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In endemic regions (West Africa and the Congo Basin), the genetic diversity of monkeypox virus (MPXV) is geographically structured into two major clades (clade I and II) that differ in virulence and host associations. Clade IIb is closely related to the B.1 lineage, which is dominating a worldwide outbreak initiated in 2022. Lineage B.1 has however accumulated mutations of unknown significance that most likely result from APOBEC3 (apolipoprotein B mRNA editing catalytic polypeptide-like 3) editing. We applied a population genetics-phylogenetics approach to investigate the evolution of MPXV during historical viral spread in Africa and to infer the distribution of fitness effects. We observed a high preponderance of codons evolving under strong purifying selection, particularly in viral genes involved in morphogenesis and replication or transcription. However, signals of positive selection were also detected and were enriched in genes involved in immunomodulation and/or virulence. In particular, several genes showing evidence of positive selection were found to hijack different steps of the cellular pathway that senses cytosolic DNA. Also, a few selected sites in genes that are not directly involved in immunomodulation are suggestive of antibody escape or other immuno-mediated pressures. Because orthopoxvirus host range is primarily determined by the interaction with the host immune system, we suggest that the positive selection signals represent signatures of host adaptation and contribute to the different virulence of clade I and II MPXV. We also used the calculated selection coefficients to infer the effects of mutations that define the predominant hMPXV1 lineage B.1, as well as the changes that have been accumulating during the worldwide outbreak. Results indicated that a proportion of deleterious mutations were purged from the predominant outbreak lineage, whose spread was not driven by the presence of beneficial changes. Polymorphic mutations with a predicted beneficial effect on fitness are few and have a low frequency. It remains to be determined whether they have any significance for ongoing virus evolution.

The ongoing worldwide monkeypox outbreak is caused by viral lineages (globally referred to as hMPXV1) that are related to but distinct from clade IIb MPXV viruses transmitted in Nigeria. Analysis of genetic differences indicated that APOBEC-mediated editing might be responsible for the unexpectedly high number of mutations observed in hMPXV1 genomes. Here, using 1624 hMPXV1 publicly available sequences, we analyzed mutations that accrued since 2017 until the emergence of the current predominant variant (B.1), as well as those that that have been accumulating during the 2022 outbreak. We found that substitutions tend to cluster and mutational hot-spots are observed.Investigation of the sequence context of C to T changes indicated a preference for 5’-TCA/G-3’ motifs, suggesting APOBEC3F- or APOBEC3A-mediated editing. The sequence context has remained unchanged since 2017, indicating that the same mutational mechanism that is driving the accumulation of substitutions during the ongoing human-to-human transmission, was already operating before the virus left Africa. We suggest that APOBEC3A is the most likely candidate, given its expression in the skin and its known role in the editing of human papillomavirus.

Primate herpes simplex viruses are species-specific and relatively harmless to their natural hosts. However, cross-species transmission is often associated with severe disease, as exemplified by the virulence of macacine herpesvirus 1 (B virus) in humans. We performed a genome-wide scan for signals of adaptation of simplexviruses to their hominin hosts. Among core genes, we found evidence of episodic positive selection in three glycoproteins, with several selected sites located in antigenic determinants. Positively selected noncore genes were found to be involved in different immune-escape mechanisms. The herpes simplex virus (HSV)-1/HSV-2 encoded product (ICP47) of one of these genes is known to down-modulate major histocompatibility complex class I expression. This feature is not shared with B virus, which instead up-regulates Human Leukocyte Antigen (HLA)-G, an immunomodulatory molecule. By in vitro expression of different ICP47 mutants, we functionally characterized the selection signals. Results indicated that the selected sites do not represent the sole determinants of binding to the transporter associated with antigen processing (TAP). Conversely, the amino acid status at these sites was sufficient to determine HLA-G up-regulation. In fact, both HSV-1 and HSV-2 ICP47 induced HLA-G when mutated to recapitulate residues in B virus, whereas the mutated version of B virus ICP47 failed to determine HLA-G expression. These differences might contribute to the severity of B virus infection in humans. Importantly, they indicate that the evolution of ICP47 in HSV-1/HSV-2 led to the loss of an immunosuppressive effect. Thus, related simplexviruses finely tune the balance between immunosuppressive and immunostimulatory pathways to promote successful co-existence with their primate hosts.

Centromeres have central functions in chromosome segregation, but centromeric DNA and centromere-binding proteins evolve rapidly in most eukaryotes. The selective pressure(s) underlying the fast evolution of centromere-binding proteins are presently unknown. An attractive possibility is that selfish centromeres promote their preferential inclusion in the oocyte and centromeric proteins evolve to suppress meiotic drive (centromere drive hypothesis). We analysed the selective patterns of mammalian genes that encode kinetochore proteins and microtubule (MT)-destabilizing factors. We show that several of these proteins evolve at the same rate or faster than proteins with a role in centromere specification. Elements of the kinetochore that bind MTs or that bridge the interaction between MTs and the centromere represented the major targets of positive selection. These data are in line with the possibility that the genetic conflict fuelled by meiotic drive extends beyond genes involved in centromere specification. However, we cannot exclude that different selective pressures underlie the rapid evolution of MT-destabilizing factors and kinetochore components. Whatever the nature of such pressures, they must have been constant during the evolution of eutherian mammals, as we found a surprisingly good correlation in dN/dS (ratio of the rate of nonsynonymous and synonymous substitutions) across orders/clades. Finally, when phylogenetic relationships were accounted for, we found little evidence that the evolutionary rates of these genes change with testes size, a proxy for sperm competition. Our data indicate that, in analogy to centromeric proteins, kinetochore components are fast evolving in mammals. This observation may imply that centromere drive plays out at multiple levels or that these proteins adapt to lineage-specific centromeric features.

Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results indicated that HSV-1 populations have limited geographic structure and the most evident clustering by geography is likely due to recent bottlenecks. For HSV-2, the only level of population structure is accounted for by the so-called “worldwide” and “African” lineages. Analysis of ancestry components and nucleotide diversity, however, did not support the view that the worldwide lineage followed early humans during out-of-Africa dispersal. Although phylogeographic analysis confirmed an African origin for both viruses, molecular dating with a method that corrects for the time-dependent rate phenomenon indicated that HSV-1 and HSV-2 migrated from Africa in relatively recent times. In particular, we estimated that the HSV-2 worldwide lineage left the continent in the 18th century, which corresponds to the height of the transatlantic slave trade, possibly explaining the high prevalence of HSV-2 in the Americas (second highest after Africa). The limited geographic clustering of HSV-1 makes it difficult to date its exit from Africa. The split between the basal clade, containing mostly African sequences, and all other strains was dated at ∼5,000 years ago. Our data do not imply that herpes simplex viruses did not infect early humans but show that the worldwide distribution of circulating strains is the result of relatively recent events.

Four coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E) are endemic in human populations. All these viruses are seasonal and generate short-term immunity. Like the highly pathogenic coronaviruses, the endemic coronaviruses have zoonotic origins. Thus, understanding the evolutionary dynamics of these human viruses might provide insight into the future trajectories of SARS-CoV-2 evolution. Because the zoonotic sources of HCoV-OC43 and HCoV-229E are known, we applied a population genetics–phylogenetic approach to investigate which selective events accompanied the divergence of these viruses from the animal ones. Results indicated that positive selection drove the evolution of some accessory proteins, as well as of the membrane proteins. However, the spike proteins of both viruses and the hemagglutinin-esterase (HE) of HCoV-OC43 represented the major selection targets. Specifically, for both viruses, most positively selected sites map to the receptor-binding domains (RBDs) and are polymorphic. Molecular dating for the HCoV-229E spike protein indicated that RBD Classes I, II, III, and IV emerged 3–9 years apart. However, since the appearance of Class V (with much higher binding affinity), around 25 years ago, limited genetic diversity accumulated in the RBD. These different time intervals are not fully consistent with the hypothesis that HCoV-229E spike evolution was driven by antigenic drift. An alternative, not mutually exclusive possibility is that strains with higher affinity for the cellular receptor have out-competed strains with lower affinity. The evolution of the HCoV-OC43 spike protein was also suggested to undergo antigenic drift. However, we also found abundant signals of positive selection in HE. Whereas such signals might result from antigenic drift, as well, previous data showing co-evolution of the spike protein with HE suggest that optimization for human cell infection also drove the evolution of this virus. These data provide insight into the possible trajectories of SARS-CoV-2 evolution, especially in case the virus should become endemic.

The aim of the study was to assess the contribution of negative emotionality at 3 months (T1) and serotonin transporter gene (SLC6A4) DNA methylation at 4.5 years of age (T2) to emotion regulation in pre-schoolers born very preterm and full-term. Forty one children (n = 21 born very preterm, n = 20 born full-term) participated in the study. Fretful behavior was assessed at T1 in response to the Face-to-FaceStill-Face (FFSF) paradigm. At T2, SLC6A4 DNA methylation was analyzed and emotion regulation was assessed using an observational procedure (i.e., the Pre-schooler Regulation of Emotional Stress, PRES). The very preterm group displayed higher emotion dysregulation during the PRES Reactivity phase than the full-term group. Higher levels of fretful behavior at 3 months were associated with greater emotional distress only for very preterm children with higher methylation at T2. No significant associations emerged in the full-term group. Despite current findings cannot be generalized owing to the relatively small sample size, this work provides preliminary longitudinal evidence about the link between negative emotionality during infancy, stress-linked epigenetic status at 4.5 years and emotion dysregulation in preschoolers born preterm.El propósito del estudio fue evaluar la contribución de la emocionalidad negativa a los 3 meses (T1) y la metilación del ADN en el gen transportador de la serotonina (SLC6A4) a los 4 años y medio de edad (T2) a la regulación de la emoción en prescolares nacidos muy antes de la gestación completa o de gestación completa. Cuarenta y un niños (n = 21 nacidos muy antes de la gestación completa, n = 20 nacidos de gestación completa) participaron en el estudio. El comportamiento irritable se evaluó a T1 como respuesta al Cara-a-Cara del paradigma de la Cara Inmóvil (FFSF). A T2, se analizó la metilación de ADN SLC6A4 y se evaluó la regulación de la emoción usando un procedimiento de observación (v.g. La Regulación del Estrés Emocional del Prescolar, PRES). El grupo nacido muy antes de la gestación completa mostró una más alta desregulación durante la fase de Reactividad PRES que el grupo nacido de gestación completa. Los niveles más altos de comportamiento irritable a los 3 meses se asociaron con una mayor angustia emocional solamente para los niños nacidos muy antes de la gestación completa con más alta metilación al T2. Ninguna asociación significativa surgió del grupo nacido de gestación completa. A pesar de que los actuales resultados no se pueden generalizar debido al tamaño relativamente pequeño del grupo muestra, este trabajo ofrece aporta evidencia longitudinal preliminar acerca de la conexión entre la emocionalidad negativa durante la infancia, el estado epigenético relacionado con el estrés a los 4 años y medio y la desregulación de la emoción en prescolares nacidos antes de la completa gestación.Le but de cette étude était d’évaluer la contribution de l’émotivité négative à 3 mois (T1) et du gène vecteur de la sérotonine (SLC6A4) méthylation de l'ADN à l’âge de 4,5 ans (T2) à la régulation de l’émotion chez les enfants d’âge préscolaire nés très prématurés et à plein terme. Quarante et un enfant (n = 21 nés très prématurés, n = 20 nés à plein terme) ont participé à l’étude. Le comportement agité a été évalué au T1 en réponse au paradigme face-à-face visage inexpressif (abrégé FFSF en anglais). Au T2, la méthylation de l'ADN SLC6A4 a été analysée et la régulation de l’émotion a été évaluée en utilisant un protocole d'observation (à savoir, la Régulation du Stress Emotionnel de l'Enfant d'Age Préscolaire, abrégé en anglais PRES). Le groupe très prématuré a fait état d'une dysrégulation de l’émotion plus élevée durant la phase de Réactivité PRES que le groupe né à plein terme. Des niveaux plus élevés de comportement agité à 3 mois étaient liés à une détresse émotionnelle plus grande uniquement pour les enfants très prématurés avec une méthylation plus élevée au T2. Aucune association importante n'a émergé dans le groupe à plein terme. En dépit du fait que les résultats actuels ne peuvent pas être généralisés à cause de la taille relativement petite de l’échantillon, ce travail offre des preuves longitudinales préliminaires sur le lien entre l’émotivité négative durant la petite enfant, le statut épigénétique lié au stress à 4,5 ans et la dysrégulation de l’émotion chez les enfants d’âge préscolaires nés avant terme.Serotonin-Transporter-Gen-Methylierung und Emotionsregulation bei Kindern im Vorschulalter, die Frühchen waren: Eine longitudinale Evaluation der Rolle negativer Emotionalität im Säuglingsalter Ziel der Studie war es, den Einfluss negativer Emotionalität im Alter von 3 Monaten (T1) und der DNA-Methylierung des Serotonin-Transporter-Gens (SLC6A4) im Alter von 4,5 Jahren (T2) auf Emotionsregulation bei Vorschulkindern zu untersuchen. Die untersuchten Kinder waren entweder als Frühchen oder voll ausgetragen auf die Welt gekommen. Einundvierzig Kinder (n = 21 sehr frühgeborene, n = 20 voll ausgetragen) nahmen an der Studie teil. Unruhiges Verhalten wurde zu T1 durch das Face-to-Face Still-Face-Paradigma (FFSF) untersucht. Zu T2 wurde die SLC6A4-DNA-Methylierung analysiert und die Emotionsregulation mittels eines Beobachtungsverfahrens beurteilt (dem Pre-schooler Regulation of Emotional Stress; PRES). Die Gruppe der Frühchen zeigte während der PRES-Reaktivitätsphase eine stärkere emotionale Dysregulation als die Gruppe der voll ausgetragenen Kinder. Höhere Werte für unruhiges Verhalten nach 3 Monaten waren nur bei Frühchen mit höherer Methylierung zu T2 mit größerem emotionalen Stress verbunden. In der Gruppe der voll ausgetragenen Kinder wurden keine signifikanten Zusammenhänge festgestellt. Obwohl die aktuellen Ergebnisse aufgrund der relativ kleinen Stichprobengröße nicht generalisiert werden können, liefert diese Arbeit vorläufige Längsschnittdaten über den Zusammenhang zwischen negativer Emotionalität im Säuglingsalter, stressbedingtem epigenetischem Status im Alter von 4,5 Jahren und emotionaler Dysregulation bei Vorschulkindern, die Frühchen waren.早産で生まれた未就学児におけるセロトニントランスポーター遺伝子のメチル化と情動調整 乳幼児期の負の情動の果たす役割についての縦断的評価 要約 本研究の目的は、超早産と満期産の未就学児の情動調整において、 (T1) 生後3ヶ月時の負の情動と (T2) 4歳半時のセロトニントランスポーター遺伝子 (SLC6A4) のDNAメチル化の寄与を評価することであった。41人の子ども (n = 21超早産児、n = 20満期産児) が研究に参加した。T1では、Face-to-Face Still-Face (FFSF) パラダイムに対する不快行動が評価された。T2では、SLC6A4 DNAメチル化が分析され、観察法 (すなわち、Pre-schooler Regulation of Emotional Stress, PRES) を用いて情動調整が評価された。超早産児群は、PRES反応期において、満期児群よりも情動調節に困難を示した。生後3ヶ月時におけるより強いレベルの不快行動は、T2においてより高いメチル化を有する超早産児においてのみ、より強い情動的苦痛と関連していた。満期産児群では、有意な関連は認められなかった。今回の結果はサンプル数が比較的少ないため一般化できないが、本研究は、早産児の乳児期における負の情動、4歳半におけるストレスに関連した後成的な状態や未就学児の情動調節の困難との関連について、縦断的な予備的証拠を提供するものである。.该研究的目的是评估3个月时 (T1) 的消极情绪以及4.5岁时 (T2) 血清素转运蛋白基因 (SLC6A4) DNA甲基化对早产和足月出生的学龄前儿童情绪调节的影响。41名儿童(21名极早产, 20名足月出生)参与了这项研究。在T1时, 根据“面对面静止脸” (FFSF) 实验范式评估了烦躁行为。在T2时, 分析SLC6A4 DNA甲基化, 并使用观察程序 (即“学龄前儿童情绪压力调节”, PRES) 评估情绪调节。与足月组相比, 极早产儿组在PRES反应阶段表现出更高的情绪调节障碍。只有在T2阶段甲基化水平较高的极早产儿, 其3个月时较高水平的烦躁行为与更大的情绪困扰有关。在足月组中无显著相关性。尽管由于样本量相对较小, 目前的研究结果还不能广泛应用, 但这项工作提供了初步的纵向证据, 表明了婴儿期的消极情绪、4.5岁时与压力相关的表观遗传状态和早产学龄前儿童情绪失调之间的联系。.المَثْيَلة الجينية لناقل السيروتونين والتنظيم العاطفي في الأطفال قبل سن المدرسة المولودين قبل الأوان: تقييم طولي لدور الانفعالية السلبية في الطفولة كان الهدف من الدراسة هو تقييم مساهمة حالة الانفعالية السلبية عند عمر 3 أشهر (T1) و مثيلة الحمض النووي لجين ناقل السيروتونين (SLC6A4) عند 4.5 سنوات من العمر (T2) في تنظيم العاطفة لدى الأطفال في سن ما قبل المدرسة المولودين قبل الأوان والمولودين بالكامل . شارك واحد وأربعون طفلاً (ن = 21 ولدًا مبتسراً ، ن = 20 ولدًا كامل المدة) في الدراسة. تم تقييم السلوك المزعج عند T1 استجابة لنموذج الوجه الثابت وجهًا لوجه (FFSF). وعند T2 ، تم تحليل مثيلة الحمض النووي لـناقل السيروتونين SLC6A4 وتقييم تنظيم العاطفة باستخدام إجراء الملاحظة (أي ، تنظيم الإجهاد العاطفي في مرحلة ما قبل المدرسة ، PRES). أظهرت المجموعة المبتسرة جدًا عدم تنظيم عاطفي أعلى أثناء مرحلة تفاعلية PRES أكثر من المجموعة كاملة المدة. وارتبطت المستويات الأعلى من السلوك المزعج في عمر ثلاثة أشهر بضيق عاطفي أكبر فقط للأطفال الخدج الذين لديهم مثيلة أعلى عند T2. لم تظهر أي ارتباطات مهمة في المجموعة كاملة المدة. على الرغم من أن النتائج الحالية لا يمكن تعميمها بسبب حجم العينة الصغير نسبيًا ، فإن هذا العمل يوفر أدلة طولية أولية حول العلاقة بين الانفعالات السلبية أثناء الطفولة ، والحالة اللاجينية المرتبطة بالإجهاد عند 4.5 سنوات ، وعدم انتظام العاطفة في الأطفال قبل سن المدرسة المولودين مبتسرين.

Understanding the evolutionary dynamics of the four human endemic coronaviruses might provide insight into the future trajectories of SARS-CoV-2 evolution. We re-assessed the timing of endemic coronavirus emergence and we show that all viruses entered human populations in a time-frame ranging from ~500 to 55 years ago. Because the three highly pathogenic coronaviruses (SARS-CoV, MERS-CoV, and SARS-CoV-2) spilled-over in tight temporal succession, the pattern of coronavirus emergence, in analogy to that of influenza pandemics, is highly irregular. To contextualize this observation in a wider perspective of viral diseases emergence since 1945, we mined epidemiology database information. After controlling for reporting bias, we find that, contrary to widespread beliefs, the occurrence of viral diseases (either zoonotic or not) has not increased over the last decades. Analysis of the recent and ongoing evolution of HCoV-229E and HCoV-OC43 indicated that positive selection most likely contributed to fine-tune the interaction with the human interferon/inflammatory response. Conversely, integration of evolutionary inference and molecular dating provided evidence that these viruses are not undergoing antigenic drift and the temporal emergence of spike protein variants is best explained by optimization of receptor binding affinity. These data provide a fresh look on viral disease emergence and on coronavirus evolution.

Primate herpes simplex viruses are relatively harmless to their natural hosts, whereas cross-species transmission can result in severe disease. We performed a genome-wide scan for signals of adaptation of simplexviruses to hominins. We found evidence of positive selection in three glycoproteins, with selected sites located in antigenic determinants. Positively selected non-core proteins were involved in different immune-escape mechanisms. By expressing mutants of one of these proteins (ICP47), we show that the amino acid status at the positively selected sites is sufficient to induce HLA-G. HSV-1/HSV-2 ICP47 induced HLA-G when mutated to recapitulate residues in B virus, whereas the mutated version of B virus ICP47 failed to determine HLA-G expression. Thus, the evolution of ICP47 in HSV-1/HSV-2 determined the loss of an immunosuppressive effect, suggesting that simplexviruses tune immune responses to promote successful co-existence with their hosts. These results also help explain the high pathogenicity of B virus in humans.

Analysis of the bat viruses most closely related to SARS‐CoV‐2 indicated that the virus probably required limited adaptation to spread in humans. Nonetheless, since its introduction in human populations, SARS‐CoV‐2 must have been subject to the selective pressure imposed by the human immune system. We exploited the availability of a large number of high‐quality SARS‐CoV‐2 genomes, as well as of validated epitope predictions, to show that B cell epitopes in the spike glycoprotein (S) and in the nucleocapsid protein (N) have higher diversity than nonepitope positions. Similar results were obtained for other human coronaviruses and for sarbecoviruses sampled in bats. Conversely, in the SARS‐CoV‐2 population, epitopes for CD4+ and CD8+ T cells were not more variable than nonepitope positions. A significant reduction in epitope variability was instead observed for some of the most immunogenic proteins (S, N, ORF8 and ORF3a). Analysis over longer evolutionary time frames indicated that this effect is not due to differential constraints. These data indicate that SARS‐CoV‐2 evolves to elude the host humoral immune response, whereas recognition by T cells is not actively avoided by the virus. However, we also found a trend of lower diversity of T cell epitopes for common cold coronaviruses, indicating that epitope conservation per se is not directly linked to disease severity. We suggest that conservation serves to maintain epitopes that elicit tolerizing T cell responses or induce T cells with regulatory activity.

Human betaherpesviruses 6A and 6B (HHV-6A and HHV-6B) are highly prevalent in human populations. The genomes of these viruses can be stably integrated at the telomeres of human chromosomes and be vertically transmitted (inherited chromosomally integrated HHV-6A/HHV-6B, iciHHV-6A/iciHHV-6B). We reconstructed the population structures of HHV-6A and HHV-6B, showing that HHV-6A diverged less than HHV-6B genomes from the projected common ancestral population. Thus, HHV-6B genomes experienced stronger drift, as also supported by calculation of nucleotide diversity and Tajima’s D. Analysis of ancestry proportions indicated that HHV-6A exogenous viruses and iciHHV-6A derived most of their genomes from distinct ancestral sources. Conversely, ancestry proportions were similar in exogenous HHV-6B viruses and iciHHV-6B. In line with previous indications, this suggests the distinct exogenous viral populations that originated iciHHV-6B in subjects with European and Asian ancestry are still causing infections in the corresponding geographic areas. Notably, for both iciHHV-6A and iciHHV-6B, we found that European and American sequences tend to have high proportions of ancestry from viral populations that experienced considerable drift, suggesting that they underwent one or more bottlenecks followed by population expansion. Finally, analysis of HHV-6B exogenous viruses sampled in Japan indicated that proportions of ancestry components of most of these viruses are different from the majority of those sampled in the USA. More generally, we show that, in both viral species, both integrated and exogenous viral genomes have different ancestry components, partially depending on geographic location. It would be extremely important to determine whether such differences account for the diversity of HHV-6A/HHV-6B-associated clinical symptoms and epidemiology. Also, the sequencing of additional exogenous and integrated viral genomes will be instrumental to confirm and expand our conclusions, which are based on a relatively small number of genomes, sequenced with variable quality, and with unequal sampling in terms of geographic origin.

Whereas the majority of herpesviruses co-speciated with their mammalian hosts, human herpes simplex virus 2 (HSV-2, genus Simplexvirus) most likely originated from the cross-species transmission of chimpanzee herpesvirus 1 to an ancestor of modern humans. We exploited the peculiar evolutionary history of HSV-2 to investigate the selective events that drove herpesvirus adaptation to a new host. We show that HSV-2 intrinsically disordered regions (IDRs)—that is, protein domains that do not adopt compact three-dimensional structures—are strongly enriched in positive selection signals. Analysis of viral proteomes indicated that a significantly higher portion of simplexvirus proteins is disordered compared with the proteins of other human herpesviruses. IDR abundance in simplexvirus proteomes was not a consequence of the base composition of their genomes (high G + C content). Conversely, protein function determines the IDR fraction, which is significantly higher in viral proteins that interact with human factors. We also found that the average extent of disorder in herpesvirus proteins tends to parallel that of their human interactors. These data suggest that viruses that interact with fast-evolving, disordered human proteins, in turn, evolve disordered viral interactors poised for innovation. We propose that the high IDR fraction present in simplexvirus proteomes contributes to their wider host range compared with other herpesviruses.

Human betaherpesviruses 6A and 6B (HHV-6A and HHV-6B) are highly prevalent in human populations. The genomes of these viruses can be stably integrated at the telomeres of human chromosomes and be vertically transmitted (inherited chromosomally integrated HHV-6, iciHHV6). We reconstructed the population structure of HHV-6 and we show that HHV-6A genomes diverged less than HHV-6B genomes from the ancestral common HHV-6A/B population. Analysis of ancestry proportions indicated that HHV-6A exogenous viruses and iciHHV-6A derived most of their genomes from distinct ancestral sources. Conversely, exogenous viral and iciHHV-6B populations were similar in terms of ancestry components, with no evident geographic structuring. Most HHV-6B genomes sampled to date derive from viral populations that experienced considerable drift. However, a population of HHV-6 exogenous viruses, currently classified as HHV-6B and sampled in New York state, formed a separate cluster (NY cluster) and harbored a considerable portion of HHV-6A-like ancestry. Recombination detection methods identified these viruses as interspecies recombinants, but phylogenetic reconstruction indicated that the recombination signals are due to shared ancestry. In analogy to iciHHV-6A, NY cluster viruses have high nucleotide diversity and constant population size. We propose that HHV-6A sequences and the NY cluster population diverged from an ancestral HHV-6A-like population. A relatively recent bottleneck of the NY (or a related) population with subsequent expansion originated most HHV-6B genomes currently sampled. Our findings indicate that the distinction between HHV-6A and -6B is not as clear-cut as previously thought. More generally, epidemiological and clinical surveys would benefit from taking HHV-6 genetic diversity into account.

JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collected information on ∼1,100 worldwide strains and we show that their geographic distribution roughly corresponds to major human migratory routes. Bayesian phylogeographic analysis inferred a Subsaharan origin for JCPyV, although with low posterior probability. High confidence inference at internal nodes provided strong support for a long-standing association between the virus and human populations. In line with these data, pairwise FST values for JCPyV and human mtDNA sampled from the same areas showed a positive and significant correlation. Likewise, very strong relationships were found when node ages in the JCPyV phylogeny were correlated with human population genetic distances (nuclear-marker based FST). Reconciliation analysis detected a significant cophylogenetic signal for the human population and JCPyV trees. Notably, JCPyV also traced some relatively recent migration events such as the expansion of people from the Philippines/Taiwan area into Remote Oceania, the gene flow between North-Eastern Siberian and Ainus, and the Koryak contribution to Circum-Arctic Americans. Finally, different molecular dating approaches dated the origin of JCPyV in a time frame that precedes human out-of-Africa migration. Thus, JCPyV infected early human populations and accompanied our species during worldwide dispersal. JCPyV typing can provide reliable geographic information and the virus most likely adapted to the genetic background of human populations.

Human betaherpesviruses 6A and 6B (HHV-6A and HHV-6B) are highly prevalent in human populations. The genomes of these viruses can be stably integrated at the telomeres of human chromosomes and be vertically transmitted (inherited chromosomally integrated HHV-6, iciHHV6). We reconstructed the population structure of HHV-6 and we show that HHV-6A genomes diverged less than HHV-6B genomes from the ancestral common HHV-6A/B population. Analysis of ancestry proportions indicated that HHV-6A exogenous viruses and iciHHV-6A derived most of their genomes from distinct ancestral sources. Conversely, exogenous viral and iciHHV-6B populations were similar in terms of ancestry components, with no evident geographic structuring. Most HHV-6B genomes sampled to date derive from viral populations that experienced considerable drift. However, a population of HHV-6 exogenous viruses, currently classified as HHV-6B and sampled in New York state, formed a separate cluster (NY cluster) and harbored a considerable portion of HHV-6A-like ancestry. Recombination detection methods identified these viruses as interspecies recombinants, but phylogenetic reconstruction indicated that the recombination signals are due to shared ancestry. In analogy to iciHHV-6A, NY cluster viruses have high nucleotide diversity and constant population size. We propose that HHV-6A sequences and the NY cluster population diverged from an ancestral HHV-6A-like population. A relatively recent bottleneck of the NY (or a related) population with subsequent expansion originated most HHV-6B genomes currently sampled. Our findings indicate that the distinction between HHV-6A and -6B is not as clear-cut as previously thought. More generally, epidemiological and clinical surveys would benefit from taking HHV-6 genetic diversity into account.

Filovirus infection is mediated by engagement of the surface-exposed glycoprotein (GP) by its cellular receptor, NPC1 (Niemann-Pick C1). Two loops in the C domain of NPC1 (NPC1-C) bind filovirus GP. Herein, we show that filovirus GP and NPC1-C evolve under mutual selective pressure. Analysis of a large mammalian phylogeny indicated that strong functional/structural constraints limit the NPC1 sequence space available for adaptive change and most sites at the contact interface with GP are under negative selection. These constraints notwithstanding, we detected positive selection at NPC1-C in all mammalian orders, from Primates to Xenarthra. Different codons evolved adaptively in distinct mammals, and most selected sites are located within the two NPC1-C loops that engage GP, or at their anchor points. In Homininae, NPC1-C was a preferential selection target, and the T419I variant possibly represents a human-specific adaptation to filovirus infection. On the other side of the arms-race, GP evolved adaptively during filovirus speciation. One of the selected sites (S142Q) establishes several atom-to-atom contacts with NPC1-C. Additional selected sites are located within epitopes recognized by neutralizing antibodies, including the 14G7 epitope, where sites selected during the recent EBOV epidemic also map. Finally, pairs of co-evolving sites in Marburgviruses and Ebolaviruses were found to involve antigenic determinants. These findings suggest that the host humoral immune response was a major selective pressure during filovirus speciation. The S142Q variant may contribute to determine Ebolavirus host range in the wild. If this were the case, EBOV/BDBV (S142) and SUDV (Q142) may not share the same reservoir(s).

Aim: The present study is part of a prospective micro-longitudinal research project and reports on the association between SLC6A4 methylation and socio-emotional stress response in very preterm (VPT) and full-term (FT) infants. Materials & methods: SLC6A4 methylation was assessed at birth and discharge in 32 VPT infants, and at birth in 27 FT infants. Socio-emotional stress response (i.e., negative emotionality) was assessed at 3 months (corrected age). Results: Negative emotionality was higher in VPTs compared with FT counterpart. In VPT infants only, stress response was associated with SLC6A4 methylation status at discharge, which was predictive of greater negative emotionality. Conclusion: The present study extends previous reports, suggesting that altered SLC6A4 methylation associates with greater socio-emotional stress sensitivity in 3-month-old VPT infants.

Hepatitis C virus (HCV) belongs to the Hepacivirus genus and is genetically heterogeneous, with seven major genotypes further divided into several recognized subtypes. HCV origin was previously dated in a range between ∼200 and 1000 years ago. Hepaciviruses have been identified in several domestic and wild mammals, the largest viral diversity being observed in bats and rodents. The closest relatives of HCV were found in horses/donkeys (equine hepaciviruses, EHV). However, the origin of HCV as a human pathogen is still an unsolved puzzle. Using a selection-informed evolutionary model, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago (CI: 3192–5221 years ago), with the oldest genotypes being endemic to Asia. EHV originated around 1100 CE (CI: 291–1640 CE). These time estimates exclude that EHV transmission was mainly sustained by widespread veterinary practices and suggest that HCV originated from a single zoonotic event with subsequent diversification in human populations. We also describe a number of biologically important sites in the major HCV genotypes that have been positively selected and indicate that drug resistance-associated variants are significantly enriched at positively selected sites. HCV exploits several cell-surface molecules for cell entry, but only two of these (CD81 and OCLN) determine the species-specificity of infection. Herein evolutionary analyses do not support a long-standing association between primates and hepaciviruses, and signals of positive selection at CD81 were only observed in Chiroptera. No evidence of selection was detected for OCLN in any mammalian order. These results shed light on the origin of HCV and provide a catalog of candidate genetic modulators of HCV phenotypic diversity.

The Mammarenavirus genus includes several pathogenic species of rodent-borne viruses. Old World (OW) mammarenaviruses infect rodents in the Murinae subfamily and are mainly transmitted in Africa and Asia; New World (NW) mammarenaviruses are found in rodents of the Cricetidae subfamily in the Americas. We applied a selection-informed method to estimate that OW and NW mammarenaviruses diverged less than ∼45,000 years ago (ya). By incorporating phylogeographic inference, we show that NW mammarenaviruses emerged in the Latin America-Caribbean region ∼41,400–3,300 ya, whereas OW mammarenaviruses originated ∼23,100–1,880 ya, most likely in Southern Africa. Cophylogenetic analysis indicated that cospeciation did not contribute significantly to mammarenavirus–host associations. Finally, we show that extremely strong selective pressure on the viral polymerase accompanied the speciation of NW viruses. These data suggest that the evolutionary history of mammarenaviruses was not driven by codivergence with their hosts. The viral polymerase should be regarded as a major determinant of mammarenavirus adaptation.

Very preterm (VPT) infants admitted to Neonatal Intensive Care Unit (NICU) are at risk for altered brain growth and less-than-optimal socio-emotional development. Recent research suggests that early NICU-related stress contributes to socio-emotional impairments in VPT infants at 3 months through epigenetic regulation (i.e., DNA methylation) of the serotonin transporter gene (SLC6A4). In the present longitudinal study we assessed: (a) the effects of NICU-related stress and SLC6A4 methylation variations from birth to discharge on brain development at term equivalent age (TEA); (b) the association between brain volume at TEA and socio-emotional development (i.e., Personal-Social scale of Griffith Mental Development Scales, GMDS) at 12 months corrected age (CA). Twenty-four infants had complete data at 12-month-age. SLC6A4 methylation was measured at a specific CpG previously associated with NICU-related stress and socio-emotional stress. Findings confirmed that higher NICU-related stress associated with greater increase of SLC6A4 methylation at NICU discharge. Moreover, higher SLC6A4 discharge methylation was associated with reduced anterior temporal lobe (ATL) volume at TEA, which in turn was significantly associated with less-than-optimal GMDS Personal-Social scale score at 12 months CA. The reduced ATL volume at TEA mediated the pathway linking stress-related increase in SLC6A4 methylation at NICU discharge and socio-emotional development at 12 months CA. These findings suggest that early adversity-related epigenetic changes might contribute to the long-lasting programming of socio-emotional development in VPT infants through epigenetic regulation and structural modifications of the developing brain.

Plasmodium falciparum, the causative agent of the deadliest form of malaria, is a member of the Laverania subgenus, which includes ape-infecting parasites. P. falciparum is thought to have originated in gorillas, although infection is now restricted to humans. Laverania parasites display remarkable host-specificity, which is partially mediated by the interaction between parasite ligands and host receptors. We analyse the evolution of BSG (basigin) and GYPA (glycophorin A) in primates/hominins, as well as of their Plasmodium-encoded ligands, PfRH5 and PfEBA175. We show that, in primates, positive selection targeted two sites in BSG (F27 and H102), both involved in PfRH5 binding. A population genetics-phylogenetics approach detected the strongest selection for the gorilla lineage: one of the positively selected sites (K191) is a major determinant of PfRH5 binding affinity. Analysis of RH5 genes indicated episodic selection on the P. falciparum branch; the positively selected W447 site is known to stabilize the interaction with human basigin. Conversely, we detect no selection in the receptor-binding region of EBA175 in the P. falciparum lineage. Its host receptor, GYPA, shows evidence of positive selection in all hominid lineages; selected codons include glycosylation sites that modulate PfEBA175 binding affinity. Data herein provide an evolutionary explanation for species-specific binding of the PfRH5-BSG ligand-receptor pair and support the hypothesis that positive selection at these genes drove the host shift leading to the emergence of P. falciparum as a human pathogen.

Dietary shifts can drive molecular evolution in mammals and a major transition in human history, the agricultural revolution, favored carbohydrate consumption. We investigated the evolutionary history of nine genes encoding brush-border proteins involved in carbohydrate digestion/absorption. Results indicated widespread adaptive evolution in mammals, with several branches experiencing episodic selection, particularly strong in bats. Many positively selected sites map to functional protein regions (e.g., within glucosidase catalytic crevices), with parallel evolution at SI (sucrase-isomaltase) and MGAM (maltase-glucoamylase). In human populations, five genes were targeted by positive selection acting on noncoding variants within regulatory elements. Analysis of ancient DNA samples indicated that most derived alleles were already present in the Paleolithic. Positively selected variants at SLC2A5 (fructose transporter) were an exception and possibly spread following the domestication of specific fruit crops. We conclude that agriculture determined no major selective event at carbohydrate metabolism genes in humans, with implications for susceptibility to metabolic disorders.

OAS (2'-5'-oligoadenylate synthases) proteins and cyclic GMP-AMP synthase (cGAS, gene symbol: MB21D1) patrol the cytoplasm for the presence of foreign nucleic acids. Upon binding to double-stranded RNA or double-stranded DNA, OAS proteins and cGAS produce nucleotide second messengers to activate RNase L and STING (stimulator of interferon genes, gene symbol: TMEM173), respectively; this leads to the initiation of antiviral responses. We analyzed the evolutionary history of the MB21D1-TMEM173 and OAS-RNASEL axes in primates and bats and found evidence of widespread positive selection in both orders. In TMEM173, residue 230, a major determinant of response to natural ligands and to mimetic drugs (e.g., DMXAA), was positively selected in Primates and Chiroptera. In both orders, selection also targeted an α-helix/loop element in RNase L that modulates the enzyme preference for single-stranded RNA versus stem loops. Analysis of positively selected sites in OAS1, OAS2, and MB21D1 revealed parallel evolution, with the corresponding residues being selected in different genes. As this cannot result from gene conversion, these data suggest that selective pressure acting on OAS and MB21D1 genes is related to nucleic acid recognition and to the specific mechanism of enzyme activation, which requires a conformational change. Finally, a population genetics-phylogenetics analysis in humans, chimpanzees, and gorillas detected several positively selected sites in most genes. Data herein shed light into species-specific differences in infection susceptibility and in response to synthetic compounds, with relevance for the design of synthetic compounds as vaccine adjuvants.

Very preterm (VPT) infants (gestational age < 32 weeks) require long-lasting hospitalization in the Neonatal Intensive Care Unit (NICU), even in absence of severe morbidities. During NICU stay, life-saving interventions occur and include invasive and painful skin-breaking procedures (NICU-related stress), which constitute a major early adverse experience for VPT infants. Telomeres are repeat-sequence at the end of chromosomes, which shorten with age and are highly susceptible to life adversities: the exposure to early adverse experiences is associated with shorter telomere length (TL). Nonetheless, previous research did not assess longitudinally the association between NICU-related stress and TL in VPT infants. In the present study, leukocyte TL was assessed from cord blood at birth in 46 VPT infants and in a group of 31 full-term (FT) infants, as well as at NICU discharge in VPTs only. NICU-related stress was measured as the number of skin-breaking procedures occurring throughout the NICU stay. A significant difference emerged for TL between VPT infants and FT counterparts at birth. TL decreased from birth to discharge in VPT infants, although the change was not significant in the group as a whole. The amount of NICU-related stress emerged as the primary predictor of TL erosion in VPT infants, even controlling for neonatal and clinical confounders. Furthermore, VPT infants exposed to high NICU-related stress exhibited a marked and significant decrease in TL, whereas VPT exposed to low NICU-related stress exhibited a non-significant increase. The present study confirms previous evidence of longer telomeres in VPT infants at birth compared to FT controls. Moreover, NICU-related stress emerged as a key regulator of TL erosion from birth to discharge in VPT infants. Future research is warranted to further explore TL erosion in VPT infants and the factors associated with individual differences in NICU-related stress susceptibility at the epigenetic level.

Background Very preterm (VPT) infants are hospitalized in Neonatal Intensive Care Units (NICUs) and are exposed to life-saving procedures eliciting pain-related stress. Recent research documented that pain-related stress might result in birth-to-discharge increased methylation of serotonin transporter gene (SLC6A4) in VPT infants, leading to poorer stress regulation at 3 months of age in VPT infants compared to their full-term (FT) counterparts. Maternal sensitivity is thought to support infants’ stress response, but its role in moderating the effects of altered SLC6A4 methylation is unknown. Main aim To assess the role of maternal sensitivity in moderating the association between altered SLC6A4 methylation and stress response in 3-month-old VPT and FT infants. Methods 53 infants (27 VPTs, 26 FTs) and their mothers were enrolled. SLC6A4 methylation was obtained from peripheral blood samples at NICU discharge for VPT infants and from cord blood at birth for FT infants. At 3 months (age corrected for prematurity), both groups participated to the face-to-face still-face (FFSF) paradigm to measure both infants’ stress response (i.e., negative emotionality) and maternal sensitivity. Results Maternal sensitivity did not significantly differ between VPT and FT infants’ mothers. In VPT infants, higher SLC6A4 methylation at hospital discharge associates with higher negative emotionality during the FFSF. In FT infants, SLC6A4 methylation and maternal sensitivity significantly interacted to predict stress response: a positive significant association between SLC6A4 methylation and negative emotionality emerged only in FT infants of less-sensitive mothers. Discussion Although no differences emerged in caregiving behavior in the two groups of mothers, maternal sensitivity was effective in moderating the effects of SLC6A4 methylation in FT infants, but not in VPT infants at 3 months. Speculatively, the buffering effect of maternal sensitivity observed in FT infants was disrupted by the altered early mother–infant contact due to NICU stay of the VPT group. These findings indirectly support that the effects of maternal sensitivity on infants’ socio-emotional development might be time dependent, and that mother–infant interventions in the NICU need to be provided precociously within a narrow sensitive period after VPT birth.

In addition to high intelligence, humans evolved specialized social-cognitive skills, which are specifically affected in children with autism spectrum disorder (ASD). Genes affected in ASD represent suitable candidates to study the evolution of human social cognition. We performed an evolutionary analysis on 68 genes associated to neurodevelopmental disorders; our data indicate that genetic diversity was shaped by distinct selective forces, including natural selection and introgression from archaic hominins. We discuss the possibility that segregation distortion during spermatogenesis accounts for a subset of ASD mutations. Finally, we detected modern-human-specific alleles in DYRK1A and TCF4. These variants are located within regions that display chromatin features typical of transcriptional enhancers in several brain areas, strongly suggesting a regulatory role. These SNPs thus represent candidates for association with neurodevelopmental disorders, and await experimental validation in future studies.

The Old World (OW) arenavirus complex includes several species of rodent-borne viruses, some of which (i.e., Lassa virus, LASV and Lymphocytic choriomeningitis virus, LCMV) cause human diseases. Most LCMV and LASV infections are caused by rodent-to-human transmissions. Thus, viral evolution is largely determined by events that occur in the wildlife reservoirs. We used a set of human- and rodent-derived viral sequences to investigate the evolutionary history underlying OW arenavirus speciation, as well as the more recent selective events that accompanied LASV spread in West Africa. We show that the viral RNA polymerase (L protein) was a major positive selection target in OW arenaviruses and during LASV out-of-Nigeria migration. No evidence of selection was observed for the glycoprotein, whereas positive selection acted on the nucleoprotein (NP) during LCMV speciation. Positively selected sites in L and NP are surrounded by highly conserved residues, and the bulk of the viral genome evolves under purifying selection. Several positively selected sites are likely to modulate viral replication/transcription. In both L and NP, structural features (solvent exposed surface area) are important determinants of site-wise evolutionary rate variation. By incorporating several rodent-derived sequences, we also performed an analysis of OW arenavirus codon adaptation to the human host. Results do not support a previously hypothesized role of codon adaptation in disease severity for non-Nigerian strains. In conclusion, L and NP represent the major selection targets and possible determinants of disease presentation; these results suggest that field surveys and experimental studies should primarily focus on these proteins.

The albuminoid gene family comprises vitamin D-binding protein (GC), alpha-fetoprotein (AFP), afamin (AFM), and albumin (ALB). Albumin is the most abundant human serum protein, and, as the other family members, acts as a transporter of endogenous and exogenous substances including thyroxine, fatty acids, and drugs. Instead, the major cargo of GC is 25-hydroxyvitamin D. We performed an evolutionary study of albuminoid genes and we show that ALB evolved adaptively in mammals. Most positively selected sites are located within albumin-binding sites for fatty acids and thyroxine, as well as at the contact surface with neonatal Fc receptor. Positive selection was also detected for residues forming the prostaglandin-binding pocket. Adaptation to hibernation/torpor might explain the signatures of episodic positive selection we detected for few mammalian lineages. Application of a population genetics–phylogenetics approach showed that purifying selection represented a major force acting on albuminoid genes in both humans and chimpanzees, with the strongest constraint observed for human GC. Population genetic analysis revealed that GC was also the target of locally exerted selective pressure, which drove the frequency increase of different haplotypes in distinct human populations. A search for known variants that modulate GC and 25-hydroxyvitamin D concentrations revealed linkage disequilibrium with positively selected variants, although European and Asian major GC haplotypes carry alleles with reported opposite effect on GC concentration. Data herein indicate that albumin, an extremely abundant housekeeping protein, was the target of pervasive and episodic selection in mammals, whereas GC represented a selection target during the recent evolution of human populations.

Summary T cell activation plays a central role in immune response and in the maintenance of self-tolerance. We analyzed the evolutionary history of T cell regulatory molecules. Nine genes involved in triggering T cell activation or in regulating the ensuing response evolved adaptively in mammals. Several positively selected sites overlap with positions interacting with the binding partner or with cellular components. Population genetic analysis in humans revealed a complex scenario of local ( FASLG , CD40LG, HAVCR2 ) and worldwide ( FAS , ICOSLG ) adaptation and H. sapiens -to-Neandertal gene flow (gene transfer between populations). Disease variants in these genes are preferential targets of pathogen-driven selection, and a Crohn's disease risk polymorphism targeted by bacterial - driven selection modulates the expression of ICOSLG in response to a bacterial superantigen. Therefore, we used evolutionary information to generate experimentally testable hypotheses concerning the function of specific genetic variants and indicate that adaptation to infection underlies the maintenance of autoimmune risk alleles.

Previous studies indicated that a few risk variants for autoimmune diseases are subject to pathogen-driven selection. Nonetheless, the proportion of risk loci that has been targeted by pathogens and the type of infectious agent(s) that exerted the strongest pressure remain to be evaluated. We assessed whether different pathogens exerted a pressure on known Crohn's disease (CD) risk variants and demonstrate that these single-nucleotide polymorphisms (SNPs) are preferential targets of protozoa-driven selection (P = 0.008). In particular, 19% of SNPs associated with CD have been subject to protozoa-driven selective pressure. Analysis of P values from genome-wide association studies (GWASs) and meta-analyses indicated that protozoan-selected SNPs display significantly stronger association with CD compared with nonselected variants. This same behavior was not observed for GWASs of other autoimmune diseases. Thus, we integrated selection signatures and meta-analysis results to prioritize five genic SNPs for replication in an Italian cohort. Three SNPs were significantly associated with CD risk, and combination with meta-analysis results yielded P values < 4 × 10 −6 . The bona fide risk alleles are located in ARHGEF2, an interactor of NOD2, NSF, a gene involved in autophagy, and HEBP1, encoding a possible mediator of inflammation. Pathway analysis indicated that ARHGEF2 and NSF participate in a molecular network, which also contains VAMP3 (previously associated to CD) and is centered around miR-31 (known to be disregulated in CD). Thus, we show that protozoa-driven selective pressure had a major role in shaping predisposition to CD. We next used this information for the identification of three bona fide novel susceptibility loci.

Humans possess a communication system based on spoken and written language. Other animals can learn vocalization by imitation, but this is not equivalent to human language. Many genes were described to be implicated in language impairment (LI) and developmental dyslexia (DD), but their evolutionary history has not been thoroughly analyzed. Herein we analyzed the evolution of ten genes involved in DD and LI. Results show that the evolutionary history of LI genes for mammals and aves was comparable in vocal-learner species and non-learners. For the human lineage, several sites showing evidence of positive selection were identified in KIAA0319 and were already present in Neanderthals and Denisovans, suggesting that any phenotypic change they entailed was shared with archaic hominins. Conversely, in FOXP2, ROBO1, ROBO2, and CNTNAP2 non-coding changes rose to high frequency after the separation from archaic hominins. These variants are promising candidates for association studies in LI and DD.

Preterm birth and Neonatal Intensive Care Unit (NICU) stay are early adverse stressful experiences, which may result in an altered temperamental profile. The serotonin transporter gene (SLC6A4), which has been linked to infant temperament, is susceptible to epigenetic regulation associated with early stressful experience. This study examined a moderation model in which the exposure to NICU-related stress and SLC6A4 methylation moderated infant temperament at 3 months of age. SLC6A4 methylation at 20 CpG sites was quantified in preterm infants (N = 48) and full-term infants (N = 30) from Italian middle-class families. Results suggested that in preterm infants NICU-related stress might be associated with alterations of serotonergic tone as a consequence of SLC6A4 methylation, which in turn, might associate with temperamental difficulties assessed at 3 months of age.

The complement system is an innate immunity effector mechanism; its action is antagonized by a wide array of pathogens and complement evasion determines the virulence of several infections. We investigated the evolutionary history of the complement system and of bacterial-encoded complement-interacting proteins. Complement components targeted by several pathogens evolved under strong selective pressure in primates, with selection acting on residues at the contact interface with microbial/viral proteins. Positively selected sites in CFH and C4BPA account for the human specificity of gonococcal infection. Bacterial interactors, evolved adaptively as well, with selected sites located at interaction surfaces with primate complement proteins. These results epitomize the expectation under a genetic conflict scenario whereby the host's and the pathogen's genes evolve within binding avoidance-binding seeking dynamics. In silico mutagenesis and protein-protein docking analyses supported this by showing that positively selected sites, both in the host's and in the pathogen's interacting partner, modulate binding.

Emotional face encoding processes in 2 types of tasks (direct and incidental) were explored in the current research through electroencephalographic (ERPs) and behavioral (response) measures. In Experiment 1 (incidental task) ERP correlates of 21 subjects were recorded when they viewed emotional (anger, sadness and happiness) or neutral facial stimuli. An emotion-specific cortical variation was found, a negative deflection at about 200 ms poststimulus (N2 effect). This effect was sensitive to the perceived emotional value of faces, since it differentiated negative high arousal (i.e., anger) from low arousal (i.e., sadness) or positive (happiness) emotions. Moreover, a specific cortical site (parietal) was activated by emotional faces but not by neutral faces. In Experiment 2 (20 subjects) a direct encoding task (emotion comprehension) was provided. We explored whether encoding for emotional faces relies on a single neural system irrespective of the task (incidental or direct), or whether it is supported by...

Ethical, legal, and social issues related to the collection, storage, and use of biospecimens and data derived from children raise critical concerns in the international debate. So far, a number of studies have considered a variety of the individual issues crucial to pediatric biobanking such as decision making, privacy protection, minor recontact, and research withdrawal by focusing on theoretical or empirical perspectives. Our research attempted to analyze such issues in a comprehensive manner by exploring practices, rules, and researcher opinions regarding proxy consent, minor assent, specimens and data handling, and return of results as faced in 10 European countries. Because of the lack of comparative analyses of these topics, a pilot study was designed. Following a qualitative methodology, a questionnaire draft mostly including open-ended queries was developed, tested, and sent by e-mail to a selected group of researchers dealing with pediatric biobanking (n=57). Returned questionnaires (n=31) highlighted that the collection, storage, distribution, and use of biospecimens and data from children were widely practiced in the contacted laboratories. In most cases, pediatric biobanking was subjected to national or local regulations covering adult biobanks (n=26). Informed consent was generally given by parents or legal representatives (n=17). Children's opinions were frequently sought and taken into account (n=16). However, minors were usually not recontacted at the age of maturity to express their own choices (n=26). Based on the collected data, dedicated recommendations are needed to govern unique ethical and regulatory issues surrounding pediatric biobanking.