Using GWAS and Machine Learning to Identify and Predict Genetic Variants Associated with Foodborne Bacteria Phenotypic Traits.

One of the main challenges in food microbiology is to prevent the risk of outbreaks by avoiding the distribution of food contaminated by bacteria. This requires constant monitoring of the circulating strains throughout the food production chain. Bacterial genomes contain signatures of natural evolution and adaptive markers that can be exploited to better understand the behavior of pathogen in the food industry. The monitoring of foodborne strains can therefore be facilitated by the use of these genomic markers capable of rapidly providing essential information on isolated strains, such as the source of contamination, risk of illness, potential for biofilm formation, and tolerance or resistance to biocides. The increasing availability of large genome datasets is enhancing the understanding of the genetic basis of complex traits such as host adaptation, virulence, and persistence. Genome-wide association studies have shown very promising results in the discovery of genomic markers that can be integrated into rapid detection tools. In addition, machine learning has successfully predicted phenotypes and classified important traits. Genome-wide association and machine learning tools have therefore the potential to support decision-making circuits intending at reducing the burden of foodborne diseases. The aim of this chapter review is to provide knowledge on the use of these two methods in food microbiology and to recommend their use in the field.

Molecular evolution and genotype shift of Porcine circoviruses type 2 in Vietnam.

Porcine Circovirus Type 2 (PCV2), a significant pathogen in the global swine industry, causes Porcine Circovirus Associated Diseases (PCVAD), contributing to substantial economic losses. This study investigates the genetic diversity and evolutionary dynamics of PCV2 in Vietnam from 2007 to 2023. We sequenced and analyzed 47 PCV2 genomes isolated from swine farms across Vietnam between 2022 and 2023, revealing predominant circulation of PCV2d (80.85%) followed by PCV2b (19.15%). Phylogenetic analysis identified PCV2 genotypes PCV2a, PCV2b, PCV2d, PCV2g, and PCV2h circulating in Vietnam, with PCV2d emerging as the most prevalent genotype. Comparison with historical data highlighted genotype shifts from PCV2b to PCV2d in 2014. Interestingly, PCV2h genotype was mainly observed between 2008 and 2012 but have not been detected since 2014. Regional analysis indicated varied PCV2 epidemiological patterns between northern and southern Vietnam. Amino acid substitutions within the capsid protein were identified, predominantly in antigenic regions critical for immune recognition. Positive selection analysis identified multiple sites under evolutionary pressure, indicating ongoing adaptation of Vietnamese PCV2 strains. These findings enhance understanding of PCV2 dynamics in Vietnam and underscore the importance of continuous surveillance and adaptive management strategies in controlling PCV2-associated diseases in swine populations.

Novel autosomal recessive SINO syndrome-associated KIDINS220 variants provide insight into the genotype-phenotype correlation.

Background: KIDINS220 encodes a transmembrane scaffold protein, kinase D-interacting substrate of 220 kDa, that regulates neurotrophin signaling. Variants in KIDINS220 have been linked to spastic paraplegia, intellectual disability, nystagmus, and obesity (SINO) syndrome or prenatal fatal cerebral ventriculomegaly and arthrogryposis (VENARG). This study aimed to investigate the genotype-phenotype correlation of pathogenic KIDINS220 variants. Methods: We performed whole-exome sequencing on a patient with SINO syndrome and epilepsy. Identified pathogenic variants were confirmed using Sanger sequencing and evaluated with in silico tools. A comprehensive literature review was conducted to analyze the genetic and phenotypic data of both the newly diagnosed patient and previously reported cases with KIDINS220 variants. Results: We identified novel compound heterozygous variants in KIDINS220, c.1556C > T (p.Thr519Met) and c.2374C > T (p.Arg792*), in the patient. Our analysis revealed that biallelic loss-of-function variants in KIDINS220 are associated with VENARG or autosomal recessive SINO (AR-SINO), whereas carboxy-terminal truncated variants that escape nonsense-mediated mRNA decay and lack amino acid residues 1507-1529 are linked to autosomal dominant SINO (AD-SINO). Patients with AR-SINO exhibit more severe clinical features compared to those with AD-SINO. Conclusions: Our study expands the spectrum of KIDINS220 variants associated with AR-SINO and provides a valuable genotype-phenotype correlation for pathogenic KIDINS220 variants.

Similarity of Phenotype in Three Male Patients With the c.320A>G Variant in ALG13: Possible Genotype-Phenotype Correlation.

BACKGROUND: Congenital disorders of glycosylation (CDG) are a group of neurometabolic diseases that result from genetic defects in the glycosylation of proteins and/or lipids. Multiple pathogenic genes contribute to the varying reported phenotypes of individuals with CDG-1 syndromes, most of which are inherited as autosomal recessive traits, although X-linked inheritance has also been reported. Pathogenic variants in the asparagine-linked glycosylation 13 homolog (ALG13) gene have been implicated in the aetiology of developmental and epileptic encephalopathy (DEE) 36 (OMIM:*300776, DEE36). The NM_001099922.3:c.320A>G; p.(Asn107Ser) variant is the most frequently described pathogenic variant in ALG13, with 59 females and 2 males with this variant reported to date. METHODS: We report on a male with a de novo, hemizygous variant in ALG13: c.320A>G; p.(Asn107Ser), whose phenotype resembles that of two previously reported males with the same variant. RESULTS: All three males have a de novo mutation, infantile spasms, DEE, drug-resistant epilepsy, intellectual disability, dysmorphic findings, recurrent infections, skeletal anomalies, brain abnormalities and a movement disorder: a phenotype not consistently reported in males with other pathogenic variants in ALG13. CONCLUSION: The similarity of phenotype in the three males with the c.320A>G variant in ALG13, suggests a possible genotype-phenotype correlation.

The prevalence of hepatitis C virus genotypes and factors associated with cirrhosis, fatty liver, and viral load: A registry-based cross-sectional cohort study in Western Iran during 1999-2023.

Background and Aims: Hepatitis C virus (HCV) is an important infectious disease that imposes a significant burden on healthcare systems. Determining the prevalence of HCV genotypes in a area is essential for the successful implementation of HCV elimination programs and allocation of financial resources to direct-acting antiviral direct-acting antivirals (DAA) treatments against prevalent HCV genotypes. Accordingly, we conducted a registry-based cross-sectional cohort study to investigate the prevalence of HCV genotypes and factors associated with cirrhosis, fatty liver, and viral load in Kermanshah Province, Western Iran. Methods: Patients presenting to the Hepatitis Clinic of the Research Center for Infectious Diseases affiliated with Kermanshah University of Medical Sciences between 1999 and 2023 were enrolled in this study. Serum samples were collected to assess HCV genotypes and viral load. Additionally, demographic data and the status of cirrhosis and fatty liver were extracted from the registry system records throughout the study period. Results: Records of 828 patients with an average age of 40.38 ± 11.72 years (range: 11-80 years) were included in the study that 721 individuals were male, and 107 were female. The prevalence of fatty liver and cirrhosis was 30.3% and 12.9%, respectively. Four genotypes (1, 2, 3, and 4) and four subtypes (1a, 1b, 3a, and 3b) were identified, with subtype 3a (55.7%) being the most prevalent, followed by subtype 1a (34.3%). None of the variables including age, gender, viral load level, and genotypes 1 and 3 were associated with fatty liver or cirrhosis. However, age, gender, and genotype were correlated with the viral load (p ≤ 0.05). Conclusion: The most common HCV subtypes in Kermanshah were 3a and 1a. Genotypes 2 and 4 were identified in one case each. Further studies on identifying HCV subtypes in different regions of the country are recommended to manage HCV infection and predict the prognosis.

A comprehensive genotype-phenotype study in 203 individuals with retinoblastoma.

Retinoblastoma is the most common intraocular tumor in children and is caused by biallelic inactivation of the RB1 gene. The identification of RB1 germline variants in patients with retinoblastoma and their families is critical for early diagnosis and prevention. In this study, genetic testing was conducted on the genomic DNA of 203 patients with retinoblastoma using a combined approach of direct sequencing and multiplex ligation-dependent probe amplification (MLPA) assays for genotype-phenotype correlation studies. Sixty-five germline variants were identified in 80 of the 203 patients, with 67 bilateral and 13 unilateral retinoblastoma cases. The variant detection rates in the bilateral and unilateral cases were 88% and 10%, respectively. Eighteen novel variants were identified. Variants were classified according to their presence, mutation pattern, location, molecular consequences, and pathogenicity. Subsequently, the genotypes and phenotypes of the 203 patients were evaluated. Variants were associated with age at diagnosis (p < 0.001), laterality (p < 0.001), and tumor size (p = 0.010). The molecular consequences of the variants were related to laterality (p < 0.001) and tumor size (p = 0.001). The pathogenicity of the variants was associated with age at diagnosis (p = 0.001), laterality (p = 0.0212), treatment response (p = 0.0470), and tumor size (p = 0.002). These results suggest that patient phenotypes are associated with the inherent characteristics of germline RB1 variants. These findings indicate the potential application of genetic testing results in clinical practice.

A novel PAX9 variant in a Chinese family with non-syndromic oligodontia and genotype-phenotype analysis of PAX9variants.

OBJECTIVES: This study aimed to identifyPAX9variants in non-syndromic tooth agenesis families of China, as well as to analyze the genotype⁃phenotype of non-syndromic tooth agenesis caused by PAX9variants, which can provide a basis for the genetic diagnosis of tooth agenesis. METHODS: We collected the data of 44 patients with non-syndromic oligodontia who underwent treatment at Stomatological Hospital of Hebei Medical University between 2018 and 2023. Whole-exome sequencing was performed on the peripheral blood of the proband and its core family members, and the variants were verified by Sanger sequencing. Pathogenicity analysis and function prediction of the variants were performed using bioinformatics tools. The correlation between the genotype of PAX9 variant and its corresponding phenotype was examined by reviewing 55 publications retrieved from PubMed. The studies involved 232 tooth agenesis patients with PAX9 variants. RESULTS: A novel PAX9 c.447delG (p.Pro150Argfs*62) and a reported PAX9 c.406C>T (p.Gln136*) were identified in two Chinese families. Through bioinformatics analysis and three-dimensional structural modeling, we postulated that the frameshift variant was pathogenic. The outcome was the premature cessation of PAX9 protein, which caused severe structural and functional deficiencies. Summarizing the PAX9 genotype-phenotype relationship revealed that patients carrying the PAX9 variant commonly led to loss of the second molars. CONCLUSIONS: We identified the novel PAX9 c.447delG (p.Pro150Argfs*62) in a Chinese family of non-syndromic oligodontia, expanding the known variant spectrum of PAX9. The most susceptible tooth position for PAX9 variants of tooth agenesis was the second molars and the deciduous molars during the deciduous dentition.

High prevalence of HPV-56 and HPV-39 in Sari, Iran: an analysis of genotype distribution.

BACKGROUND: Human papillomavirus (HPV) is responsible for the most common sexually transmitted infection, particularly among sexually active individuals. Understanding the geographical distribution and epidemiology of the most prevalent HPV genotypes is essential for developing effective prevention strategies. Consequently, this study aimed to examine the distribution of HPV genotypes among HPV-positive women and men in Sari, the capital city of Mazandaran province in northern Iran. MATERIALS AND METHODS: HPV DNA was extracted (PZP Company, Molecular IVD, Iran) from genital and cervical samples of the study participants. Genotyping was conducted for 90 cases utilizing the High + Low Papilloma Strip test (Operon Company, Spain). Demographic data were statistically analyzed in correlation with the virological data (STATA version 17). RESULTS: Overall, 67.7% (61 out of 90) of the cases tested positive for HPV, with 75% of those being classified as high-risk. The participant group consisted of 92% females (83) and 8% males (7). The highest HPV prevalence, 75% (36), was observed in females and males aged under 31, with the majority of positive cases belonging to high-risk genotypes. The most frequently identified genotypes were HPV-11 (23%), HPV-6 (21%), HPV-56 (18%), HPV-39 (16%), HPV-16, HPV-91, and HPV-66 each comprising (14%). HPV-56 was the most common high-risk genotype, accounting for 11 cases (18%), followed by HPV-39, which was present in 10 cases (16%). CONCLUSION: The prevalence of HPV infection was particularly high among individuals under the age of 31 for both genders, with men exhibiting a 100% infection rate. These findings emphasize the urgent need for targeted education aimed at the younger population and the implementation of infection control measures. Specifically, widespread HPV vaccination targeting HPV-6, HPV-11, HPV-39, and HPV-56 should be prioritized for the general population.

Effect of Severe Fever With Thrombocytopenia Syndrome Virus Genotype on Disease Severity, Viral Load, and Cytokines in South Korea.

Background: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne disease caused by Bandavirus dabieense (SFTS virus [SFTSV]). Recently, at least 6 different genotypes of SFTSV have been identified, with genotypes A, D, and F dominant in China and B dominant in Japan and Korea. This study investigated the effect of SFTSV genotypes circulating in South Korea on disease severity, viral load, and cytokine profile. Methods: We prospectively enrolled 70 patients with SFTS from July 2015 to June 2022. Serial plasma samples were obtained during hospitalization and analyzed. Viral load was measured by real-time reverse-transcription polymerase chain reaction. Partial sequences of the viral genome were analyzed for genotyping. Plasma concentrations of 17 cytokines were measured by multiplex-bead immunoassay. Results: Of 70 samples, 51 could be genotyped. Genotype B was predominant (80.4%) and other genotypes were uncommon. Intensive care unit admission rates (51.2% vs 50.0%) and mortality rates (26.8% vs 40.0%) did not show any significant differences between genotype B and non-B genotypes. The initial viral load did not show any significant differences (3.59 vs 3.64 log copies/µL), whereas viral load measured at hospital day 3-4 tended to be higher in genotype B than non-B genotypes (3.83 vs 1.83 log copies/µL, P = .07). Additionally, the plasma concentrations of interferon-α, interleukin 10, and interferon-γ-induced protein 10, which are closely related to mortality in cases of SFTS, did not show any significant differences. Conclusions: SFTSV genotype B was the prevalent genotype in South Korea, with no genotype-specific difference in clinical outcomes, initial viral load, or cytokine profiles.

Among- and within-population variation in germination response shapes ecological resilience in the Mediterranean cliff species Brassica incana Ten.

BACKGROUND AND AIMS: Understanding how plant species respond to extreme conditions is crucial for predicting their ecological resilience under climate change. Here, we aim to forecast the ecological resilience of the Mediterranean cliff species Brassica incana (Brassicaceae) by estimating population variation in germination response under novel extreme environmental conditions. METHODS: We investigated the thermal germination responses in 14 populations of B. incana by exposing seeds to temperatures within and outside conditions experienced in their local environment. Then, we quantified among- and within-population variation in germination response to extreme temperatures, estimated genotype-by-environment interactions (G × E) and tested if population performance at extreme temperatures is explained by local climate. KEY RESULTS: We found significant among-population differences in germination response, a different level of within-population variability, and different mechanisms underlying G × E patterns. Also, populations experiencing warmer temperatures in their local environment showed a better performance at both cold and hot extremes while populations experiencing colder temperatures showed a limited ability to germinate under extreme conditions. CONCLUSIONS: Our results suggest that populations experiencing warmer temperatures in their local environment have a higher potential to face future thermal extreme conditions and their role is thus crucial to promote species ecological resilience.

Ranking the attribution of high-risk genotypes among women with cervical precancers and cancers: a cross-sectional study in Ningbo, China.

BACKGROUND: The region-specific importance of carcinogenic HPV genotypes is required for optimizing HPV-based screening and promoting appropriate multivalent HPV prophylactic vaccines. This information is lacking for Ningbo, one of the first cities of China's Healthy City Innovation Pilot Program for Cervical Cancer Elimination. Here, we investigated high-risk HPV (HR-HPV) genotype-specific distribution and attribution to biopsy-confirmed cervical intraepithelial neoplasia grade 2 or worse (CIN2+) before mass vaccination in Ningbo, China. METHODS: A total of 1393 eligible CIN2+ archived blocks (including 161 CIN2, 1107 CIN3, and 125 invasive cervical cancers [ICC]) were collected from 2017 to 2020 in Ningbo. HR-HPV DNA was genotyped using the SPF10-DEIA-LiPA25 version 1 detection system and the SureX HPV 25X Genotyping Kit. Genotype-specific attribution to CIN2+ was estimated using a fractional contribution approach. RESULTS: Ranking by the attributable proportions, HPV16 remained the most important genotype in both cervical precancers and cancers, accounting for 36.8% of CIN2, 53.2% of CIN3, and 73.3% of ICC cases. Among cervical precancers, HPV52 (17.3% in CIN2, 12.7% in CIN3) and HPV58 (13.9%, 14.9%) ranked second and third, while HPV33 (8.3%, 7.9%) and HPV31 (6.5%, 4.1%) ranked fourth and fifth, respectively. However, among ICCs, HPV18 (5.7%) accounted for the second highest proportion, followed by HPV33 (5.4%), HPV58 (4.0%), and HPV45 (3.2%). HPV18/45 together accounted for 46.8% of adenocarcinomas, which was slightly lower than that of HPV16 (47.7%). The remaining HR-HPV genotypes (HPV35/39/51/56/59/66/68) combined accounted for only 6.7% of CIN2, 2.9% of CIN3, and 4.2% of ICC. CONCLUSIONS: With Ningbo's strong medical resources, it will be important to continue HPV16/18 control efforts, and could broaden to HPV31/33/45/52/58 for maximum health benefits. However, different strategies should be proposed for other HR-HPV genotypes based on their lower carcinogenic risks.

Human papillomavirus type-specific distribution in cervical intraepithelial neoplasia and cancer in The Gambia prior to HPV immunization programme: a baseline for monitoring the quadrivalent vaccine.

BACKGROUND: Cervical cancer is the leading cause of cancer deaths in Gambian women. Current estimates indicate that 286 women are annually diagnosed with cervical cancer with a fatality rate of 70%. In an attempt to address this, in 2019 the quadrivalent HPV vaccine was incorporated into the Gambia's Expanded Programme on Immunisation. The study aims to retrospectively assess the prevalence and distribution of high-risk HPV genotype in archived, formalin fixed paraffin embedded cervical biopsy tissues diagnosed with cervical cancer in the Gambia from year 2013-2022. METHOD: A total of 223 samples with histologically diagnosis of cervical cancer with adequate tissues were sectioned and deparaffinised, followed by HPV DNA extraction and the detection of HR-HPV by real-time multiplex PCR. The human ß-globin gene was amplified in 119 samples, which were subsequently tested for HPV DNA. RESULTS: HPV was prevalent in 87.4% (104 of 119) cervical cancer cases, 12.6% (15/119) samples tested negative. Amongst cervical cancer cases, HPV 16 genotype was the most frequent type accounting for 53.8% (56 /104), followed by other HR-HPV genotypes 17.3% (18/104), and HPV genotype 18 was 15.4% (16/104). Furthermore, multiple HPV infections involving HPV 16 and /or 18 was detected in 14 cases as follows: HPV genotypes 16 and 18 (3.8%, 4 /104), HPV 16 and other HR-HPV (6.7%, 8/104), and HPV 18 and other HR-HPV (1.9%, 2/104). A significant association between age and diagnosis with cervical cancer (p = 0.02), and HPV genotype 16 (p = 0.04) was observed. CONCLUSION: There was no difference in the distribution of HPV 16 and 18 genotypes in cervical cancer cases in The Gambia in comparison with the global distribution. However, the high prevalence of cervical cancer cases with other HR-HPV, and combined infections of HPV 16 with other HR-HPV genotypes seen in this study, clearly shows that the nonavalent HPV vaccine could be more beneficial for The Gambia. This study provides The Gambia with a baseline data to use in policy decisions regarding future evaluation of the quadrivalent HPV vaccine in the country.

HIV drug resistance: analysis of viral genotypes and mutation loci in people living with HIV in Chongqing, China (2016-2023).

BACKGROUND: Large-scale HIV genotype drug resistance study has not been conducted in Chongqing. METHODS: A retrospective study was conducted on people living with HIV(PLWH) who received HIV-1 genotype resistance testing at Chongqing Public Health Medical Center from May 2016 to June 2023. The HIV-1pol gene was amplified through RT-PCR and analyzed in terms of genotypic drug resistance. RESULTS: Of the 3015 PLWH tested for HIV-1 drug resistance, 1405 (46.6%) were resistant to at least one antiviral drug. Among non-nucleoside reverse transcriptase inhibitors (NNRTIs), 43.8% were resistant, compared to 29.5% for nucleoside reverse transcriptase inhibitors (NRTIs) and 3.4% for protease inhibitors (PIs). V179D/E and K103N/S were identified as the common mutation sites in the NNRTIs class of drugs, M184V/I and K65R/N were reported as the most common mutation sites in NRTIs, while thymidine analogue mutation (TAM) group was identified in 373 samples. L10FIV was the most common mutation in PIs. The dominant HIV-1 subtype was CRF07_BC. CONCLUSIONS: The high prevalence of HIV-1 drug resistance in Chongqing underscores the imperative for rigorous surveillance of the local HIV epidemic. Furthermore, TAMs are associated with HIV-1 multidrug resistance, and timely detection of drug resistance is helpful to reduce the emergence and spread of such drug-resistant strains.

The Comparative Full-Length Genome Characterization of African Swine Fever Virus Detected in Thailand.

African swine fever virus (ASFV) has been responsible for the globally devastating epidemics in wild and domesticated pigs. Of the 24 identified ASFV genotypes, genotype II is the primary cause for the pandemic occurring in Europe and Asia since its emergence in Georgia in 2007. The current study aimed to characterize the full-length genomic pattern of the ASFV strain from Thailand, TH1_22/CR (Accession No. PP915735), which was then compared with genomic diversity across other Asian isolates using Georgia 2007/1 (Accession No. FR682468) as the reference. Viral DNA was isolated from the pig spleen sample following library preparation and paired-end sequencing using the MiSeq Illumina platform. The sequenced TH1_22/CR isolate spanned 189,395 nucleotides encoding 193 open reading frames (ORFs), exhibiting maximum nucleotide similarity (99.99%) with Georgian (Georgia 2007/1) and Chinese (Wuhan 2019-1 and China HLJ) isolates. Based on phylogenetic analysis, the TH1_22/CR isolate (Accession No. PP915735) was characterized as genotype II, serogroup 8, and IGR-II due to the presence of three tandem repeat sequences (TRSs). Genetic variations including SNPs and single and polynucleotide indels were identified in TH1_22/CR in agreement with other Asian isolates. For comprehensive analysis, the genome was divided into four regions (I-IV) based on gene location. Overall, the TH1_22/CR isolate demonstrated eight SNPs and indels in its genome. Two unique SNPs were reported in the coding regions of the TH1_22/CR isolate, out of which, a C-591-T substitution was seen in MGF 360-4L and a C-297-T was found in A238L, and four unique SNPs were reported in non-coding regions (NCRs). Furthermore, a 29 bp deletion was observed in the IGR between MGF 110-13La and MGF 110-13Lb, as well as 52 bp deletion in the ASFV G ACD 00350 gene. This comparative analysis establishes the foundational information for future studies on the diversity and phylogeography of this regionally significant genetic sub-group of ASFV.

Distinguishing mutants that resist drugs via different mechanisms by examining fitness tradeoffs.

There is growing interest in designing multidrug therapies that leverage tradeoffs to combat resistance. Tradeoffs are common in evolution and occur when, for example, resistance to one drug results in sensitivity to another. Major questions remain about the extent to which tradeoffs are reliable, specifically, whether the mutants that provide resistance to a given drug all suffer similar tradeoffs. This question is difficult because the drug-resistant mutants observed in the clinic, and even those evolved in controlled laboratory settings, are often biased towards those that provide large fitness benefits. Thus, the mutations (and mechanisms) that provide drug resistance may be more diverse than current data suggests. Here, we perform evolution experiments utilizing lineage-tracking to capture a fuller spectrum of mutations that give yeast cells a fitness advantage in fluconazole, a common antifungal drug. We then quantify fitness tradeoffs for each of 774 evolved mutants across 12 environments, finding these mutants group into classes with characteristically different tradeoffs. Their unique tradeoffs may imply that each group of mutants affects fitness through different underlying mechanisms. Some of the groupings we find are surprising. For example, we find some mutants that resist single drugs do not resist their combination, while others do. And some mutants to the same gene have different tradeoffs than others. These findings, on one hand, demonstrate the difficulty in relying on consistent or intuitive tradeoffs when designing multidrug treatments. On the other hand, by demonstrating that hundreds of adaptive mutations can be reduced to a few groups with characteristic tradeoffs, our findings may yet empower multidrug strategies that leverage tradeoffs to combat resistance. More generally speaking, by grouping mutants that likely affect fitness through similar underlying mechanisms, our work guides efforts to map the phenotypic effects of mutation.

Mutations in an organism's DNA make the individual more likely to survive and reproduce in its environment, passing on its mutations to the next generation. Mutations can alter the proteins that a gene codes for in many ways. This leads to a situation where seemingly similar mutations ­ such as two mutations in the same gene ­ can have different effects. For example, two different mutations could affect the primary function of the encoded protein in the same way but have different side effects. One mutation might also cause the protein to interact with a new molecule or protein. Organisms possessing one or the other mutation will thus have similar odds of surviving and reproducing in some environments, but differences in environments where the new interaction is important. In microorganisms, mutations can lead to drug resistance. If drug-resistant mutations have different side effects, it can be challenging to treat microbial infections, as drug-resistant pathogens are often treated with sequential drug strategies. These strategies rely on mutations that cause resistance to the first drug all having susceptibility to the second drug. But if similar seeming mutations can have diverse side effects, predictions about how they will respond to a second drug are more complicated. To address this issue, Schmidlin, Apodaca et al. collected a diverse group of nearly a thousand mutant yeast strains that were resistant to a drug called fluconazole. Next, they asked to what extent the fitness ­ the ability to survive and reproduce ­ of these mutants responded similarly to environmental change. They used this information to cluster mutations into groups that likely have similar effects at the molecular level, finding at least six such groups with unique trade-offs across environments. For example, some groups resisted only low drug concentrations, and others were unique in that they resisted treatment with two single drugs but not their combination. These diverse types of fluconazole-resistant yeast lineages highlight the challenges of designing a simple sequential drug treatment that targets all drug-resistant mutants. However, the results also suggest some predictability in how drug-resistant infections can evolve and be treated.

Monovalent rotavirus vaccine effectiveness and long-term impact among children <5 years old in Antananarivo, Madagascar, 2010-2022.

BACKGROUND: Monovalent rotavirus vaccine substantially reduced rotavirus disease burden after introduction (May 2014) in Madagascar. We examined the effectiveness and long-term impact on acute watery diarrhea and rotavirus-related hospitalizations among children <5 years old at two hospitals in Antananarivo, Madagascar (2010-2022). METHODS: We used a test-negative case-control design to estimate monovalent rotavirus vaccine effectiveness (VE) against laboratory-confirmed rotavirus hospitalizations among children age 6-23 months with documented vaccination status adjusted for year of symptom onset, rotavirus season, age group, nutritional status, and clinical severity. To evaluate the impact, we expanded to children age 0-59 months with acute watery diarrhea. First, we used admission logbook data to compare the proportion of all hospitalizations attributed to diarrhea in the pre-vaccine (January 2010-December 2013), transition period (January 2014-December 2014), and post-vaccine (January 2015-December 2022) periods. Second, we used active surveillance data (June 2013-May 2022) to describe rotavirus positivity and detected genotypes by vaccine introduction period and surveillance year (1 June-31 May). RESULT: Adjusted VE of at least one dose against hospitalization due to rotavirus diarrhea among children age 6-23 months was 61 % (95 % CI: -39 %-89 %). The annual median proportion of hospitalizations attributed to diarrhea declined from 28 % in the pre-vaccine to 10 % in the post-vaccine period. Rotavirus positivity among hospitalized children age 0-59 months with acute watery diarrhea was substantially higher during the pre-vaccine (59 %) than the post-vaccine (23 %) period. In the pre-vaccine period, G3P[8] (76 %) and G2P[4] (12 %) were the dominant genotypes detected. Although genotypes varied by surveillance year, G1P[8] and G2P[4] represented >50 % of the genotypes detected post-introduction. CONCLUSIONS: Rotavirus vaccine has been successfully implemented in Madagascar's routine childhood immunization program and had a large impact on rotavirus disease burden, supporting continued use of rotavirus vaccines in Madagascar.

Genotype-Guided Antiplatelet Therapy: JACC Review Topic of the Week.

The clinical efficacy and safety of antiplatelet agents vary among patients. Consequently, some patients are at increased risk of recurrent ischemic events during treatment. This interindividual variability can be a result of genetic variants in enzymes that play a role in drug metabolism. The field of pharmacogenomics explores the influence of these genetic variants on an individual's drug response. Tailoring antiplatelet treatment based on genetic variants can potentially result in optimized dosing or a change in drug selection. Most evidence supports guiding therapy based on the CYP2C19 allelic variants in patients with an indication for dual antiplatelet therapy. In ticagrelor-treated or prasugrel-treated patients, a genotype-guided de-escalation strategy can reduce bleeding risk, whereas in patients treated with clopidogrel, an escalation strategy may prevent ischemic events. Although the clinical results are promising, few hospitals have implemented these strategies. New results, technological advancements, and growing experience may potentially overcome current barriers for implementation in the future.

Genotype and phenotype analysis of α-thalassemia fusion gene in southern China.

OBJECTIVE: The α-globin fusion gene between the HBA2 and HBAP1 genes, is clinically important in thalassemia screening because this fusion gene can cause severe hemoglobin (Hb) H disease when combined with α0 -thalassemia (α0 -thal). In this study, we evaluate the red blood cell parameters of α-thalassemia fusion gene in southern China. METHOD: Study samples suspected of α-thalassemia fusion gene were collected and confirmed by PCR-sequencing from one medical lab center in southern China. Their genotypes and phenotypes were analyzed. RESULTS: A total of 266 cases of α-thalassemia fusion gene were confirmed in our lab from 2017 to 2023, most of them were from Hainan province (169 cases) and Huadu district of Guangzhou (21 cases), the nationality of 143 cases from Hainan was identified, with 71.3% (102/143) being from the Li minority. The Hb, MCV, MCH for αα/(αα)fusion in adult males were 143.5±11.83g/L, 81.51±4.39 fl, and 26.26±1.29 pg, respectively; and in females, they were 126.69±12.89 g/L, 80.10±4.05 fl, 25.8±2.04 pg, respectively. All 12 cases (αα) Fusion/ --SEA showed anemia with decreased Hb, MCV and MCH. CONCLUSION: The carriers of α-globin fusion gene heterozygotes are clinically silent and exhibit an α+ phenotype. Individuals with (αα)Fusion/--SEA show apparent anemia. This α-globin fusion gene is relatively common in southern China, specifically among the Li minority of Hainan province. Therefore, it should be taken into account for genetic counseling purposes.

When is an SNP not an SNP?

Genomic duplications are important sources of structural change and gene innovation. In humans, the most recent and highly identical sequences (>90% homology, >1 kb long) are known as segmental duplications (SDs). Single-nucleotide variants or single-nucleotide polymorphisms within SDs have not been systematically assessed due to limitations around mapping short-read sequencing data. Single-nucleotide variant rs62486260 was flagged in a study of familial renal stone disease but it was unclear whether it was real or an artifact resulting from the presence of a SD. We describe in silico and wet-lab approaches to investigate this, using segment-specific long-PCR assays, followed by short PCR for Sanger sequencing. Our conclusion was that rs62486260 is an artifact. Our approach can be generalized to deal with other such situations.

The method described includes a two-step procedure for determining whether an apparent single-nucleotide polymorphism may be an artifact resulting from the presence of a duplicated genomic region/pseudogene. Step one involves identifying sequence differences between the two duplicated regions and designing a long PCR assay to specifically amplify each region separately. Step 2 involves amplifying a short PCR product which flanks the single-nucleotide polymorphism of interest, from the long products generated in step 1.