Use of whole genome sequencing to estimate the contribution of immune evasion and waning immunity on decreasing COVID-19 vaccine effectiveness.

BACKGROUND: The impact variant-specific immune evasion and waning protection have on declining COVID-19 vaccine effectiveness remains unclear. Using whole-genome-sequencing (WGS), we examined the contribution of these factors on the decline observed following the introduction of the Delta variant. Further, we evaluated the utility of calendar-period-based classification as an alternative to WGS. METHODS: We conducted a test-negative-case-control study among people who received SARS-CoV-2 RT-PCR testing in the Yale New Haven Health System between April 1 and August 24, 2021. Variant classification was performed using WGS and calendar-period. RESULTS: Overall, 2,029 cases (RT-PCR positive, sequenced samples [infections]) and 343,985 controls (negative RT-PCRs) were included. VE 14-89 days after 2nd dose was significantly higher against WGS-classified Alpha-infection (84.4%, CI: 75.6-90.0%) than Delta-infection (68.9%, CI: 58.0-77.1%, p-value = 0.013). The odds of WGS-classified Delta-infection were significantly higher 90-149 than 14-89 days after 2nd dose (p-value = 0.003). VE estimates against calendar-period-classified infections approximated estimates against WGS-classified infections, however, calendar-period-based classification was subject to outcome misclassification (35%: Alpha-period, 4%: Delta-period). CONCLUSIONS: Both waning protection and variant-specific immune evasion contributed to the lower effectiveness. While VE estimates against calendar-period-classified infections mirrored those against WGS-classified infections, our analysis highlights the need for WGS when variants are co-circulating and misclassification is likely.

Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose.

The emergence of the SARS-CoV-2 Omicron sublineages resulted in increased transmission rates and reduced protection from vaccines. To counteract these effects, multiple booster strategies were used in different countries, although data comparing their efficiency in improving protective immunity remain sparse, especially among vulnerable populations, including older adults. The inactivated CoronaVac vaccine was among the most widely distributed vaccine worldwide and was essential in the early control of SARS-CoV-2-related hospitalizations and deaths. However, it is not well understood whether homologous versus heterologous booster doses in those fully vaccinated with CoronaVac induce distinct humoral responses or whether these responses vary across age groups. We analyzed plasma antibody responses from CoronaVac-vaccinated younger or older individuals who received a homologous CoronaVac or heterologous BNT162b2 or ChAdOx1 booster vaccine. All three evaluated boosters resulted in increased virus-specific IgG titers 28 days after the booster dose. However, we found that both IgG titers against SARS-CoV-2 Spike or RBD and neutralization titers against Omicron sublineages were substantially reduced in participants who received homologous CoronaVac compared with the heterologous BNT162b2 or ChAdOx1 booster. This effect was specifically prominent in recipients >50 years of age. In this group, the CoronaVac booster induced low virus-specific IgG titers and failed to elevate neutralization titers against any Omicron sublineage. Our results point to the notable inefficiency of CoronaVac immunization and boosting in mounting protective antiviral humoral immunity, particularly among older adults, during the Omicron wave. These observations also point to benefits of heterologous regimens in high-risk populations fully vaccinated with CoronaVac.

Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection

The chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately two-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution result in the emergence and persistence of at least three genetically distinct genotypes suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants. Graphical To understand the intrahost evolution of SARS-CoV-2 from a single patient chronically infected for at least 471 days, Chaguza et al. use whole genome sequencing to estimate the evolutionary rate, the genetic divergence of viral lineages, relative mutation rates, and frequency of mutational variants during the course of the infection.

Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection.

The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants.

Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons.

Background: The SARS-CoV-2 Omicron variant became a global concern due to its rapid spread and displacement of the dominant Delta variant. We hypothesized that part of Omicron's rapid rise was based on its increased ability to cause infections in persons that are vaccinated compared to Delta. Methods: We analyzed nasal swab PCR tests for samples collected between December 12 and 16, 2021, in Connecticut when the proportion of Delta and Omicron variants was relatively equal. We used the spike gene target failure (SGTF) to classify probable Delta and Omicron infections. We fitted an exponential curve to the estimated infections to determine the doubling times for each variant. We compared the test positivity rates for each variant by vaccination status, number of doses, and vaccine manufacturer. Generalized linear models were used to assess factors associated with odds of infection with each variant among persons testing positive for SARS-CoV-2. Findings: For infections with high virus copies (Ct < 30) among vaccinated persons, we found higher odds that they were infected with Omicron compared to Delta, and that the odds increased with increased number of vaccine doses. Compared to unvaccinated persons, we found significant reduction in Delta positivity rates after two (43.4%-49.1%) and three vaccine doses (81.1%), while we only found a significant reduction in Omicron positivity rates after three doses (62.3%). Conclusion: The rapid rise in Omicron infections was likely driven by Omicron's escape from vaccine-induced immunity. Funding: This work was supported by the Centers for Disease Control and Prevention (CDC).

De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report.

SARS-CoV-2 remdesivir resistance mutations have been generated in vitro but have not been reported in patients receiving treatment with the antiviral agent. We present a case of an immunocompromised patient with acquired B-cell deficiency who developed an indolent, protracted course of SARS-CoV-2 infection. Remdesivir therapy alleviated symptoms and produced a transient virologic response, but her course was complicated by recrudescence of high-grade viral shedding. Whole genome sequencing identified a mutation, E802D, in the nsp12 RNA-dependent RNA polymerase, which was not present in pre-treatment specimens. In vitro experiments demonstrated that the mutation conferred a ~6-fold increase in remdesivir IC50 but resulted in a fitness cost in the absence of remdesivir. Sustained clinical and virologic response was achieved after treatment with casirivimab-imdevimab. Although the fitness cost observed in vitro may limit the risk posed by E802D, this case illustrates the importance of monitoring for remdesivir resistance and the potential benefit of combinatorial therapies in immunocompromised patients with SARS-CoV-2 infection.

Fears, Reassurance, and Milestones: A Twitter Analysis around World Prematurity Day during the COVID-19 Pandemic.

Preterm birth (birth <37 completed weeks' gestation) is common, affecting 10.6% of live births globally (nearly 15 million babies per year). Having a new baby admitted to a neonatal unit often triggers stress and anxiety for parents. This paper seeks to explore experiences of preterm birth via Twitter. The intermingling of COVID-19 restrictions and World Prematurity Day allows for an understanding of both the additional stresses incurred as a consequence of the pandemic and the more "everyday" experiences in the NICU and beyond. The content analysis of the data included 3161 tweets. Three themes were identified: 1. COVID-19 was not the only trauma; 2. Raising awareness, especially World Prematurity Day; and, 3. Baby milestones. These themes highlight the multi-level challenges faced by parents of premature babies and the healthcare professionals involved in their care. The COVID-19 pandemic and the consequent restrictions imposed on parents' contact with their babies have resulted in immense emotional strain for families. The reported COVID-19 pandemic "baby blind spot" appears to particularly impact this group of babies. Improved understanding of the lived experiences of preterm babies and their families should inform greater awareness and improved support.

Evidence-based approach to providing informed consent for hip fracture surgery during the COVID-19 era.

BACKGROUND: Hip fractures are the most common reason for inpatient orthopaedic trauma admission. Urgent surgical intervention for hip fractures has remained a clinical priority throughout the coronavirus disease 2019 (COVID-19) pandemic. Despite this, there is a paucity of clinical guidance addressing the informed consent process for hip fracture surgery in COVID-19 positive patients. This is of paramount medicolegal importance in a high-risk patient population. AIM: To quantify the additional perioperative risks for COVID-19 positive patients undergoing hip fracture surgery and provide clinicians with an evidence-based framework to establish an informed consent process. METHODS: Two hundred and fifty nine consecutive patients undergoing surgical intervention for hip fractures in four hospitals in the United Kingdom were recruited. 51 patients were confirmed positive for COVID-19. Predefined outcomes were analyzed over a 30-d postoperative period. COVID-19 positive and COVID-19 negative patients were compared after adjustment for confounding factors. RESULTS: COVID-19 positive patients had more intensive care admissions (27% vs 5%, P < 0.001), longer inpatient stays (median 23 d vs 9 d, P < 0.001) and a higher 30-d mortality (29% vs 10%, P = 0.001) than COVID-19 negative patients. Postoperative complications were evident in 74.5% of COVID-19 positive patients. 35.3% of COVID-19 positive patients suffered postoperative lower respiratory tract infections with 13.7% developing acute respiratory distress syndrome (ARDS) and 9.8% experiencing symptomatic thromboembolic events. CONCLUSION: The COVID-19 pandemic has created uncertainty in the medical community worldwide and poses unique challenges in providing informed consent for surgery. COVID-19 positive patients undergoing hip fracture surgery should be consented for the additional risk of postoperative complications (including lower respiratory tract infection, ARDS, deep vein thrombosis and pulmonary embolism), increased requirement for intensive care admission, longer inpatient stay and higher risk of mortality. Further, clinicians must be transparent about the potential for unknown risks as research into the long-term surgical outcomes of COVID-19 positive patients continues to evolve.

Structural modeling and analysis of the SARS-CoV-2 cell entry inhibitor camostat bound to the trypsin-like protease TMPRSS2.

The type II transmembrane serine protease TMPRSS2 facilitates the entry of coronaviruses, such as SARS-CoV-2, into host cells by cleaving the S1/S2 interface of the viral spike protein. Based on structural data derived from X-ray crystallographic data of related trypsin-like proteases, a homology model of TMPRSS2 is described and validated using the broad spectrum COVID-19 drug candidate camostat as a probe. Both active site recognition and catalytic function are examined using quantum mechanics/molecular mechanics molecular dynamic (QM/MM MD) simulations of camostat and its active metabolite, 4-(4-guanidinobenzoyloxy) phenylacetate (GBPA). Substrate binding is shown to be primarily stabilized through salt bridge formation between the shared guanidino pharmacophore and D435 in pocket A (flanking the catalytic S441). Based on the binding mode of GBPA, residues K342 and W461 have been identified as potential contacts involved in TMPRSS2 selective binding and activity. Additional data is reported that indicates the transition state structure is stabilized through H-bonding interactions with the backbone N-H groups within an oxyanion hole following bottom-side attack of the carbonyl by S441. This is supported by prior work on related serine proteases suggesting further strategies to exploit in the design of more potent inhibitors. Taken overall, the proposed structure along with the key contact sites and mechanistic features identified should prove highly advantageous to the design and rational development of safe and effective therapeutics that target TMPRSS2 and avoid inhibition of other trypsin-dependent processes.

The effects of COVID-19 on perioperative morbidity and mortality in patients with hip fractures.

AIMS: During the COVID-19 pandemic, many patients continue to require urgent surgery for hip fractures. However, the impact of COVID-19 on perioperative outcomes in these high-risk patients remains unknown. The objectives of this study were to establish the effects of COVID-19 on perioperative morbidity and mortality, and determine any risk factors for increased mortality in patients with COVID-19 undergoing hip fracture surgery. METHODS: This multicentre cohort study included 340 COVID-19-negative patients versus 82 COVID-19-positive patients undergoing surgical treatment for hip fractures across nine NHS hospitals in Greater London, UK. Patients in both treatment groups were comparable for age, sex, body mass index, fracture configuration, and type of surgery performed. Predefined perioperative outcomes were recorded within a 30-day postoperative period. Univariate and multivariate analysis were used to identify risk factors associated with increased risk of mortality. RESULTS: COVID-19-positive patients had increased postoperative mortality rates (30.5% (25/82) vs 10.3% (35/340) respectively, p < 0.001) compared to COVID-19-negative patients. Risk factors for increased mortality in patients with COVID-19 undergoing surgery included positive smoking status (hazard ratio (HR) 15.4 (95% confidence interval (CI) 4.55 to 52.2; p < 0.001) and greater than three comorbidities (HR 13.5 (95% CI 2.82 to 66.0, p < 0.001). COVID-19-positive patients had increased risk of postoperative complications (89.0% (73/82) vs 35.0% (119/340) respectively; p < 0.001), more critical care unit admissions (61.0% (50/82) vs 18.2% (62/340) respectively; p < 0.001), and increased length of hospital stay (mean 13.8 days (SD 4.6) vs 6.7 days (SD 2.5) respectively; p < 0.001), compared to COVID-19-negative patients. CONCLUSION: Hip fracture surgery in COVID-19-positive patients was associated with increased length of hospital stay, more admissions to the critical care unit, higher risk of perioperative complications, and increased mortality rates compared to COVID-19-negative patients. Risk factors for increased mortality in patients with COVID-19 undergoing surgery included positive smoking status and multiple (greater than three) comorbidities. Cite this article: Bone Joint J 2020;102-B(9):1136-1145.

Impact of COVID-19 Pandemic on Laboratory Utilization.

BACKGROUND: Coronavirus disease 2019 (COVID-19) was formally characterized as a pandemic on March 11, 2020. Since that time, the COVID-19 pandemic has led to unprecedented demand for healthcare resources. The purpose of this study was to identify changes in laboratory test utilization in the setting of increasing local incidence of COVID-19. METHODS: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Data were extracted from the laboratory information system database over a 10-week period, spanning the primordial inflection of COVID-19 incidence in our region. Total testing volumes were calculated during the first 2 and last 2 weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the prepandemic and COVID-19 surge periods. RESULTS: Between February 2, 2020, and April 11, 2020, there were 873 397 tests ordered and final verified. The in-house SARS-CoV-2 PCR positivity rate for admitted patients in the last week of the observation period was 30.8%. Significant increases in workload were observed in the send-out laboratory section and for COVID-19 diagnosis (PCR) and management-related testing. Otherwise, there was a net decrease in overall demand across nearly all laboratory sections. Increases in testing were noted for tests related to COVID-19 management. Viral transport media and citrated blue top containers demonstrated increases in utilization. CONCLUSION: Increasing local incidence of COVID-19 had a profound impact on laboratory operations. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. During events such as COVID-19, monitoring of such patterns can help inform laboratory management, staffing, and test stewardship recommendations for managing resource and supply availability.