Background The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatment. Herein we present the initial results correlating RT-PCR quality control metrics with sample collection and sequencing methods from full SARS-CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021. Methods RT-PCR confirmed (N Gene Ct value < 30) positive patient samples, with nucleic acid extracted from saliva, nasopharyngeal and oropharyngeal swabs were selected for viral whole genome SARS-CoV-2 sequencing. Sequencing was performed using Illumina COVIDSeq™ protocol on either the NextSeq550 or NovaSeq6000 systems. Informatic variant calling, and lineage analysis were performed using DRAGEN COVID Lineage applications on Illumina’s Basespace cloud analytical system. All sequence data and variant calls were uploaded to NCBI and GISAID. Results An association was observed between higher sequencing coverage, quality, and samples with a lower Ct value, with < 27 being optimal, across both sequencing platforms and sample collection methods. Both nasopharyngeal swabs and saliva samples were found to be optimal samples of choice for SARS-CoV-2 surveillance sequencing studies, both in terms of strain identification and sequencing depth of coverage, with NovaSeq 6000 providing higher coverage than the NextSeq 550. The most frequent variants identified were the B.1.617.2 Delta (India) and P.1 Gamma (Brazil) variants in the samples sequenced between April 2021 and June 2021. At the time of submission, the most common variant > 99% of positives sequenced was Omicron. Conclusion These initial analyses highlight the importance of sequencing platform, sample collection methods, and RT-PCR Ct values in guiding surveillance efforts. These surveillance studies evaluating genetic changes of SARS-CoV-2 have been identified as critical by the CDC that can affect many aspects of public health including transmission, disease severity, diagnostics, therapeutics, and vaccines.

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Background The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatment. Herein we present the initial results from full SARS- CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021. Methods RT-PCR confirmed (N Gene Ct value <30) positive patient samples, with nucleic acid extracted from saliva, nasopharyngeal and oropharyngeal swabs were selected for viral whole genome SARS-CoV-2 sequencing. Sequencing was performed using Illumina COVIDSeqtm protocol on either the NextSeq550 or NovaSeq6000 systems. Informatic variant calling, and lineage analysis were performed using DRAGEN COVID Lineage applications on Illumina’s Basespace cloud analytical system. All sequence data and variant calls were uploaded to NCBI and GISAID. Results An association was observed between higher sequencing coverage, quality, and samples with a lower Ct value, with <27 being optimal, across both sequencing platforms and sample collection methods. Both nasopharyngeal swabs and saliva samples were found to be optimal samples of choice for SARS-CoV2 surveillance sequencing studies, both in terms of strain identification and sequencing depth of coverage, with NovaSeq 6000 providing higher coverage than the NextSeq 550. The most frequent variants identified were the B.1.617.2 Delta (India) and P.1 Gamma (Brazil) variants. Conclusion These initial analyses highlight the importance of sequencing platform, sample collection methods, and RT-PCR Ct values in guiding surveillance efforts to inform the public of variant transmission rates, with the potential to facilitate correlation of sequencing data with vaccine efficacy rate and efficacy of infection prevention precautions.

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Introduction Hypogonadism is common in men with male factor infertility and hormone therapies may improve semen parameters and pregnancy rates in affected men. However, compared to paternal factors such as advanced age, male infertility or obesity, it is uncertain whether hypogonadism itself impacts perinatal birth outcomes and complications. Objective This study evaluates the association between male hypogonadism and perinatal birth complications in the United States. Methods We performed a retrospective analysis of the IBM MarketScan™ Commercial Claims and Encounters database between 2011-2017. We identified birth records using birth or pregnancy-related major diagnostic categories associated with persons age 0. Fathers were considered to be adult (&gt; 18) male individuals with the same family identifier as the neonates listed as either the primary insurance beneficiary or spouse. Birth records were excluded if there was no family identifier or the father was unable to be linked. For each birth, we recorded whether they were preterm, diagnosed as low birth weight, or diagnosed with birth defects. For the fathers linked with each birth record, we determined paternal age, hypogonadism status, geographic region, and other associated comorbidities. Births were stratified based on whether the father had hypogonadism or not and we performed univariate tests for variation. Additionally, we conducted a multivariate logistic model of birth complication (preterm, low weight, or growth defect) against father's age, hypogonadism status, and paternal comorbidities. Results Between 2011 and 2017, paternal hypogonadism was found in 3.97% of fathers among 468,546 birth records. In contrast, no paternal hypogonadism was found in 96.03% of fathers among 468,546 birth records. Overall, our study reveals that paternal hypogonadism is positively associated with perinatal birth complications (odds ratio (OR) 1.10; 95% CI: 1.06, 1.13). Additionally, low birth weight was found in 46, 96% of birth among 196,607 birth records with paternal hypogonadism, follow by preterm birth with 7.64% of birth among 26,886 birth records with paternal hypogonadism. Conclusions Male hypogonadism was associated with a statistically significant increase in perinatal birth complications. However, these results should be interpreted with caution because patients with male hypogonadism are also likely to have male infertility. For hypogonadism to be considered as a separate risk factor for perinatal birth complications further investigation will be needed. Disclosure No