-GIT) for the screening of latent tuberculosis in recent immigrants to Italy.

To evaluate the agreement between QuantiFERON-TB Gold In-Tube test (QFT-GIT) and tuberculin skin test (TST) for the screening of latent tuberculosis infection (LTBI) in recent immigrants to Italy, 279 subjects were submitted to concomitant TST and QFT-GIT. The agreement was analyzed using k statistics. A total of 72/279 (25.8%) individuals were TST positive, while 107/279 (38.3%) were QFT-GIT positive. The overall agreement between QFT-GIT and TST was 70.9%, with k statistic of 0.35. Using different TST and QFT-GIT cut-offs, the best concordance value was obtained for QFT-GIT at > 2.64 IU/ml and TST at > 10mm (k = 0.409). Discordant results were found for 58 subjects (21%) with QFT-GIT positive/TST negative and 23 (8%) with QFT-GIT negative/TST positive. A high amount of discordance QFT-GIT+/TST- was described. QFT-GIT might increase the identification of LTBI cases among recent immigrants.

Prevalence of HBV genotypes in South American immigrants affected by HBV-related chronic active hepatitis.

This study evaluated the prevalence of HBV infection in a population of South American immigrants in Italy and to determine in patients with detectable serum HBV-DNA the HBV genotypes. Between April 2005 and April 2006 a total of 130 South American immigrants were tested for HBsAg. In HBsAg positive patients the biochemical and virological activity of infection and the possible presence of co-infections (HCV, HDV, HIV) were evaluated. In patients with detectable serum HBV DNA, the HBV genotype was determined by INNOLiPA. Among the 130 subjects tested, 14 (10.7%) resulted HBsAg positive. All were men, with a mean age of 22 years (range 19-37) and 12 (85.7 %) came from Brazil, while 2 (14.3%) came from Ecuador. All patients infected by HBV had elevated alanine-aminotransferase serum levels (mean level was 127 IU/L, range 74-312) and serum HBV DNA detectable by PCR-Real Time (mean level 1,037,652 copies/mL, range 19,876-1,377,648). Genotype distribution was as follow: genotype D, 9 (64.2%), genotype A, 5 (35.8%). All patients infected by genotype D came from Brazil, while among the patients infected by genotype A, three came from Brazil and two from Ecuador. Our study evidences a moderate prevalence of HBV-infection in South American immigrants with the identification of two genotypes, D and A. These genotypes are not the most prevalent in the South America and this is probably the expression of a possible geographical redistribution of HBV genotypes.

Prevalence of HBV-genotypes in immigrants affected by HBV-related chronic active hepatitis.

BACKGROUND: The genetic heterogeneity of the HBV genome has been established and eight genotypes can be classified according to the criterion of >8% differences in the complete nucleotide sequence of the viral genome. AIMS: To evaluate the prevalence of HBV-infection in a population of immigrants and to determine in patients with detectable serum HBV-DNA the HBV-genotypes. METHODS: Between January 2005 and December 2005 a total of 556 immigrants were tested for HBsAg. In HBsAg positive patients the biochemical and virological activity of infection and the possible presence of co-infections (HCV, HDV, HIV) were evaluated. In patients with detectable serum HBV DNA, the HBV-genotype was determined by INNOLiPA. RESULTS: Among the 556 subjects tested, 60 (10.7%) resulted HBsAg positive. All were men, and 42 (70%) come from Africa, 10 (16.6%) from Asia and 9 (14.4%) from East-Europe. 28/60 (46.6%) patients presented normal ALT levels (<40 IU/L) and undetectable serum HBV DNA (<100 copies/mL in real-time PCR), while 32 (53.4%) patients had ALT levels above laboratory normal values and detectable serum HBV DNA. Genotype distribution was as follow: genotype E, 16 (50%), genotype D, 9 (28.1%), genotype A, 7 (21.9%). CONCLUSION: Our study evidences a moderate prevalence of HBV-infection in immigrants, particularly in sub-Saharan African people, and the potentiality of migratory flow in the introduction of genotype non-D hepatitis B virus, potentially characterized by a different natural history and, possibly, a different response to antiviral treatment.

Prevalence of HBV genotypes in South American immigrants affected by HBV-related chronic active hepatitis

This study evaluated the prevalence of HBV infection in a population of South American immigrants in Italy and to determine in patients with detectable serum HBV-DNA the HBVgenotypes. Between April 2005 and April 2006 a total of 130 South American immigrants were tested for HBsAg. In HBsAg positive patients the biochemical and virological activity of infection and the possible presence of co-infections (HCV, HDV, HIV) were evaluated. In patients with detectable serum HBV DNA, the HBV genotype was determined by INNOLiPA. Among the 130 subjects tested, 14 (10.7 percent) resulted HBsAg positive. All were men, with a mean age of 22 years (range 19-37) and 12 (85.7 percent) came from Brazil, while 2 (14.3 percent) came from Ecuador. All patients infected by HBV had elevated alanine-aminotransferase serum levels (mean level was 127 IU/L, range 74-312) and serum HBV DNA detectable by PCR-Real Time (mean level 1,037,652 copies/mL, range 19,876-1,377,648). Genotype distribution was as follow: genotype D, 9 (64.2 percent), genotype A, 5 (35.8 percent). All patients infected by genotype D came from Brazil, while among the patients infected by genotype A, three came from Brazil and two from Ecuador. Our study evidences a moderate prevalence of HBV-infection in South American immigrants with the identification of two genotypes, D and A. These genotypes are not the most prevalent in the South America and this is probably the expression of a possible geographical redistribution of HBV genotypes.

Prevalence of HBV-genotypes in immigrants affected by HBV-related chronic active hepatitis

BACKGROUND: The genetic heterogeneity of the HBV genome has been established and eight genotypes can be classified according to the criterion of >8 percent differences in the complete nucleotide sequence of the viral genome. AIMS: To evaluate the prevalence of HBV-infection in a population of immigrants and to determine in patients with detectable serum HBV-DNA the HBV-genotypes. METHODS: Between January 2005 and December 2005 a total of 556 immigrants were tested for HBsAg. In HBsAg positive patients the biochemical and virological activity of infection and the possible presence of co-infections (HCV, HDV, HIV) were evaluated. In patients with detectable serum HBV DNA, the HBV-genotype was determined by INNOLiPA. RESULTS: Among the 556 subjects tested, 60 (10.7 percent) resulted HBsAg positive. All were men, and 42 (70 percent) come from Africa, 10 (16.6 percent) from Asia and 9 (14.4 percent) from East-Europe. 28/60 (46.6 percent) patients presented normal ALT levels (<40 IU/L) and undetectable serum HBV DNA (<100 copies/mL in real-time PCR), while 32 (53.4 percent) patients had ALT levels above laboratory normal values and detectable serum HBV DNA. Genotype distribution was as follow: genotype E, 16 (50 percent), genotype D, 9 (28.1 percent), genotype A, 7 (21.9 percent). CONCLUSION: Our study evidences a moderate prevalence of HBV-infection in immigrants, particularly in sub-Saharan African people, and the potentiality of migratory flow in the introduction of genotype non-D hepatitis B virus, potentially characterized by a different natural history and, possibly, a different response to antiviral treatment.

RACIONAL: A heterogeneidade do genoma do vírus da hepatite B (VHB) foi estabelecida e oito genótipos podem ser classificados de acordo com o critério de diferenças de percentagem maior ou igual a 8 na seqüência completa do nucleotídeo do genoma vira!. OBJETIVOS: Verificar a prevalência da infecção pelo vírus da hepatite B (VHB) em uma população de imigrantes na Itália e determinar os genótipos do VHB em pacientes com níveis séricos detectáveis do VHB-DNA. MÉTODOS: Entre janeiro e dezembro de 2005, o total de 556 imigrantes foram testados para o HbsAg. Se positivos, a atividade bioquímica e viral da infecção e a possível presença de co-infecções (HVC, HVD e HIV) foram examinadas. Nos pacientes positivos para o VHB-DNA, o genótipo do VHB foi determinado pelo método INNOLiPA. RESULTADOS: Entre os 556 pacientes, 60 (10,7 por cento) tinham HbsAg positivo. Todos eram do sexo masculino e 42 (70 por cento), provenientes da Africa, 10 (16,6 por cento) da Asia e 9 (14,4 por cento) do Leste Europeu. 28/60 (46,6 por cento) apresentaram níveis de ALT normais (<40 UI/L) e soro negativo ou indetectável para o VHB-DNA (<100 copies/mL PCR "real-time"), enquanto 32 (53,4 por cento) tinham níveis mais elevados de ALT e soro positivo para VHB-DNA. A distribuição do genótipo foi a seguinte: genótipo E, 16 (50 por cento), genótipo D, 9 (28,1 por cento), genótipo A, 7 (21,1 por cento). CONCLUSÃO: O estudo evidencia a prevalência moderada do HVB em imigrantes, particularmente na população africana, sub-Sahara e o potencial fluxo migratório na introdução da hepatite B, genótipo não-D, potencialmente caracterizada pela história natural e possivelmente levar à diferença no tratamento anti-viral.