Background Understanding the cellular host factors that promote and inhibit viral entry is important for identifying viral countermeasures. CRISPR whole genome screens can be used to rapidly discover host factors that contribute to or impair viral entry. However, when using the live viruses and cellular lethality for selection, these screens can identify an overwhelming number of genes without specificity for the stage of the viral infection cycle. New screening methods are needed to identify host machinery contributing to specific steps of viral infection. Here, we developed a CRISPR whole genome screen and counter screen strategy based on a pseudoviral platform that allowed identification of genes specific to SARS-CoV-2 spike and vesicular stomatitis virus glycoprotein VSV-G mediated entry. Methods To focus the screen onto the entry step, we used non-lytic fluorescent reporters in combination with a comparative counter screen strategy to distinguish host genes affecting the pseudoviral reporter from those unique to envelope-mediated entry. Screening of SARS-CoV-2 spike and VSV-G on the same lentiviral pseudovirus allowed identification of entry-specific genes relative to genes associated with retro-transcription, integration, and reporter expression from the lentiviral pseudovirus. Second, a Cre-Gag fusion protein in the pseudovirus was used to bypass retro-transcription and integration by directly activating a floxed GFP reporter upon entry to reduce the number of gene hits and increase specificity for viral entry. Results Our approach correctly identified SARS-CoV-2 and VSV-G receptors ACE2 and LDLR, respectively and distinguished genes associated with retroviral reporter expression from envelope-mediated entry. Moreover, the CRE-Gag fusion/flox reporter increased the screen specificity for viral entry associated genes. Validation of a few hits demonstrates that this approach distinguishes envelope-specific host factors from genes affecting reporter expression. Conclusion Overall, this approach provides a new strategy for identifying host genes influencing viral entry without the confounding complexity of live-viral screens which produce long gene lists associated with all aspects of viral pathogenesis and replication. This approach provides a pathway for increasing the specificity of CRISPR whole genome screens for identifying host genes contributing to specific steps in viral infection.

A document by Haleema Qayyum Abbasi. Click on the document to view its contents.

During the Belgian winter and spring season 2022-2023, we investigated the potential of used paper tissue (UPT) as a non-invasive sampling method for the diagnosis of acute respiratory infections. Screening for respiratory pathogens was done using an in-house developed respiratory panel for simultaneous detection of 22 respiratory viruses and 7 non-viral pathogens. The method allowed the identification and typing of respiratory pathogens in symptomatic individuals, as well as in collective samples taken at a community level. Pathogens that were identified in nasal swabs could also be detected in concurrent UPT from the same patient. In all cases that tested positive on an antigen-detection rapid diagnostic test, the corresponding virus could be detected in UPT. The collection of UPT could be useful in epidemiological surveillance of SARS-CoV-2 and other coronaviruses, as well as other respiratory pathogens such as influenzavirus, respiratory syncytial virus, entero/rhinoviruses including EV D68, parainfluenzaviruses and Streptococcus pneumoniae. Multiple respiratory pathogens could be detected in UPTs of collectivities, confirming its applicability for community testing. This is especially interesting for screening in nursing homes, centers for the disabled, schools or other settings were taking nasal or nasopharyngeal samples is cumbersome.

The number of SARS-CoV-2 recombinants identified during the pandemic has increased since the era of Omicron variants, but XBB.1.5 (or Omicron 23A) is the first lineage comprised of hybrid genomes to predominate at the country and global scales. Very interestingly, the XBB.1.5 recombinant, like the Marseille-4B subvariant (B.1.160/20A.EU2) and the pandemic variant B.1.1.7 (20I/Alpha) previously, has its ORF8 gene inactivated by a stop codon. XBB.1.5 was generated through two successive main events: a recombination between SARS-CoV-2 of lineages BA.2.10.1.1 (BJ.1) and BA.2 75.3.1.1.1 (BM.1.1.1) that generated the XBB (22F) lineage; then ORF8 gene inactivation by a stop codon. We further identified that a stop codon was present at 89 (74%) codons of the ORF8 gene in ≥1 of 15,222,404 genomes available in GISAID, and at 15 codons (12%) in ≥1,000 genomes. Thus, it is very likely that stop codons in ORF8 gene contributed on at least 3 occasions and independently during the SARS-CoV-2 pandemic to the evolutionary success of a lineage that became transiently predominant, most recently XBB.1.5. Such association of gene loss with evolutionary success, which suits the recently described Mistigri rule, is an important biological phenomenon very unknown in virology while largely described in cellular organisms.

Evaluate clinical effectiveness of Azvudine with data rather than speculationDaishi Li, MD1,2,3*, Yihuang Liu, MD1,2,3*, Minxue Shen, MD1,2,3,4#, Guangtong Deng, MD1,2,3#1 Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China2 National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China3 Furong Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China.4 Department of Social Medicine and Health Management, Xiangya School of Public Health, Central South University, Changsha, Hunan, ChinaDaishi Li and Yihuang Liu contributed equally to this study.#Correspondence to Guangtong Deng, Minxue Shen, MD, Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China. E-mail: dengguangtong@outlook.com; shenmx1988@csu.edu.cn.To the Editor,We appreciate the interest in our article entitled “Real-world effectiveness of Azvudine versus nirmatrelvir-ritonavir in hospitalized patients with COVID-19: A retrospective cohort study”.In their study, Ma et al. stated that antiviral therapies must be administered within five days of symptom onset to be effective. However, our study population included approximately 90% of patients beyond this treatment window. Moreover, we were unable to provide virological results, leading to Ma et al.’s speculation that treatment was unlikely to benefit patients in our study. They further praised the benefits of nirmatrelvir-ritonavir in COVID-19 patients and demonstrated their results supporting a faster time to nucleic acid negative conversion compared to patients receiving Azvudine. In a phase III trial, patients treated with Azvudine only showed a 50% reduction in viral load on the fifth day of treatment, making it difficult to achieve significant clinical efficacy. Ma et al. also concluded that the dose of Azvudine was insufficient for its antiviral effects, using data from drug experimental and pharmacokinetic studies. Finally, they called for the time to make more effective drugs available to COVID-19 patients.1As a retrospective study, we sought to collect more information, particularly on cycle thresholds in COVID-19 patients. However, as we previously reported, the cycle threshold value was no longer used as a discharge criterion during the period and was not regularly checked.2 Moreover, most electronic health records of COVID-19 patients only recorded quantitative results (positive or negative) upon admission, hence virological data was lacking. Nevertheless, it was not necessary for our study, which aimed to evaluate the real-world clinical effectiveness (composite outcomes and mortality). 3Azvudine and nirmatrelvir-ritonavir were recommended for the treatment of COVID-19 patients as early as possible, but these drugs were not strictly used according to the instructions during the special period. We acknowledged several limitations in our retrospective study, including the possibility of selection bias and confounding by indication. We also emphasized that our conclusions were solely based on data from our hospital and that the generalization of our findings required more high-quality and multi-center clinical trials.3 As clinicians, with limited knowledge about drug experimental and pharmacokinetics studies, we refrain from making any response on the topic of its antiviral effect. If there are any questions concerning the antiviral effect, we suggest contacting the corresponding authors of these studies.4,5 We can, however, discuss the clinical effectiveness of the drugs.We agree that numerous studies from other countries support the benefits of nirmatrelvir-ritonavir in treating COVID-19 patients.6 However, a multi-center randomized controlled study based on Chinese patients failed to detect a significant reduction in the risk of all-cause mortality on day 28 and the duration of virus clearance in severe adult COVID-19 patients.7 As our study mainly included severe COVID-19 patients in China, the limited efficacy of nirmatrelvir-ritonavir is not surprising.3,8 While Ma et al. found a faster time to nucleic acid negative conversion in patients receiving nirmatrelvir-ritonavir compared to those receiving Azvudine,1 it did not entirely negate our findings that support the better clinical benefit of Azvudine.3Evaluating a drug’s effectiveness requires clinical data, rather than piecing together several basic articles to make a speculation solely based on its antiviral effect. For instance, remdesivir can effectively inhibit COVID-19 infection in vitro but has no significant effect on COVID-19 patients who are already being ventilated.9Similarly, metformin, the most commonly used oral type 2 diabetic drug, functions in many diseases, including avoiding long COVID.10 Nowadays, compared with other anti-COVID-19 drugs, there is limited clinical study on Azvudine. Therefore, we call for more real-world studies to evaluate the effectiveness of Azvudine in COVID-19 patients.Finally, we appreciate the feedback from some readers regarding the flowchart of patient screening in Figure 1. To avoid any confusion, we would like to clarify that patients were repeatedly counted if they met individual exclusion criteria in the study. Additionally, pregnant patients were mistakenly classified to patients with history diseases. After matching, none of pregnant patients were included in Azudine and nirmatrelvir-ritonavir group. Therefore, our conclusions were still consistent.Declaration of Competing Interest: None.Acknowledgement: This work was supported by the National Natural Science Foundation of China (Grant Nos. 82102803, 82272849 to G. D.), National Natural Science Foundation of Hunan Province (Grant Nos. 2021JJ40976 to G. D.) and Natural Science Fund for Outstanding Youths in Hunan Province (2023JJ20093 to G.D.).Role of the funding source: The funding sources had no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the article for publication. All the authors had full access to all the data in the study and agree to submit the manuscript for publication.

SARS-CoV2 infection has caused an increase in mortality and morbidity but with vaccination, the disease severity has significantly reduced. But with emergence of various variants of concerns (VOCs), the vaccine breakthrough infection has also increased. Here, we studied circulating spike specific T follicular response (cTfh) in infection naïve vaccinees and convalescent vaccinees (individuals who got delta breakthrough infection after 2 doses of BBV152 vaccine) to understand their response as they are the most crucial cells that are involve in vaccine mediated protection by helping in B-cell maturation. Our results indicated that cTfh cells in both the groups recognized wild type and delta spike protein but memory response to wild type spike was superior in infection naïve than in convalescent group. The cytokine response particularly IL-21 from cTfh cells was also higher in infection naïve than convalescent vaccines indicating a dampened cTfh response in convalescent vaccines after breakthrough infection. Also, there was positive correlation between IL-21 from cTfh cells and neutralizing antibodies of infection naïve vaccinees. Multiple cytokine analysis also revealed higher inflammation in convalescent vaccinees. Our data indicated necessity of third booster dose may be individual specific depending in the steady state functional phenotype of immune cells.

Rabies is an ancient neuroinvasive viral (genus Lyssavirus, family Rhabdoviridae) disease affecting approximately 59,000 people worldwide. The central nervous system (CNS) is targeted, and rabies has a case fatality rate of almost 100% in humans and animals. Rabies is entirely preventable through proper vaccination, and thus, the highest incidence is typically observed in developing countries, mainly in Africa and Asia. However, there are still cases in European countries and the US. Recently, demographic, increasing income levels, and the coronavirus disease 2019 (COVID-19) pandemic have caused a massive raising in the animal population, enhancing the need for preventive measures (e.g., vaccination, surveillance, animal control programs), post-exposure prophylaxis, and a better understanding of rabies pathophysiology to identify therapeutic targets, since there is no effective treatment after the onset of clinical manifestations. Here we review the neuroimmune biology and mechanisms of rabies. Its pathogenesis involves a complex and poorly understood modulation of immune and brain functions associated with metabolic, synaptic, and neuronal impairments, resulting in fatal outcomes without significant histopathological lesions in the CNS. In this context, the neuroimmunological and neurochemical aspects of excitatory/inhibitory signaling (e.g., GABA/glutamate crosstalk) are likely related to the clinical manifestations of rabies infection. Uncovering new links between immunopathological mechanisms and neurochemical imbalance will be essential to identify novel potential therapeutic targets to reduce rabies morbidity and mortality.

People with mpox are likely to be stigmatized because of analogies to other sexually transmitted infections. Stigma is driven by beliefs about the perceived severity of the condition and perceived responsibility for acquiring the condition, both in broader society and individual responsibility. We explored these beliefs and compared them across mpox, HIV, syphilis, gonorrhoea, and chlamydia in an online survey, conducted in July, 2022, with 394 men-who-have-sex-with-men (MSM) in the Netherlands. We compared mean scores between infections using repeated measures ANOVA and conducted hierarchical regression analyses to identify determinants of both mpox perceived responsibility endpoints. Results showed that participants expected that mpox would be seen as a ‘gay disease’ and will be used to blame gay men. Compared to other infections, mpox was considered less severe than HIV, but more severe than syphilis, gonorrhoea, and chlamydia. Perceived responsibility was comparable across infections, but, for each infection, participants perceived attributed responsibility for infection to be higher in society than individual responsibility. Both perceived responsibility endpoints were highly correlated with each other and with other stigma beliefs. These results provide insight on the underlying determinants of mpox stigma, and demonstrate that mpox stigma is present in the Netherlands.

Sexually transmitted infections (STIs) are a major global public health concern, with human papillomavirus (HPV) being one of the most common STIs affecting both men and women worldwide [1]. It is estimated that about 75% of sexually active people will contract HPV at some point in their lives [1]. The impact of HPV on health can be severe, causing various health problems such as genital warts, cervical, anal, penile, and oropharyngeal cancers [2].Several studies conducted in Africa have shown significant HPV prevalence rates among men who have sex with men (MSM). In sub-Saharan Africa, HPV was detected in a range of 19.1% to 100% of men, with a pooled prevalence of 78.2% among HIV-positive men and 49.4% among HIV-negative men [3]. Another study in South Africa found that HPV genotypes were detected in 72.8% of anal, 11.5% of oro-pharyngeal, and 15.3% of urine specimens of MSM, with multiple HPV types being more common in the anal canal [4]. Additionally, a study in Nigeria reported a higher prevalence of anal high-risk HPV (HR-HPV) among HIV-positive MSM compared to HIV-negative MSM [5], while another study in Mali found that a significant percentage of MSM had anal HPV infection of any genotypes, with a large portion being HR-HPV positive [6]. The increasing prevalence of anal HR-HPV among MSM in Africa highlights the urgent need for increased HPV screening and prevention measures targeted at this population, particularly HIV-positive MSM.HPV vaccination programs are highly effective in reducing the burden of HPV and associated diseases in both men and women [3]. The vaccine offers long-lasting protection against HPV infections that are most commonly associated with cancer [7]. Although the vaccine is primarily known for preventing cervical cancer in women, it can also prevent HPV-related cancers in men, such as anal, penile, and oropharyngeal cancers [7]. Moreover, vaccinating men can lead to herd immunity, which can protect women from HPV-related diseases [2]. Therefore, it is essential to prioritize the HPV vaccine for MSM who engage in anal sex to prevent HPV-related cancers and reduce the overall burden of HPV in Africa.However, the low uptake of the HPV vaccine in Africa, especially among high-risk individuals, is concerning despite the vaccine’s effectiveness in preventing HPV-related diseases. Only 14 of the 54 African nations have included the HPV vaccine in their national immunization programs for girls as of 2021, and no countries in western and central Africa have included widespread HPV vaccination in their national immunization programs [8 10]. Furthermore, currently, no countries in Africa offer HPV vaccination to men [8]. This means that individuals engaging in anal sex, who are at a higher risk of developing anal cancer, are not receiving the protection they need, despite the high prevalence of HPV infection among MSM. This underscores the urgent need to prioritize the inclusion of the HPV vaccine in national immunization programs in Africa, and to ensure equitable access to the vaccine for all persons, including MSM.To improve access to healthcare services and HPV vaccination for MSM in Africa, it is crucial to address both the structural and social barriers that hinder their access to these services. Some of the barriers that HPV-infected MSM face include a lack of information, general vaccine hesitancy, a lack of advice from healthcare professionals, expense and logistics, and the perception that HPV vaccination may encourage promiscuity [9]. Furthermore, discrimination and the criminalization of same-sex behavior can further prevent MSM from accessing healthcare programs [10].A comprehensive approach is necessary to overcome these barriers and improve access to healthcare services and HPV vaccination for MSM in Africa. This includes community-based interventions [11], and healthcare professional training to increase awareness about HPV, the benefits of vaccination, and to reduce vaccine hesitancy among MSM [12]. Healthcare professionals should also receive training to provide culturally competent care to meet the unique healthcare needs of MSM in a non-judgmental manner [12]. Policy changes are also necessary to eliminate discrimination and criminalization of same-sex behavior and enable MSM to access healthcare services without fear of stigma or persecution [10]. Moreover, to increase vaccine coverage in Africa, the HPV vaccine should be made affordable and accessible to all individuals, regardless of their socioeconomic status [10]. This can be achieved by implementing community-based vaccination programs, mobile clinics, and school-based vaccination programs. Overall, these interventions can help to improve vaccination rates and increase access to healthcare services for MSM in Africa, ultimately leading to better health outcomes and reducing health disparities.

Background: It is unknown whether Torque Teno virus (TTV) DNA load monitoring could anticipate the development of infectious events in hematological patients undergoing treatment with small molecular targeting agents. We characterized the kinetics of plasma TTV DNA in patients treated with ibrutinib or ruxolitinib and assessed whether TTV DNA load monitoring could predict the occurrence of Cytomegalovirus (CMV) DNAemia or the magnitude of CMV-specific T-cell responses. Methods: Multicenter, retrospective, observational study, recruiting 20 patients treated with ibrutinib and 21 with ruxolitinib. Plasma TTV and CMV DNA loads were quantified by real-time PCR at baseline and days +15, +30, +45, +60, +75, +90, +120, +150, and +180 after treatment inception. Enumeration of CMV-specific IFN-γ-producing CD8 + and CD4 + T cells in whole blood was performed by flow cytometry. Results: Median TTV DNA load in ibrutinib-treated patients increased significantly ( P=0.025) from baseline (median, 5.76 log 10 copies/ml) to day +120 (median, 7.83 log 10 copies/ml). A moderate inverse correlation (Rho=-0.46; P<0.001) was found between TTV DNA load and absolute lymphocyte count (ALC). In ruxolitinib-treated patients, TTV DNA load quantified at baseline was not significantly different from that measured after treatment inception ( P ≥0.12). TTV DNA loads were not predictive of the subsequent occurrence of CMV DNAemia in either patient group. No correlation was observed between TTV DNA loads and CMV-specific IFN-γ-producing CD8 + and CD4 + T cell counts in either patient group. Conclusion: The data did not support the hypothesis that TTV DNA load monitoring in hematological patients treated with ibrutinib or ruxolitinib could be useful to predict either the occurrence of CMV DNAemia or the level of CMV-specific reconstitution.

COVID-19 bivalent ancestral/Omicron mRNA booster vaccinations became available to boost and expand the immunity against SARS-CoV-2 Omicron infections. In a prospective cohort study including 59 healthcare workers, we assessed SARS-CoV-2 ancestral and Omicron BA.5-specific neutralizing antibody and T cell responses in previously infected and infection-naive individuals. Also, we assessed the effect of an ancestral/Omicron BA.1 bivalent mRNA booster vaccination on these immune responses. 10 months after previous monovalent mRNA vaccinations, ancestral SARS-CoV-2 S1-specific T cell and anti-RBD IgG responses remained detectable in most individuals and a previous SARS-CoV-2 infection was associated with increased T cell responses. T cell responses, anti-RBD IgG, and Omicron BA.5 neutralization activity increased after receiving an ancestral/Omicron BA.1 bivalent booster mRNA vaccination. An Omicron BA.5 infection in addition to bivalent vaccination led to a higher ratio of Omicron BA.5 to ancestral strain neutralization activity compared to bivalent vaccination without a recent SARS-CoV-2 infection. In conclusion, SARS-CoV-2 T cell and antibody responses persist for up to 10 months after a monovalent booster mRNA vaccination. An ancestral/Omicron BA.1 bivalent booster mRNA vaccination increases these immune responses and also induces Omicron BA.5 cross-neutralization antibody activity. Finally, our data indicate that hybrid immunity is associated with improved preservation of T cell immunity.

Clinical and histopathological evidence suggest that the male reproductive system may be negatively impacted in patients with coronavirus disease (COVID-19). The objective of this study is to investigate the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on semen parameters by comparing semen analyses before and after COVID-19 diagnosis in the same patient. We retrospectively analyzed 342 semen analyses by reviewing medical records. The study included two groups of patients: (i) those who underwent two consecutive semen analyses within 6 months, one before (n=114) and one after (n=114) COVID-19 diagnosis, and (ii) a control group (n=114) that was age-matched and did not receive a diagnosis of COVID-19. The study results indicated a significant decrease in semen volume, total sperm count per ejaculate, progressive motile sperm count, total motile sperm count, and normal sperm morphology after SARS-CoV-2 infection in comparison to their respective values before the infection. Subgroup analyses showed that the duration of COVID-19 diagnosis (short-term vs long-term) did not impact the changes in semen parameters. However, fever during the COVID-19 process had a negative effect on semen parameters, particularly sperm concentration, unlike in patients without fever. In conclusion, our findings suggest that SARS-CoV-2 infection is associated with a decline in semen quality, which may potentially impact male fertility. Furthermore, it’s important to note that the negative effects on semen parameters may persist in the long-term. Our results also indicate that fever during active infection could be a significant risk factor that negatively affects spermatogenesis.

In May 2022, several countries reported mpox cases from patients without history of traveling to endemic areas. France was one of the most affected European countries. In this study, we described the clinical characteristics of mpox cases in France, and studied the genetic diversity of the virus. Patients diagnosed with mpox infection (qPCR ct<28) between 21 th May and 4 th July 2022 and between 16 th August and 10 th September 2022 were included to this study. Twelve amplicons corresponding to the most polymorphic regions of the mpox genome and covering ~30,000 nucleotides were generated and sequenced using the S5 XL Ion Torrent technology to evaluate the genetic diversity of mpox sequences. One hundred and fourty-eight patients were diagnosed with mpox-infection. 95% were men, 5% transgender (M-to-F), 50% were taking HIV pre-exposure prophylaxis, and 25% were HIV seropositive. One hundred and sixty-two samples were sequenced and compared to GenBank sequences. Thirty-two distinct mutational patterns were identified. Overall, low genetic diversity of mpox sequences was found compared with pre-epidemic Western-African sequences, with 32 distinct mutational patterns. Our results provide a first glance at the mutational landscape of early mpox 2022 circulating strains in Paris (France).

Since 1999, Vaccinia virus (VACV) has been described as a causative agent of bovine vaccinia (BV), a zoonotic disease that occurs mainly in rural areas of Brazil. However, the circulation of VACV in urban environments and its associated burden has been poorly explored. Moreover, the current Mpox outbreak has raised questions regarding the immune status of the worldwide population previous vaccinated against smallpox. Hence, we conducted a cross-sectional study to better understand the prevalence of anti-OPV neutralizing antibodies (NA) in a susceptible urban population of Brazil. A total of 372 individuals were sampled, yielding an overall seroprevalence of 16.9% (CI95%=13.4–21.1), and antibodies titers ranging from 100 to 800 NU/ml. The prevalence of NA among vaccinated individuals (≥36yo) was 24.9% (IC 95%=19.5–31.2), and among those unvaccinated (<36yo) was 6.7% (IC 95%=3.7–11.8). Multivariate logistic regression analysis indicated that age ≥36yo and the presence of vaccine take were independently associated with the presence of anti-OPV NA. Our findings suggest that vulnerable populations could be subclinically exposed to VACV in urban areas, drawing attention to alternative routes of zoonotic VACV exposure. Our data is also important for better strategies in order to mitigate zoonotic OPV infections mainly among vulnerable populations.

Omicron BF.7 became the predominant SARS-CoV-2 variant in Beijing after the adjustment of COVID-19 response strategies in December 2022. The ability of antibodies elicited by BF.7 infection to cross-react with SARS-CoV-2-like viruses is unknown. This study aimed to investigate the cross-reactive neutralizing antibodies against SARS-CoV-2-related pangolin coronavirus GX_P2V in sera from vaccinated and/or SARS-CoV-2 infected individuals. All vaccinated individuals who recovered from Omicron BF.7 breakthrough infections exhibited substantially higher levels of neutralizing antibodies against GX_P2V among collected subject populations (geometric mean titer [GMT] = 362). Uninfected individuals who received four-mixed-dose vaccines also demonstrated higher levels of neutralizing antibodies (GMT = 44) against GX_P2V than those who received two- or three-dose vaccines and those who recovered from wild type SARS-CoV-2. This finding highlights the significance of prior and hybrid booster vaccinations with wild-type SARS-CoV-2 vaccines in generating potent cross-protective immunity against future spillovers of SARS-CoV-2-like viruses.

Severe fever with thrombocytopaenia syndrome virus (SFTSV) and Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause the hyperproduction of inflammatory cytokines, which have pathological effects in patient including severe or fatal cytokine storms. To characterize the effect of SFTSV and SARS-CoV-2 infection on the production of cytokines in SFTS and COVID-19 patients, we performed an analysis of cytokines in SFTS and COVID-19 patients and also investigated the role of IL-10 in vitro studies: LPS-induced THP-1-derived macrophages, SFTSV infection of THP-1 cells, and SARS-CoV-2 infection of THP-1 cells. In this study, we found that levels of both IL-10 and IL-6 were significantly elevated, the level of TGF-β was significantly decreased and IL-10 was elevated earlier than IL-6 in severe and critical COVID-19 and fatal SFTS patients, and inhibition of IL-10 signalling decreased the production of IL-6 and elevated that of TGF-β. Therefore, the hyperproduction of IL-10 and IL-6 and the low production of TGF-β have been linked to cytokine storm-induced mortality in fatal SFTS and severe and critically ill COVID-19 patients and that IL-10 can play an important role in the host immune response to severe and critical SARS-CoV-2 and fatal SFTSV infection.

Rotavirus molecular surveillance remains important in the post vaccine era in order to monitor the changes in transmission patterns, identify vaccine induced antigenic changes and discover potentially pathogenic vaccine related strains. The Canadian province of Alberta introduced rotavirus vaccination into its provincial vaccination schedule June 2015. To evaluate the impact of this program on stool rotavirus positivity rate, strain diversity and seasonal trends, we analyzed a prospective cohort of children with acute gastroenteritis recruited between December 2014 and August 2018. We identified dynamic changes in rotavirus positivity and genotype trends during pre- and post- rotavirus vaccine introduction periods. Genotypes G9P[8], G1P[8], G2P[4] and G12P[8] predominated consecutively each season with overall lower rotavirus incidence rates in 2016 and 2017. The demographic and clinical features of rotavirus gastroenteritis were comparable among wild type rotaviruses; however, children with G12P[8] infections were older (P<0.001). Continued efforts to monitor changes in the molecular epidemiology of rotavirus using whole genome sequence characterization is needed to further understand the impact of the selection pressure of vaccination on rotavirus evolution.

In somatic cells, microRNAs (miRNAs) bind to the genomes of RNA viruses and influence their translation and replication. Here we demonstrate that a significant number of miRNA binding sites locate in the NSP4 region of the SARS-CoV-2 genome, and the intestinal human miRNAs exert evolutionary pressure on this region. Notably, in infected cells, NSP4 promotes the formation of double-membrane vesicles, which serve as the scaffolds for replication-transcriptional complexes and protect viral RNA from intracellular destruction. In three years of selection, the loss of many miRNA binding sites, in particular, those within the NSP4, has shaped the SARS-CoV-2 genomes to promote the descendants of the BA.2 variants as the dominant strains that define current momentum of the pandemics. Findings highlight the possibility that intestinal tissue may significantly impact evolution of the SARS-CoV-2 genome and may play a pivotal role in the long COVID.