The authors have undertaken in-depth sequencing of more than 1000 hospital patients' isolates to find out how the virus is mutating within individuals. Overall, there seem to be consistent and reproducible patterns of within-host virus diversity. The authors observed only one or two variants in most samples, but a few carried many variants.

This preliminary study suggests that a single dose of BNT162b2 vaccine may be sufficient to obtain a high level of S-protein IgG antibody in nursing home residents previously diagnosed with COVID-19 based on RT-PCR results.

We investigated SARS-CoV-2 infection clusters involving 95 HCP and 137 possible patient contact sequences. The majority of HCP infections could not be linked to a patient or co-worker (55/95; 57.9%) and were genetically similar to viruses circulating concurrently in the community. We found 10.5% of infections could be traced to a coworker (10/95). Strikingly, only 4.2% of HCP infections could be traced to a patient source (4/95).

Based on the Italian case study, we outline several scenarios: mass vaccination campaigns with different paces, different transmission rates due to new variants and different enforced countermeasures, including the alternation of opening and closure phases. Our results demonstrate that non-pharmaceutical interventions have a higher effect on the epidemic evolution than vaccination alone, advocating for the need to keep NPIs in place during the first phase of vaccination.

Phylogenetic analysis from WGS and epidemiological data was used to identify an initial transmission that occurred in the admissions ward. It also showed high prevalence of asymptomatic staff infection with genetically identical viral sequences which may have contributed to the propagation of the outbreak. Actions were taken to help reduce the risk of nosocomial transmission by the introduction of rapid testing in the admissions ward and introduction of portable HEPA14 filters.

We conducted whole-exome sequencing in 233 hospitalized COVID-19 patients and identified four PID gene (UNC13D, AP3B1, RNF168, DHX58) variants were significantly enriched in COVID-19 patients experiencing severe cytokine storms. The total percentage of COVID-19 patients with variants in UNC13D or AP3B1, two typical HLH genes, was dramatically higher in high-level cytokine group than in low-level group (33.3 vs. 5.7%, P?<?0.001).

Saliva testing was successfully adopted for SARS-CoV-2 detection in numerous countries. In the US, saliva testing gained traction to facilitate the reopening of educational institutions, with its potential for pooling samples for processing, enabling sustainable testing program. As a preferable method for frequent, repeat testing, saliva could be particularly well suited for detecting SARS-CoV-2 during the prodromal phase,8 decreasing risk of further transmission.

It is often stated that vaccines do not save lives, vaccinations do. Our modeling reinforces this point. We project that despite considerable uncertainty about the timing and severity of variant waves in the United States, rapid vaccination must remain high to save the most lives and limit future time under partial lockdown.

"We investigated the potential role of asymptomatic infection and silent transmission in London care homes that reported no cases of COVID-19 during the first wave of the pandemic.... We found high rates of asymptomatic infection and transmission even in care homes with no COVID-19 cases. The higher seropositivity rates compared to RT-PCR positivity highlights the true extent of the silent outbreak."

We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease.

We identified an emerging SARS-CoV-2 variant in 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. The variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6-24% increased transmissibility relative to wild-type circulating strains. The variant carries 3 mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo.

In a COVID-19 outbreak at a Kentucky skilled nursing facility involving a newly introduced variant to the region, unvaccinated residents and health care personnel (HCP) had 3.0 and 4.1 times the risk of infection as did vaccinated residents and HCP. Vaccine was 86.5% protective against symptomatic illness among residents and 87.1% protective among HCP.

Twenty-two possible breakthrough SARS-CoV-2 infections occurred among fully vaccinated persons =14 days after their second dose of COVID-19 vaccine. Two thirds of persons were asymptomatic. A minority of persons with breakthrough infection experienced mild to moderate COVID-19–like symptoms; two COVID-19–related hospitalizations and one death occurred. No facility-associated secondary transmission was identified.

Emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of clinical concern. In a cohort of 417 persons who had received the second dose of mRNA vaccine at least 2 weeks previously, we identified 2 women with vaccine breakthrough infection. Despite evidence of vaccine efficacy in both women, symptoms of coronavirus disease 2019 developed, and they tested positive for SARS-CoV-2 by polymerase-chain-reaction testing. Viral sequencing revealed variants of likely clinical importance, including E484K in 1 woman and three mutations (T95I, del142–144, and D614G) in both.

The authors have undertaken in-depth sequencing of more than 1000 hospital patients' isolates to find out how the virus is mutating within individuals. Overall, there seem to be consistent and reproducible patterns of within-host virus diversity. The authors observed only one or two variants in most samples, but a few carried many variants.

This preliminary study suggests that a single dose of BNT162b2 vaccine may be sufficient to obtain a high level of S-protein IgG antibody in nursing home residents previously diagnosed with COVID-19 based on RT-PCR results.

We investigated SARS-CoV-2 infection clusters involving 95 HCP and 137 possible patient contact sequences. The majority of HCP infections could not be linked to a patient or co-worker (55/95; 57.9%) and were genetically similar to viruses circulating concurrently in the community. We found 10.5% of infections could be traced to a coworker (10/95). Strikingly, only 4.2% of HCP infections could be traced to a patient source (4/95).

Based on the Italian case study, we outline several scenarios: mass vaccination campaigns with different paces, different transmission rates due to new variants and different enforced countermeasures, including the alternation of opening and closure phases. Our results demonstrate that non-pharmaceutical interventions have a higher effect on the epidemic evolution than vaccination alone, advocating for the need to keep NPIs in place during the first phase of vaccination.

Phylogenetic analysis from WGS and epidemiological data was used to identify an initial transmission that occurred in the admissions ward. It also showed high prevalence of asymptomatic staff infection with genetically identical viral sequences which may have contributed to the propagation of the outbreak. Actions were taken to help reduce the risk of nosocomial transmission by the introduction of rapid testing in the admissions ward and introduction of portable HEPA14 filters.

We conducted whole-exome sequencing in 233 hospitalized COVID-19 patients and identified four PID gene (UNC13D, AP3B1, RNF168, DHX58) variants were significantly enriched in COVID-19 patients experiencing severe cytokine storms. The total percentage of COVID-19 patients with variants in UNC13D or AP3B1, two typical HLH genes, was dramatically higher in high-level cytokine group than in low-level group (33.3 vs. 5.7%, P?<?0.001).

Saliva testing was successfully adopted for SARS-CoV-2 detection in numerous countries. In the US, saliva testing gained traction to facilitate the reopening of educational institutions, with its potential for pooling samples for processing, enabling sustainable testing program. As a preferable method for frequent, repeat testing, saliva could be particularly well suited for detecting SARS-CoV-2 during the prodromal phase,8 decreasing risk of further transmission.

It is often stated that vaccines do not save lives, vaccinations do. Our modeling reinforces this point. We project that despite considerable uncertainty about the timing and severity of variant waves in the United States, rapid vaccination must remain high to save the most lives and limit future time under partial lockdown.

"We investigated the potential role of asymptomatic infection and silent transmission in London care homes that reported no cases of COVID-19 during the first wave of the pandemic.... We found high rates of asymptomatic infection and transmission even in care homes with no COVID-19 cases. The higher seropositivity rates compared to RT-PCR positivity highlights the true extent of the silent outbreak."

We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease.

We identified an emerging SARS-CoV-2 variant in 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. The variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6-24% increased transmissibility relative to wild-type circulating strains. The variant carries 3 mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo.

In a COVID-19 outbreak at a Kentucky skilled nursing facility involving a newly introduced variant to the region, unvaccinated residents and health care personnel (HCP) had 3.0 and 4.1 times the risk of infection as did vaccinated residents and HCP. Vaccine was 86.5% protective against symptomatic illness among residents and 87.1% protective among HCP.

Twenty-two possible breakthrough SARS-CoV-2 infections occurred among fully vaccinated persons =14 days after their second dose of COVID-19 vaccine. Two thirds of persons were asymptomatic. A minority of persons with breakthrough infection experienced mild to moderate COVID-19–like symptoms; two COVID-19–related hospitalizations and one death occurred. No facility-associated secondary transmission was identified.

Emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of clinical concern. In a cohort of 417 persons who had received the second dose of mRNA vaccine at least 2 weeks previously, we identified 2 women with vaccine breakthrough infection. Despite evidence of vaccine efficacy in both women, symptoms of coronavirus disease 2019 developed, and they tested positive for SARS-CoV-2 by polymerase-chain-reaction testing. Viral sequencing revealed variants of likely clinical importance, including E484K in 1 woman and three mutations (T95I, del142–144, and D614G) in both.

The authors have undertaken in-depth sequencing of more than 1000 hospital patients' isolates to find out how the virus is mutating within individuals. Overall, there seem to be consistent and reproducible patterns of within-host virus diversity. The authors observed only one or two variants in most samples, but a few carried many variants.

This preliminary study suggests that a single dose of BNT162b2 vaccine may be sufficient to obtain a high level of S-protein IgG antibody in nursing home residents previously diagnosed with COVID-19 based on RT-PCR results.

We investigated SARS-CoV-2 infection clusters involving 95 HCP and 137 possible patient contact sequences. The majority of HCP infections could not be linked to a patient or co-worker (55/95; 57.9%) and were genetically similar to viruses circulating concurrently in the community. We found 10.5% of infections could be traced to a coworker (10/95). Strikingly, only 4.2% of HCP infections could be traced to a patient source (4/95).

Based on the Italian case study, we outline several scenarios: mass vaccination campaigns with different paces, different transmission rates due to new variants and different enforced countermeasures, including the alternation of opening and closure phases. Our results demonstrate that non-pharmaceutical interventions have a higher effect on the epidemic evolution than vaccination alone, advocating for the need to keep NPIs in place during the first phase of vaccination.

Phylogenetic analysis from WGS and epidemiological data was used to identify an initial transmission that occurred in the admissions ward. It also showed high prevalence of asymptomatic staff infection with genetically identical viral sequences which may have contributed to the propagation of the outbreak. Actions were taken to help reduce the risk of nosocomial transmission by the introduction of rapid testing in the admissions ward and introduction of portable HEPA14 filters.

We conducted whole-exome sequencing in 233 hospitalized COVID-19 patients and identified four PID gene (UNC13D, AP3B1, RNF168, DHX58) variants were significantly enriched in COVID-19 patients experiencing severe cytokine storms. The total percentage of COVID-19 patients with variants in UNC13D or AP3B1, two typical HLH genes, was dramatically higher in high-level cytokine group than in low-level group (33.3 vs. 5.7%, P?<?0.001).

Saliva testing was successfully adopted for SARS-CoV-2 detection in numerous countries. In the US, saliva testing gained traction to facilitate the reopening of educational institutions, with its potential for pooling samples for processing, enabling sustainable testing program. As a preferable method for frequent, repeat testing, saliva could be particularly well suited for detecting SARS-CoV-2 during the prodromal phase,8 decreasing risk of further transmission.

It is often stated that vaccines do not save lives, vaccinations do. Our modeling reinforces this point. We project that despite considerable uncertainty about the timing and severity of variant waves in the United States, rapid vaccination must remain high to save the most lives and limit future time under partial lockdown.

"We investigated the potential role of asymptomatic infection and silent transmission in London care homes that reported no cases of COVID-19 during the first wave of the pandemic.... We found high rates of asymptomatic infection and transmission even in care homes with no COVID-19 cases. The higher seropositivity rates compared to RT-PCR positivity highlights the true extent of the silent outbreak."

We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease.

We identified an emerging SARS-CoV-2 variant in 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. The variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6-24% increased transmissibility relative to wild-type circulating strains. The variant carries 3 mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo.

In a COVID-19 outbreak at a Kentucky skilled nursing facility involving a newly introduced variant to the region, unvaccinated residents and health care personnel (HCP) had 3.0 and 4.1 times the risk of infection as did vaccinated residents and HCP. Vaccine was 86.5% protective against symptomatic illness among residents and 87.1% protective among HCP.

Twenty-two possible breakthrough SARS-CoV-2 infections occurred among fully vaccinated persons =14 days after their second dose of COVID-19 vaccine. Two thirds of persons were asymptomatic. A minority of persons with breakthrough infection experienced mild to moderate COVID-19–like symptoms; two COVID-19–related hospitalizations and one death occurred. No facility-associated secondary transmission was identified.

Emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of clinical concern. In a cohort of 417 persons who had received the second dose of mRNA vaccine at least 2 weeks previously, we identified 2 women with vaccine breakthrough infection. Despite evidence of vaccine efficacy in both women, symptoms of coronavirus disease 2019 developed, and they tested positive for SARS-CoV-2 by polymerase-chain-reaction testing. Viral sequencing revealed variants of likely clinical importance, including E484K in 1 woman and three mutations (T95I, del142–144, and D614G) in both.