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• The Pangolin classification clustered the South Kivu sequences into seven lineages. • The Delta variant is responsible for COVID-19 outbreaks during the third wave. • D614G is the most frequent mutation observed, followed by L4715L. • There are multiple introductions of SARS-CoV-2 and subsequent circulating variants. We used whole-genome sequencing of SARS-CoV-2 to identify variants circulating in the Democratic Republic of the Congo and obtain molecular information useful for diagnosis, improving treatment, and general pandemic control strategies. A total of 74 SARS-CoV-2 isolates were sequenced using Oxford Nanopore platforms. Generated reads were processed to obtain consensus genome sequences. Sequences with more than 80% genome coverage were used for variant calling, phylogenetic analysis, and classification using Pangolin lineage annotation nomenclature. Phylogenetic analysis based on Pangolin classification clustered South Kivu sequences into seven lineages (A.23.1, B.1.1.6, B.1.214, B.1.617.2, B.1.351, C.16, and P.1). The Delta (B.1.617.2) variant was the most dominant and responsible for outbreaks during the third wave. Based on the Wuhan reference genome, 289 distinct mutations were detected, including 141 missenses, 123 synonymous, and 25 insertions/deletions when our isolates were mapped to the Wuhan reference strain. Most of these point mutations were located within the coding sequences of the SARS-CoV-2 genome that includes spike, ORF1ab, ORF3, and nucleocapsid protein genes. The most common mutation was D614G (1841A>G) observed in 61 sequences, followed by L4715L (14143 C>T) found in 60 sequences. Our findings highlight multiple introductions of SARS-CoV-2 into South Kivu through different sources and subsequent circulation of variants in the province. These results emphasize the importance of timely monitoring of genetic variation and its effect on disease severity. This work set a foundation for the use of genomic surveillance as a tool for future global pandemic management and control. [ABSTRACT FROM AUTHOR]

• SARS-CoV-2 vaccines ameliorate infection and adverse outcomes. • The booster dose induces increased humoral immune responses. • The booster dose induces an increased adaptative immune response. • The booster dose leads to early activation of the memory CD8+ T subset. Vaccines against SARS-CoV-2 ameliorate infection and adverse outcomes from SARS-CoV-2. Elicitation of high affinity and durable protective antibody responses is a hallmark of a successful humoral immune response to vaccination. To assess the relevance of serum levels of SARS-CoV-2 specific antibodies and to further characterize the immune response to SARS-CoV-2 vaccines, we report i) the levels of spike-binding and neutralizing antibodies to SARS-COV-2 in the sera of 30 healthy volunteers at nine months after the second vaccination dose of mRNA vaccine and one month after the booster dose; ii) the levels of IFN-γ production by blood T cells exposed to SARS-CoV-2 spike antigen (Wuhan, Alpha B.1.1.7, Delta B.1.617.2, and Omicron B1.1.529 variants); and iii) the specific phenotype of T cells related with exposure to SARS-CoV-2 spike antigen. We observed that the booster dose induced increased humoral and adaptive immune responses and led to early activation of the memory CD8+ T subset. [ABSTRACT FROM AUTHOR]

[Display omitted] • The mean latent/removed periods of the COVID-19 epidemic in China were 5.40/2.13 days. • There were 1.72 latent/infected persons per 10,000 Wuhan travelers up to January 20th. • Space-time R 0 estimates indicated an initial value between 2 and 3.5 in most cities. • There were 196 cities that had an estimated R 0 < 1 on February 29th. • A clear descent in temporal R 0 started one week after the outbreak and lasted for two weeks. The novel coronavirus (COVID-19) epidemic is reaching its final phase in China. The epidemic data are available for a complete assessment of epidemiological parameters in all regions and time periods. This study aims to present a spatiotemporal epidemic model based on spatially stratified heterogeneity (SSH) to simulate the epidemic spread. A susceptible-exposed/latent-infected-removed (SEIR) model was constructed for each SSH-identified stratum (each administrative city) to estimate the spatiotemporal epidemiological parameters of the outbreak. We estimated that the mean latent and removed periods were 5.40 and 2.13 days, respectively. There was an average of 1.72 latent or infected persons per 10,000 Wuhan travelers to other locations until January 20th, 2020. The space-time basic reproduction number (R 0) estimates indicate an initial value between 2 and 3.5 in most cities on this date. The mean period for R 0 estimates to decrease to 80%, and 50% of initial values in cities were an average of 14.73 and 19.62 days, respectively. Our model estimates the complete spatiotemporal epidemiological characteristics of the outbreak in a space-time domain. These findings will help enhance a comprehensive understanding of the outbreak and inform the strategies of prevention and control in other countries worldwide. [ABSTRACT FROM AUTHOR]

• Non-pharmaceutical interventions are associated with the decline of COVID-19 cases. • These interventions directly reduced the transmission of respiratory pathogens. • These interventions are cost-effective. • These interventions should be implemented before more effective approaches become available. The emergence of a novel coronavirus, SARS-CoV-2, and its subsequent spread outside of Wuhan, China, led to the human society experiencing a pandemic of coronavirus disease 2019 (COVID-19). While the development of vaccines and pharmaceutical treatments are ongoing, government authorities in China have implemented unprecedented non-pharmaceutical interventions as primary barriers to curb the spread of the deadly SARS-CoV-2 virus. Although the decline of COVID-19 cases coincided with the implementation of such interventions, we searched for evidence to demonstrate the efficacy of these interventions, since artifactual factors, such as the environment, the pathogen itself, and the phases of epidemic, may also alter the patterns of case development. We surveyed common viral respiratory infections that have a similar pattern of transmission, tropism, and clinical manifestation, as COVID-19 under a series of non-pharmaceutical interventions during the current pandemic season. We then compared this data with historical data from previous seasons without such interventions. Our survey showed that the rates of common respiratory infections, such as influenza and respiratory syncytial virus infections, decreased dramatically from 13.7% (95% CI, 10.82–16.58) and 4.64% (95% CI, 2.88–7.64) in previous years to 0.73% (95% CI, 0.02–1.44) and 0.0%, respectively, in the current season. Our surveillance provides compelling evidence that non-pharmaceutical interventions are cost-effective ways to curb the spread of contagious agents, and may represent the only practical approach to limit the evolving epidemic until specific vaccines and pharmaceutical treatments are available. [ABSTRACT FROM AUTHOR]

• Full therapeutic low molecular weight heparin to be considered if platelets >50,000. • Blood products for overt disseminated intravascular coagulation with active bleeding. • Anti-coagulation dose should be half of the therapeutic dose if platelets <50,000. • Only prophylactic dose if platelets <30,000. • Platelet transfusion and an inferior vena cava filter considered if platelets <30,000. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2), a novel coronavirus, originated as an epidemic respiratory illness in Wuhan, China. COVID-19 eventually spread to almost all countries and has now been declared a global pandemic disease by the World Health Organisation. A plethora of research has explored the dynamics of different clinical entities related to SARS-COV-2, in particular, COVID-19 associated coagulopathy. A large scale of patients have been reported to have developed pulmonary embolism without any other standard triggers or risk factors, leading to speculation that COVID-19 is an independent risk factor for venous thromboembolism. In addition to the development of thromboembolic complications such as pulmonary embolism, COVID-19 has also been reported to have triggered disseminated intravascular coagulation (DIC); however, it is unclear whether pulmonary embolism was due to COVID-19-induced thrombosis or a result of coagulopathy secondary to DIC. We describe a unique case of a COVID-19 associated coagulopathy in a patient with confirmed pulmonary embolism along with an overt DIC. Following diagnosis, the challenge was to identify the appropriate treatment modality for this unique situation. The patient was treated with anticoagulants and steroids along with blood products. The patient's condition markedly improved and was clinically stable on discharge. [ABSTRACT FROM AUTHOR]

• Whole-genome sequencing was performed for COVID-19-positive patients by ARTIC amplicon-based sequencing. • The spike region of 32 isolates showed one or multiple alterations in nucleotide bases compared with the Wuhan reference strain. • RBD of all Indian isolates showed binding affinity for angiotensin-converting enzyme 2 (ACE2) of humans, bats, hamsters and pangolins. • The mutated receptor-binding domain of one isolate showed stronger binding affinity for human ACE2. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected the whole world, including Odisha, a state in eastern India. Many people have migrated to the state from different countries as well as other states during this SARS-CoV-2 pandemic. The aim of this study was to analyse the receptor-binding domain (RBD) sequence of the spike protein from isolates collected from throat swab samples of COVID-19-positive patients and further to assess the RBD affinity for angiotensin-converting enzyme 2 (ACE2) of different species, including humans. Whole-genome sequencing for 35 clinical SARS-CoV-2 isolates from COVID-19-positive patients was performed by ARTIC amplicon-based sequencing. Sequence analysis and phylogenetic analysis were performed for the spike region and the RBD region of all isolates. The interaction between the RBD and ACE2 of five different species was also analysed. The spike region of 32 isolates showed one or multiple alterations in nucleotide bases in comparison with the Wuhan reference strain. One of the identified mutations, at position 1204 (Ref A, RMRC 22 C), in the RBD coding region of the spike protein showed stronger binding affinity for human ACE2. Furthermore, RBDs of all the Indian isolates showed binding affinity for ACE2 of different species. As mutant RBD showed stronger interaction with human ACE2, it could potentially result in higher infectivity. The binding affinity of the RBDs for ACE2 of all five species studied suggests that the virus can infect a wide variety of animals, which could also act as natural reservoir for SARS-CoV-2. [ABSTRACT FROM AUTHOR]

• We investigated the prevalence and recovery time of olfactory and gustatory dysfunction in COVID-19 patients in Wuhan, China. • The prevalence of olfactory and gustatory disorders in COVID-19 patients in China is much lower than that in Western countries. • Recovery from olfactory and/or gustatory dysfunction takes more than 4 weeks in more than half of the patients. • Cardiovascular disease might be related to the development of olfactory or taste disorders in patients with COVID-19. To investigate olfactory and gustatory dysfunction in patients with coronavirus disease 2019 (COVID-19) in Wuhan using a telephone interview. This retrospective telephone survey investigated 196 consecutive patients with COVID-19 at 3 months after discharge from two hospitals in Wuhan, China. The characteristics of the patient's disease course and time to recovery from olfactory and/or gustatory dysfunction (OD and/or GD) were collected by telephone interview. Demographic data were collected from the patient medical records. A total of 196 patients with COVID-19 completed the study. The most prevalent general symptoms were fever, cough, and fatigue. Overall, 19.9% of the patients reported OD and/or GD. In 87.2% of these cases, OD or GD appeared after the general symptoms. The time to recovery from OD and/or GD was more than 4 weeks in 51.4% of the patients. Patients with COVID-19 and OD and/or GD had significantly higher rates of cardiovascular disease than patients without OD and/or GD (p = 0.002). Recovery from chemosensory dysfunction (OD and/or GD) was slow, with over half of the patients taking more than 4 weeks to recover. Cardiovascular disease might be related to the development of olfactory or taste disorders in patients with COVID-19. [ABSTRACT FROM AUTHOR]

• A high rate of asymptomatic SARS-CoV-2 carriers was found in healthcare workers. • Asymptomatic individuals had lower antibody levels in the acute phase. • Asymptomatic IgG titration reduced during the early convalescent phase. To investigate the proportion and characteristics of asymptomatic infection among healthcare workers (HCWs). This study retrospectively investigated 1407 HCWs who were screened for COVID-19 by chest computed tomography (CT) scans and nasopharyngeal swabs for SARS-CoV-2 nucleic acid. Demographics, CT features, nasopharyngeal swabs, baseline symptoms, and laboratory data were collected. Of 1407 HCWs, 235 had symptoms and 1172 were asymptomatic close contacts, of which, 107 were symptomatic cases and 84 were close contacts who had abnormal CT findings. Of 152 symptomatic individuals and 908 close contacts tested for SARS-CoV-2 nucleic acid, 122 symptomatic cases and 38 close contacts had positive reverse-transcriptase real-time polymerase chain (RT-PCR) test results. The rate of confirmed asymptomatic infections was 4.2% (38/908). Both symptomatic and asymptomatic infected cases had high titrations of specific IgG or had ≥four-fold increase in IgG during convalescence compared with the acute phase. Combining the RT-PCR tests and serological findings, the rate of asymptomatic infections was 9.7% (88/908). In terms of the duration of viral shedding, there was no significant difference between symptomatic mild/moderate participants and asymptomatic infections. The findings demonstrated that a high rate of asymptomatic SARS-CoV-2 carriers existed among healthcare worker close contacts during the outbreak of COVID-19. [ABSTRACT FROM AUTHOR]

• Twelve air samples and 355 surface samples from a hospital were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). • Only one air sample, which was obtained during an intubation procedure, tested positive. • A low level of surface contamination was found, and most occurred on high-touch surfaces. • No association was found between surface contamination and patient characteristics. Few studies have explored air and surface contamination by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare settings. Air and surface samples were collected from the isolation wards and intensive care units designated for coronavirus disease 2019 (COVID-19) patients. Clinical data and the results of nasopharyngeal specimen and serum antibody testing were also collected for the patient sample. A total of 367 air and surface swab samples were collected from the patient care areas of 15 patients with mild COVID-19 and nine patients with severe/critical COVID-19. Only one air sample taken during the intubation procedure tested positive. High-touch surfaces were slightly more likely to be contaminated with SARS-CoV-2 RNA than low-touch surfaces. Contamination rates were slightly higher near severe/critical patients than near mild patients, although this difference was not statistically significant (p > 0.05). Surface contamination was still found near the patients with both positive IgG and IgM. Air and surface contamination with viral RNA was relatively low in these healthcare settings after the enhancement of infection prevention and control. Environmental contamination could still be found near seroconverted patients, suggesting the need to maintain constant vigilance in healthcare settings to reduce healthcare-associated infection during the COVID-19 pandemic. [ABSTRACT FROM AUTHOR]

CORONA virus disease -19 (COVID-19) is a disease caused by SARS-CoV-2. The outbreak started from Wuhan, China in Dec'2019 and became a pandemic. Human to human transmission occurs through droplet, fomites, aerosol and contaminated surfaces.This study shows that use of portable air purifier in patient's room can actually reduce the viral load in the room air that might minimize the risk of acquiring COVID through air-borne transmission by heath care professional taking care of the COVID patients. The study was carried out in room/cabins of special ward in LN Hospital, New Delhi where recently detected (within 48 Hr of RT-PCR +Ve results) COVID-19 patient with cough were admitted for treatment.The COVID-19 patients were asked to cough on the petri dish fixed with a polyvinylidene fluoride (PVDF) membrane filter (80 mm in diameter and 3 um pore size) keeping it within 2 feet distances from his/her nose for 15 mins. Then the membrane was then removed and added to falcon tube (15ML) containing 3 ML of viral transport medium (VTM). The tube were sent to PCR lab in an ice box. Air sampler was run for 1Hr keeping it at 3 Meter distance from recently diagnosed COVID-19 patient. RT-PCR done from particulate matters collected in VTM from the air sampler.Air sampler was run similarly and RT-PCR was done from PM collected in the filter of air sampler. The primary air suction was done at two different air flow 16.7 and 27 litre per minute (LPM), after which both RDRP and E gene were positive, after the use of purifier both the genes were still positive but with increased Ct values. With continous use of the air purifier the viral load of COVID-19 present in the air of ICU with paitents is primarily reduced but not completely eliminated. [ABSTRACT FROM AUTHOR]

• The true incidence of SARS-COV-2 is much higher than the reported number of cases. • Large sample size studies have shown 1.2–12.9% incidence of SARS-COV-2 among asymptomatic people. • Studies with a small sample size showed up to 87.9% incidence among asymptomatic people. • Asymptomatic individuals could be a potential source of infection to the community. The recent outbreak of the coronavirus disease 2019 (COVID-19) has quickly spread globally since its discovery in Wuhan, China, in December 2019. A comprehensive strategy – including surveillance, diagnostics, research, and clinical treatment – is urgently needed to win the battle against COVID-19. Recently, numerous studies have reported the incidence of SARS-CoV-2 in asymptomatic patients. Yet, the incidence and viral transmission from the asymptomatic cases are not yet apparent. To estimate the incidence of COVID-19 among asymptomatic cases and describe its epidemiological and clinical significance this review systematically examined the published literature on SARS-CoV-2 in asymptomatic patients. The literature was searched through four scientific databases: PubMed, Web of Science, Scopus, and Science Direct. Sixty-three studies satisfied the inclusion criteria. The majority of the reported studies were from China. However, there was a lack of SARS-CoV-2 epidemiological studies, from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. Studies with a large sample size (>1000) estimated that the percentage of people contracting SARS-CoV-2 and likely to be asymptomatic ranged from 1.2–12.9%. However, other studies with a smaller sample size reported a much higher incidence and indicated that up to 87.9% of COVID-19 infected individuals could be asymptomatic. Most of these studies indicated that asymptopatics are a potential source of infection to the community. This review highlighted the need for more robust and well-designed studies to better estimate COVID-19 incidence among asymptomatic patients worldwide. Early identification of asymptomatic cases, as well as monitoring and tracing close contacts, could help in mitigating the spread of COVID-19. [ABSTRACT FROM AUTHOR]

• The clinical manifestations of COVID-19 children are milder than those of influenza A children under 5 years. • The laboratory tests of COVID-19 children are milder than those of influenza A children under 5 years. • Imaging results more commonly presented as ground-glass opacities in COVID-19 patients. Since the outbreak of Coronavirus Disease 2019 (COVID-19) in Wuhan, considerable attention has been paid to its epidemiology and clinical characteristics in children. However, it is also crucial for clinicians to differentiate COVID-19 from other respiratory infectious diseases, such as influenza viruses. This was a retrospective study. Two groups of COVID-19 patients (n = 57) and influenza A patients (n = 59) were enrolled. We analyzed and compared their clinical manifestations, imaging characteristics and treatments. The proportions of cough (70.2%), fever (54.4%) and gastrointestinal symptoms (14.1%) in COVID-19 patients were lower than those of influenza A patients (98.3%, P < 0.001; 84.7%, P < 0.001; and 35.6%, P = 0.007; respectively). In addition, COVID-19 patients showed significantly lower levels of leukocytes (7.87 vs. 9.89 × 109 L–1, P = 0.027), neutrophils (2.43 vs. 5.16 × 109 L–1, P < 0.001), C-reactive protein (CRP; 3.7 vs. 15.1 mg/L, P = 0.001) and procalcitonin (PCT; 0.09 vs. 0.68 mm/h, P < 0.001), while lymphocyte levels (4.58 vs. 3.56 × 109 L–1; P = 0.006) were significantly higher compared with influenza A patients. In terms of CT imaging, ground-glass opacification in chest CT was more common in COVID-19 patients than in influenza A patients (42.1% vs. 15%, P = 0.032). In contrast, consolidation was more common in influenza A patients (25%) than in COVID-19 patients (5.2%, P = 0.025). The clinical manifestations and laboratory tests of COVID-19 children are milder than those of influenza A children under 5 years. Additionally, imaging results more commonly presented as ground-glass opacities in COVID-19 patients. [ABSTRACT FROM AUTHOR]

• Employing statistical modeling analyses, we elucidated the effects of a 'wet market' on coronavirus disease (COVID-19) transmission dynamics in China, by stratifying cases with contact history with the Huanan Seafood Wholesale Market. • For market-to-human transmission, we estimated mean R at 0.24 (95% CrI: 0.01–1.38), with the reporting rate identified as being 2–34-fold higher compared with human-to-human transmission. • The proportion of asymptomatic/mild-symptom patients constitutes a substantial component of the COVID-19 disease burden. The novel coronavirus (SARS-CoV-2) originating from Wuhan spread rapidly throughout China. While its origin remains uncertain, accumulating evidence links a wet market with the early spread of SARS-CoV-2 in Wuhan. Similarly, the influence of the marketplace on the early transmission dynamics is yet to be investigated. Using the daily series of COVID-19 incidence, stratified according to contact history with the market, we have conducted quantitative modeling analyses to estimate the reproduction numbers (R) for market-to-human and human-to-human transmission, the reporting probability, and the early effects of public health interventions. We estimated R at 0.24 (95% CrI: 0.01–1.38) for market-to-human transmission and 2.37 (95% CrI: 2.08–2.71) for human-to-human transmission during the early spread in China (2019–2020). Moreover, we estimated that the reporting rate for cases stemming from market-to-human transmission was 2–34 fold higher than that for cases stemming from human-to-human transmission, suggesting that contact history with the wet market played a key role in identifying COVID-19 cases. Our R estimate tied to market-to-human transmission had substantial uncertainty, but it was significantly lower compared with the reproduction number driving human-to-human transmission. Our results also suggest that asymptomatic and subclinical infections constitute a substantial component of the COVID-19 morbidity burden. [ABSTRACT FROM AUTHOR]

• Air quality is tightly associated with COVID-19 transmission. • PM 2.5 and NO 2 strongly promote COVID-19 transmission. • Temperature is inversely associated with COVID-19 transmission. Although COVID-19 is known to be caused by human-to-human transmission, it remains largely unclear whether ambient air pollutants and meteorological parameters could promote its transmission. A retrospective study was conducted to study whether air quality index (AQI), four ambient air pollutants (PM 2.5 , PM 10 , NO 2 and CO) and five meteorological variables (daily temperature, highest temperature, lowest temperature, temperature difference and sunshine duration) could increase COVID-19 incidence in Wuhan and XiaoGan between Jan 26th to Feb 29th in 2020. First, a significant correlation was found between COVID-19 incidence and AQI in both Wuhan (R 2 = 0.13, p < 0.05) and XiaoGan (R 2 = 0.223, p < 0.01). Specifically, among four pollutants, COVID-19 incidence was prominently correlated with PM 2.5 and NO 2 in both cities. In Wuhan, the tightest correlation was observed between NO 2 and COVID-19 incidence (R 2 = 0.329, p < 0.01). In XiaoGan, in addition to the PM 2.5 (R 2 = 0.117, p < 0.01) and NO 2 (R 2 = 0.015, p < 0.05), a notable correlation was also observed between the PM 10 and COVID-19 incidence (R 2 = 0.105, p < 0.05). Moreover, temperature is the only meteorological parameter that constantly correlated well with COVID-19 incidence in both Wuhan and XiaoGan, but in an inverse correlation (p < 0.05). AQI, PM 2.5 , NO 2 , and temperature are four variables that could promote the sustained transmission of COVID-19. [ABSTRACT FROM AUTHOR]

• A high proportion of COVID-19 patients were co-infected with influenza in Tongji Hospital (Wuhan). • Critically ill COVID-19 patients with influenza were more prone to cardiac injury than those without influenza. • Co-infection with the influenza virus may induce an earlier and more frequently occurring cytokine storm in critically ill COVID-19 patients. • Do not ignore detection of the influenza virus in patients with COVID-19. To delineate the clinical characteristics of critically ill COVID-19 patients co-infected with influenza. This study included adult patients with laboratory-confirmed COVID-19 form Tongji Hospital (Wuhan, China), with or without influenza, and compared their clinical characteristics. Among 93 patients, 44 died and 49 were discharged. Forty-four (47.3%) were infected with influenza virus A and two (2.2%) with influenza virus B. Twenty-two (50.0%) of the non-survivors and 24 (49.0%) of the survivors were infected with the influenza virus. Critically ill COVID-19 patients with influenza were more prone to cardiac injury than those without influenza. For the laboratory indicators at admission the following were higher in non-survivors with influenza than in those without influenza: white blood cell counts, neutrophil counts, levels of tumor necrosis factor-α, D-dimer value, and proportion of elevated creatinine. The results showed that a high proportion of COVID-19 patients were co-infected with influenza in Tongji Hospital, with no significant difference in the proportion of co-infection between survivors and non-survivors. The critically ill COVID-19 patients with influenza exhibited more severe inflammation and organ injury, indicating that co-infection with the influenza virus may induce an earlier and more frequently occurring cytokine storm. [ABSTRACT FROM AUTHOR]

• This study focused on the duration of viral shedding and risk factors in patients with COVID-19 outside of Wuhan, China. • The median duration of viral shedding in the current study was 17 days. • The highest temperature at admission, time from symptoms onset to admission and hospital length of stay were risk factors. To investigate factors associated with the duration of viral shedding in patients with COVID-19, outside of Wuhan. In this retrospective cohort study, patients with laboratory-confirmed COVID-19 in Changsha, China were included. Clinical characteristics, laboratory findings, treatment, and outcome were retrieved. Univariate and multivariate analyses were performed to explore potential factors. Overall, 147 patients with COVID-19 were included. The median duration of viral shedding (the number of days from symptoms onset until the successive negative detection of SARS-CoV-2 RNA) was 17 days (interquartile range [IQR], 12–21). Multivariate Logistic regression analysis indicated that the highest temperature at admission (odds ratio [OR], 5.200; 95% confidence interval [CI]: 1.190−22.726; p = 0.028), time from symptom onset to admission (OR, 1.740; 95% CI: 1.296−2.337; p < 0.001) and hospital length of stay (OR, 1.604; 95% CI: 1.262−2.040; p < 0.001) were risk factors for prolonged duration of viral shedding. This study, with a relatively large sample size, focused on the duration of viral shedding and related factors in patients with COVID-19, outside of Wuhan, China. Potential risk factors were identified and should be taken into consideration for the strategy of quarantining infected patients. [ABSTRACT FROM AUTHOR]

• LBS-requesting mobile device data is helpful to identify the generations of the early COVID-19 epidemic spread. • A third-generation epidemic spread had appeared in Wuhan from January 17–20, 2020 and in Hubei from January 23–24. • The mixed first and second-generation spreads strongly interacted to enhance the epidemic in Hubei excluding Wuhan. • The trend of the interactions between the first and second-generation spreads was evident in Hubei's adjacent provinces. • The mixed first and second-generation spreads appeared in most cities at the beginning of the outbreak. The outbreak of atypical pneumonia caused by the novel coronavirus (COVID-19) has currently become a global concern. The generations of the epidemic spread are not well known, yet these are critical parameters to facilitate an understanding of the epidemic. A seafood wholesale market and Wuhan city, China, were recognized as the primary and secondary epidemic sources. Human movements nationwide from the two epidemic sources revealed the characteristics of the first-generation and second-generation spreads of the COVID-19 epidemic, as well as the potential third-generation spread. We used spatiotemporal data of COVID-19 cases in mainland China and two categories of location-based service (LBS) data of mobile devices from the primary and secondary epidemic sources to calculate Pearson correlation coefficient, r , and spatial stratified heterogeneity, q , statistics. Two categories of device trajectories had generally significant correlations and determinant powers of the epidemic spread. Both r and q statistics decreased with distance from the epidemic sources and their associations changed with time. At the beginning of the epidemic, the mixed first-generation and second-generation spreads appeared in most cities with confirmed cases. They strongly interacted to enhance the epidemic in Hubei province and the trend was also significant in the provinces adjacent to Hubei. The third-generation spread started in Wuhan from January 17–20, 2020, and in Hubei from January 23–24. No obvious third-generation spread was detected outside Hubei. The findings provide important foundations to quantify the effect of human movement on epidemic spread and inform ongoing control strategies. The spatiotemporal association between the epidemic spread and human movements from the primary and secondary epidemic sources indicates a transfer from second to third generations of the infection. Urgent control measures include preventing the potential third-generation spread in mainland China, eliminating it in Hubei, and reducing the interaction influence of first-generation and second-generation spreads. [ABSTRACT FROM AUTHOR]

• ACE2 are highly expressed in human small intestinal enterocytes. • 2019-nCoV may have same tissue tropism such as small intestine with SARS-CoV. • The gastrointestinal tract may be an alternative route for 2019-nCoV. • Distribution pattern of ACE2 gene insinuates the possibility of a fecal–oral transmission for COVID-19. The coronavirus disease 2019 (COVID-19) was first reported in Wuhan, China and rapidly spread in other countries in December 2019. The infected patients presented with fever, respiratory symptoms, sometimes with digestive and other systemic manifestations, and some progressed with a severe acute respiratory syndrome or even death. Associated digestive symptoms were frequently observed in the patients, with an unknown significance and mechanism. ACE2, as the major known functional receptor of the 2019 novel coronavirus (2019-nCoV) attracted our attention. We collected the clinical data of the 2019-nCoV-infected patients from published studies and extracted the data about the incidence of gastrointestinal symptoms. Furthermore, we used online datasets to analyze ACE2 expression in different human organs, especially in the small intestine, to explore the relationship between ACE2 expression patterns and clinical symptoms. We found that diarrhea accounted for a notable proportion of COVID-19 patients, ranging from 8.0% to 12.9%. The results reveal that ACE2 mRNA and protein are highly expressed in the small intestinal enterocytes but not in the goblet cells or intestinal immune cells. High expression of ACE2 on the surface cells in the digestive tract may lead to gastrointestinal symptoms and inflammation susceptibility. Overall, digestive symptoms were common in the COVID-19 patients. ACE2 expression on surface cells of the small intestine may mediate the invasion and amplification of the virus and activation of gastrointestinal inflammation. It is a possible mechanism of digestive symptoms in the COVID-19 patients and explains the presence of the virus in patients' stool samples. The study also highlights the necessity of taking stool samples for suspected patients to help in early diagnosis and assessment of disease status. [ABSTRACT FROM AUTHOR]

• An outbreak of pneumonia of COVID-19 was recently reported in China, with highly infectious. • This was a multi-centered study included 234 inpatients confirmed with COVID-19 from 13 hospitals during 17 days (from January 10th to February 7th 2020) in Jiangsu province. Most of these cases were introduced from Wuhan, and they might have some distinctive clinical and imaging features. • The comprehensive chest CT characteristics and clinical features of patients with COVID-19 were described in this study. A pneumonia associated with the coronavirus disease 2019 (COVID-19) recently emerged in China. It was recognized as a global health hazard. 234 inpatients with COVID-19 were included. Detailed clinical data, chest HRCT basic performances and certain signs were recorded Ground-glass opacity (GGO), consolidation, fibrosis and air trapping were quantified. Both clinical types and CT stages were evaluated. Most patients (approximately 90%) were classified as common type and with epidemiologic history. Fever and cough were main symptoms. Chest CT showed abnormal attenuation in bilateral multiple lung lobes, distributed in the lower and/or periphery of the lungs (94.98%), with multiple shapes. GGO and vascular enhancement sign were most frequent seen, followed by interlobular septal thickening and air bronchus sign as well as consolidation, fibrosis and air trapping. There were significant differences in most of CT signs between different stage groups. The SpO2 and OI were decreased in stage IV, and the CT score of consolidation, fibrosis and air trapping was significantly lower in stage I (P < 0.05). A weak relevance was between the fibrosis score and the value of PaO2 and SpO2 (P < 0.05). Clinical performances of patients with COVID-19, mostly with epidemiologic history and typical symptoms, were critical valuable in the diagnosis of the COVID-19. While chest HRCT provided the distribution, shape, attenuation and extent of lung lesions, as well as some typical CT signs of COVID-19 pneumonia. [ABSTRACT FROM AUTHOR]

• Novel coronavirus (SARS-Coronavirus-2:SARS-CoV-2) which emerged in Wuhan, China, has spread to multiple countries rapidly. • This is the first case of meningitis associated with SARS-CoV-2 who was brought in by ambulance. • The specific SARS-CoV-2 RNA was not detected in the nasopharyngeal swab but was detected in a CSF. • This case warns the physicians of patients who have CNS symptoms. Novel coronavirus (SARS-Coronavirus-2:SARS-CoV-2) which emerged in Wuhan, China, has spread to multiple countries rapidly. We report the first case of meningitis associated with SARS-CoV-2 who was brought in by ambulance due to a convulsion accompanied by unconsciousness. He had never been to any foreign countries. He felt generalized fatigue and fever (day 1). He saw doctors nearby twice (day 2 and 5) and was prescribed Laninamivir and antipyretic agents, His family visited his home and found that he was unconsciousness and lying on the floor in his vomit. He was immediately transported to this hospital by ambulance (day 9). Under emergency transport, he had transient generalized seizures that lasted about a minute. He had obvious neck stiffness. The specific SARS-CoV-2 RNA was not detected in the nasopharyngeal swab but was detected in a CSF. Anti- HSV 1 and varicella-zoster IgM antibodies were not detected in serum samples. A brain MRI showed hyperintensity along the wall of right lateral ventricle and hyperintense signal changes in the right mesial temporal lobe and hippocampus, suggesting the possibility of SARS-CoV-2 meningitis. This case warns the physicians of patients who have CNS symptoms. [ABSTRACT FROM AUTHOR]

• There are more than 100,000 confirmed COVID-19 cases, with spread to over 100 countries as of 2020-03-08. • Asymptomatic carriers during the incubation period can be a potential infection source of COVID-19. • Person-to-person transmission has been documented; asymptomatic carriers should be a focus for disease prevention. With the ongoing outbreak of COVID-19 around the world, it has become a worldwide health concern. One previous study reported a family cluster with an asymptomatic transmission of COVID-19. Here, we report another series of cases and further demonstrate the repeatability of the transmission of COVID-19 by pre-symptomatic carriers. A familial cluster of five patients associated with COVID-19 was enrolled in the hospital. We collected epidemiological and clinical characteristics, laboratory outcomes from electronic medical records, and also verified them with the patients and their families. Among them, three family members (Case 3/4/5) had returned from Wuhan. Additionally, two family members, those who had not traveled to Wuhan, also contracted COVID-19 after contacting with the other three family members. Case 1 developed severe pneumonia and was admitted to the ICU. Case 3 and Case 5 presented fever and cough on days two through three of hospitalization and had ground-glass opacity changes in their lungs. Case 4 presented with diarrhea and pharyngalgia after admission without radiographic abnormalities. Case 2 presented no clinical nor radiographic abnormalities. All five cases had an increasing level of C-reactive protein. Our findings indicate that COVID-19 can be transmitted by asymptomatic carriers during the incubation period. [ABSTRACT FROM AUTHOR]

• COVID -19 cases are now confirmed in multiple countries. • Assessed the prevalence of comorbidities in infected patients. • Comorbidities are risk factors for severe compared with non-severe patients. • Help the health sector guide vulnerable populations and assess the risk of deterioration. An outbreak of coronavirus disease 2019 (COVID-19) occurred in Wuhan, China; the epidemic is more widespread than initially estimated, with cases now confirmed in multiple countries. The aim of this meta-analysis was to assess the prevalence of comorbidities in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected patients and the risk of underlying diseases in severe patients compared to non-severe patients. A literature search was conducted using the databases PubMed, EMBASE, and Web of Science through February 25, 2020. Odds ratios (ORs) and 95% confidence intervals (CIs) were pooled using random-effects models. Seven studies were included in the meta-analysis, including 1 576 infected patients. The results showed the most prevalent clinical symptom was fever (91.3%, 95% CI: 86–97%), followed by cough (67.7%, 95% CI: 59–76%), fatigue (51.0%, 95% CI: 34–68%) and dyspnea (30.4%, 95% CI: 21–40%). The most prevalent comorbidities were hypertension (21.1%, 95% CI: 13.0–27.2%) and diabetes (9.7%, 95% CI: 7.2–12.2%), followed by cardiovascular disease (8.4%, 95% CI: 3.8–13.8%) and respiratory system disease (1.5%, 95% CI: 0.9–2.1%). When compared between severe and non-severe patients, the pooled OR of hypertension, respiratory system disease, and cardiovascular disease were 2.36 (95% CI: 1.46–3.83), 2.46 (95% CI: 1.76–3.44) and 3.42 (95% CI: 1.88–6.22) respectively. We assessed the prevalence of comorbidities in the COVID-19 patients and found that underlying disease, including hypertension, respiratory system disease and cardiovascular disease, may be risk factors for severe patients compared with non-severe patients. [ABSTRACT FROM AUTHOR]

• The latest summary of the COVID-19 outbreak in China; • There might be an oral-fecal transmission of the virus; • Aggregates and consolidates the epidemiology, clinical manifestations, diagnosis, treatments and preventions of this new type of coronavirus. There is a current worldwide outbreak of the novel coronavirus Covid-19 (coronavirus disease 2019; the pathogen called SARS-CoV-2; previously 2019-nCoV), which originated from Wuhan in China and has now spread to 6 continents including 66 countries, as of 24:00 on March 2, 2020. Governments are under increased pressure to stop the outbreak from spiraling into a global health emergency. At this stage, preparedness, transparency, and sharing of information are crucial to risk assessments and beginning outbreak control activities. This information should include reports from outbreak site and from laboratories supporting the investigation. This paper aggregates and consolidates the epidemiology, clinical manifestations, diagnosis, treatments and preventions of this new type of coronavirus. [ABSTRACT FROM AUTHOR]

• All types and characteristics of available laboratory testing for SARS-CoV-2 were reviewed. • The selection strategies of testing and sampling sites were examined at different disease stages. • The choice of test depends on technical characteristics, clinical scenarios and requirements. The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which began in Wuhan, Hubei Province, China, has rapidly spread to produce a global pandemic. It is now clear that person-to-person transmission of SARS-CoV-2 has been occurring and that the virus has been dramatically growing in recent months. Early, rapid and accurate diagnosis is of great significance for curtailing the spread of SARS-CoV-2. There are currently several diagnostic techniques (e.g. viral culture and nucleic acid amplification test) being used to detect the virus. However, the sensitivity and specificity of these methods are quite different, with the sample source and detection limit varying greatly. This study reviewed all types and characteristics of the currently available laboratory diagnostic assays for detecting SARS-CoV-2 infection and summarized the selection strategies of testing and sampling sites at different disease stages to improve the diagnostic accuracy of Coronavirus Disease 2019 (COVID-19). [ABSTRACT FROM AUTHOR]

• We reported our experience of the course of PCR assays and the duration of viral shedding in 23 asymptomatic or mild COVID-19 patients from the cruise ship. • The median duration of viral shedding was 19 days (range, 6–37 days) from initial viral detection. • Eight of the 23 cases (35%) had another positive PCR result after testing negative once. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the cause of novel coronavirus disease 2019 (COVID-19), was first reported in Wuhan, China, and now has spread across the world as a global pandemic. The propagation from asymptomatic polymerase chain reaction (PCR)-positive individuals represents a complicating factor in the efforts to control the COVID-19 pandemic. We examined the course of PCR assays and the duration of viral shedding in 23 asymptomatic or mild COVID-19 patients from the cruise ship who were admitted to our hospital. Among these 23 cases, the median duration of viral shedding was 19 days (range, 6–37 days) from initial viral detection. Eight cases (35%) had another positive PCR result after testing negative once. Although the duration of viral shedding was approximately three weeks, the infectivity and transmissibility period from asymptomatic and mild COVID-19 cases is unclear. Further studies are needed to determine how long such asymptomatic and mild COVID-19 cases have infectivity. [ABSTRACT FROM AUTHOR]

An outbreak of coronavirus disease (COVID-19) in Wuhan, China caused by SARS-CoV-2 has led to a serious epidemic in China and other countries, resulting in worldwide concern. With active efforts of prevention and control, more and more patients are being discharged. However, how to manage these patients normatively is still challenging. This paper reports an asymptomatic discharged patient with COVID-19 who retested positive for SARS-CoV-2, which arouses concern regarding the present discharge standards of COVID-19. [ABSTRACT FROM AUTHOR]

• Patients who are infected by SARS-Cov-2 and HIV tend to have a longer disease course and slower generation of specific antibodies • For suspected cases of COVID-19, nucleic acid detection, gene sequencing and antibody detection can confirm the diagnosis, respectively • SARS-Cov-2 may damage lymphocytes, especially T-lymphocytes, and the immune system is impaired during the period of disease The ongoing outbreak of COVID-19 that began in Wuhan, China, become an emergency of international concern when thousands of people were infected around the world. This study reports a case simultaneously infected by SARS-Cov-2 and HIV, which showed a longer disease course and slower generation of specific antibodies. This case highlights that a co-infection of SARS-Cov-2 and HIV may severely impair the immune system. [ABSTRACT FROM AUTHOR]

• Zhejiang was the third worst-affected province of COVID-19 in China • This study monitored transmissibility of COVID-19, accounting transmission from imported cases • An interruption of local transmission was observed in early/mid-February 2020 • Early response followed by large-scale measures was effective for the interruption Owing to the frequent travel connections between Wuhan and Zhejiang, Zhejiang was the third worst-affected province in China with 1,205 cases confirmed before 26 February 2020. The transmissibility of the 2019 novel coronavirus disease was monitored in Zhejiang, accounting for the transmissions from imported cases. Even though Zhejiang was one of the worst-affected provinces, an interruption of disease transmission (i.e. instantaneous reproduction numbers <1) was observed in early/mid-February after a comprehensive set of interventions combating the outbreak. [ABSTRACT FROM AUTHOR]

• Nasopharyngeal swab showed higher positive rate than oropharyngeal swab. • Nasopharyngeal swab from male showed higher positive rate than female. • The consistency between from nasopharyngeal and oropharyngeal swabs were poor. Since the outbreak of coronavirus disease (COVID-19) in Wuhan in December 2019, by March 10, 2020, a total of 80,932 confirmed cases have been reported in China. Two consecutively negative RT-PCR test results in respiratory tract specimens is required for the evaluation of discharge from hospital, and oropharyngeal swabs were the most common sample. However, false negative results occurred in the late stage of hospitalization, and avoiding false negative result is critical essential. We reviewed the medical record of 353 patients who received tests with both specimens simultaneously, and compared the performance between nasopharyngeal and oropharyngeal swabs. Of the 353 patients (outpatients, 192; inpatients, 161) studied, the median age was 54 years, and 177 (50.1%) were women. Higher positive rate (positive tests/total tests) was observed in nasopharyngeal swabs than oropharyngeal swabs, especially in inpatients. Nasopharyngeal swabs from inpatients showed higher positive rate than outpatients. Nasopharyngeal swabs from male showed higher positive rate than female, especially in outpatients. Detection with both specimens slightly increased the positive rate than nasopharyngeal swab only. Moreover, the consistency between from nasopharyngeal and oropharyngeal swabs were poor (Kappa = 0.308). In conclusion, our study suggests that nasopharyngeal swabs may be more suitable than oropharyngeal swab at this stage of COVID-19 outbreak. [ABSTRACT FROM AUTHOR]

• People with positive SARS-CoV-2 RNA from respiratory tract specimens are infectious sources of COVID-19. • SARS-CoV-2 RNA from respiratory tract specimens may be persistent or recurrently positive during the course of this disease. • Active surveillance of SARS-CoV-2 RNA should be performed for infectivity assessment. The ongoing outbreak of COVID-19 that began in Wuhan, China, has constituted a Public Health Emergency of International Concern, with cases confirmed in multiple countries. Currently, patients are the primary source of infection. We report a confirmed case of COVID-19 whose oropharyngeal swab test of SARS-CoV-2 RNA turned positive in convalescence. This case highlights the importance of active surveillance of SARS-CoV-2 RNA for infectivity assessment. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 is a zoonotic pathogen able to infect humans, pets and other animal species, mustelids and felids being highly susceptible. Experimentally, it has been shown that SARS-CoV-2 replicates efficiently in cats, inducing humoral immunity and causing a variable clinical presentation. Here we report the case of two cats (G1 and G2) naturally infected with SARS-CoV-2 after contact with their COVID-19 positive owner diagnosed in September 2020. Oral swabs soaked in PBS were collected daily from 1 to 16 days after the owner tested positive for SARS-CoV-2. Urine and feces were taken several times during this period. Samples were analyzed by in-house real-time RT-PCR (based on CDC 2019-nCoV_N1). Serum samples, collected at day 30, were tested by IDVet multi-species ELISA. Vero E6 cells was used for virus isolation. Partial spike gene was sequenced by Sanger and compared with the owner sequence and the reference Wuhan 2019 (NC_045512.2). G1 showed apathy, anorexia, lack of grooming and mild respiratory symptoms (tearing and sneezing) for 5 days and then recovered gradually. G2 remained clinically asymptomatic. Viral RNA peak in oral swabs was detected in both cats at day 2 showing similar Ct value (25). SARS-CoV-2 was consistently shedding in G1 for 9 days, after sporadically detected until day 16. Viral shedding in G2 decreased quickly during the first 6 days. Faeces were positive to SARS-CoV-2 until 9 (G1) or 12 (G2) days post-viral detection. Viral RNA in urine was sporadically detected in G2 with high Ct values. Specific antibodies were detected in both cats one month after infection. Virus isolation was not successful. Cats and owner sequences of the spike protein were homologous with two mutations (A222V and D614G) that classify the virus within the 20A.EU1 clade. SARS-CoV-2 natural infection of two cats occurred after close contact with their infected owner. Both cats developed humoral immune response but they showed different clinical presentation and viral shedding pattern. Oral swabs and feces are proper samples for SARS-CoV-2 detection in cats. Variant 20A.EU1 detected in this study emerged in early summer 2020, presumably in Spain, and subsequently spread throughout Europe. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) causes COVID-19, which was first reported in humans in 2019, in Wuhan, China. This RNA virus has highly efficient transmission. Sporadic cases of infection in pets have been described. Human to animal transmission seems to occur, however, the epidemiologic role of pets remains unclear. This study aimed to screen dogs and cats from the North and Centre regions of Portugal for the exposure to SARS-CoV-2, during the peak of SARS-CoV-2 human infection in Portugal, which occurred between October 2020 and March 2021. A cross-sectional study was conducted in dogs and cats presented to veterinary medical centres from Portugal between October 2020 and March 2021, that required blood sampling as part of their diagnostic plan. Only surplus sera or plasma samples were used in this research. Sera or plasma were tested for the presence of specific antibodies anti-SARS-CoV-2 using a commercial ELISA adapted for multi-species detection (ID Screen SARS-CoV-2Double Antigen Multispecies®, IDVet). Laboratory results were expressed in S/P values and samples with an S/P% ≥ 60% were classified as positive. A total of 107 animals were sampled (dogs n=60; cats n=47). The canine population was composed by 25 purebred and 35 crossbreed dogs, with ages ranging from 5 months to 15 years of age. Cats were mainly of the domestic short-hair breed (n=45), with ages ranging between 6 months and 9 years old. The estimated rate of exposure was of 5.0% (95% CI: 1.71-13.7%) in dogs (n=3) and 2.13% (95% CI: 1.18-14.26%) in cats (n=1). A doubtful result (50≥S/P%<60%) was obtained in 6.7% (95% CI: 2.6-15.9%) of dogs (n=4) and in 4.26% (95% CI: 2.6-15.9%) of cats (n=3). To our best knowledge, this is the first serosurvey conducted in pets in Portugal. An exposure to the agent has been evidenced in dogs and in cats. Further studies must clarify the impact of the exposure in animal health and the role of the pets in spreading the virus. [ABSTRACT FROM AUTHOR]

• SARS-CoV-2 RNA could be detected on the surfaces of pagers and in drawers in the isolation wards 28 days after exposure. • First report of the presence of SARS-CoV-2 RNA in isolation ward environment 28 days after exposure. • The thorough disinfection of the ward environment included air and surface disinfection. • After thorough disinfection, SARS-CoV-2 RNA tested negative in the isolation ward environment. Recent studies have reported that surfaces and objects in the rooms of infected patients that are frequently touched by both medical staff and patients could be contaminated with SARS-CoV-2. In December 2019, Wuhan China suffered the earliest from this COVID-19 pandemic, and we took that opportunity to investigate whether the SARS-CoV-2 RNA exists in the ward environment after a long time from exposure. We found that on the 28th day following the discharge of COVID-19 patients, SARS-CoV-2 RNA could still be detected on the surfaces of pagers and in drawers in the isolation wards. Thorough disinfection of the ward environment was subsequently performed, after which these surfaces in the isolation wards tested negative for the presence of SARS-CoV-2 RNA. The findings remind us that the contaminated environment in the wards may become potential infectious resources and that despite a long time from exposure, the thorough disinfection in the COVID-10 units after is still necessary. [ABSTRACT FROM AUTHOR]