Category: Corona Virus

Background and objective

Over the past few decades, new infectious diseases have emerged,and these have played a key role in changing behavior and lifestyle in all age groups. More recently, with the emergence of the coronavirus disease 2019 (COVID-19) pandemic, governments around the world have made unprecedented efforts to contain the epidemic by implementing quarantine measures, social distancing, and isolating infected individuals. Social behavioral adaptations (e.g., social distancing, isolation, etc.) impact children's and adolescents' lifestyle activities and lead to increased incidence of psychosocial problems, worsening of preexisting mental illness, and fears of infection, uncertainty, isolation, and stress. In light of this, this study aimed to assess the impact of COVID-19 on the behaviors and lifestyles of the children and adolescent population of Pakistan.

A cross-sectional study was conducted involving 323 children and adolescents bytargeting parents of children and adolescents in the age group of 4-18 yearsliving in Pakistan.The study was conducted from April 2021 to September 2021. A well-designed structured questionnaire was used to collect data about the sociodemographic profile, attitudes, and behavioral factors impacted by COVID-19 in children and adolescents. SPSS Statistics version 23 (IBM, Armonk, NY)was used to enter and analyze data.

Parents or caregivers of a total of 189 male and 134 female childrenaged between four and 18 years took part in this study.During COVID-19, the consumption of fast food and fried foods by children and adolescentsincreased significantly.In this study, out of 323 participants, almost all (289, 89.5%) had increased their screen time significantly.Nearly half of the total individuals experienced the feeling of depression and loneliness during the pandemic. Additionally, some children and adolescents felt fearful when leaving home. COVID-19 lockdowns have led to many changes in children's and adolescents' lifestyle habits. They reduced physical contact with others due to the fear of transmission of COVID-19. Based on our findings, the pandemic and its containment strategies have adversely affected the behaviors, lifestyles, and attitudes of children and adolescents.

Governments around the world have imposed social distancing during the COVID-19 pandemic, leading to adverse short-term and long-term negative mental health issues such as unhappiness, fear, worry, irritability, depressive symptoms, anxiety, and post-traumatic stress disorder (PTSD). Interventions are needed to focus on building resilience in children and adolescents, addressing their fears and concerns through better communication, encouraging routine and physical activity, and taking measures to alleviate loneliness.

Human behavior represents the latent and expressive capacity of various physiological, psychological, and social activities at all stages of human life; however, the earlier the habits are formed, the more likely they are to take root and flourish [1]. Over the past few decades, new infectious diseases such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome(MERS), zika, and, more recently, the coronavirus disease 2019 (COVID-19) have emerged[2]. As of May 2021, the COVID-19 pandemic has infected more than 164 million people in more than 200 countries around the world and caused more than 3,881,091 deaths, according to the World Health Organization (WHO). As a result, governments around the world have made unprecedented efforts to contain the epidemic by implementing quarantine measures, social distancing, and isolating infected individuals[3].

By the end of April 2020, an estimated 1.5 billion children (aged 5-12 years) and adolescents (aged 13-17 years) worldwide had switched to distance learning following school closures. School closures and additional social behavioral adaptations (e.g., social distancing, isolation, etc.) impacted children's and adolescents' lifestyles and activities [4]. Preliminary evidence of deep concern suggests that social restrictions needed to reduce the spread of COVID-19 have increasedsedentary behavior, disrupted sleep patterns, and caused changes in lifestyles at home and outside, especially among children and adolescents [5].

A study in China found that only 17% of children achieved adequate levels of physical activity, and 66% of them were rated "inactive" during the pandemic. Canadian children reported a similar decline in physical activity [6]. The available evidence shows that 43.5% of Polish respondents said that they ate more during quarantine, and 51.8% admitted to eatingsnacksmore frequently between meals [7]. A multicontinental survey of adolescents (n=1,047) showed that during the COVID-19 pandemic, daily sitting time increased by 28.6% and the frequency and duration of physical activity decreased by 24% and 33.5%, respectively [8]. Obese children have decreased their exercise time and increased screen and sleep time during the COVID-19-associated lockdowns [9].

The two key pillars of human civilization - social interaction and structured schedules - have been distorted by the pandemic, which has led to significant psychological effects on children and adolescents. The increased incidence of psychosocial problems, worsening of preexisting mental illnesses, and fears of infection, uncertainty, isolation, stress, and mass panic have all significantly increased due to the ongoing pandemic [10].

A web-based survey was conducted targeting the parents of children and adolescents aged 4-18 years. The data were collected from April 2021 to September 2021. An informed written consent form was developed in the English language describing the objectives of this research, and IRBapproval from the Ethical Review Board of General Hospital, Lahore (00/89/20) was obtained before the data collection.

A descriptive cross-sectional study design was adopted for this research. A nonprobability, convenience sampling method was used for data collection. The Raosoft sample size calculator was used to estimate the sample size; maintaining a 5% margin of error, a 95% confidence level, and a prevalence of 31.3%, the minimum sample size of 250 was determined. We, however, conducted our study on 323 children. Parents of children and adolescents (aged 4-18 years) living in Pakistan presenting at the speech therapy clinic of our hospital were included in the study,while those who denied consent were excluded.

A standardized electronic questionnaire including queries about thesociodemographic profile, changes in eating style and behavior, changes in physical activities and screen time, lifestyle changes, and disturbances in sleep and mental healthwere used to collect data through a web-based survey using Google Forms. Data were entered into the SPSS Statistics version 23 (IBM, Armonk, NY). The data were coded and refined for further analysis. Results were presented in the form of frequency tables and bar/pie charts of different variables representing the research topic, and quantitative values were presented asmeans and standard deviations.

Parents of 323 children participated in this online survey. The mean age of the children was 11.2 years, with a standard deviation of 4.2. Among them, 38.4%were between the ages of three to nine years and the rest were between the ages of 10-19; 41.5% (n=134) were females and 58.5% (n=189) were males; 58.2% (n=188) were dwelling in the metropolitan city while 41.8% (n=135) lived in small cities. The demographic factors are presented in Table 1.

During COVID-19, the consumption of fast food and fried foods by children and adolescents has increased significantly. According to this survey, during COVID-19, a higher consumption level of fizzy drinks has been observed. Our findings are presented in Table 2.

In this study, out of 323 participants, almost all (289, 89.5%) had increased their screen time significantly. Similarly, among the323 individuals, 52 (16.1%) spent less than two hours in front of the screen, 112 (34.7%) spent two to five hours, 93 (28.8%) spent five to eight hours, and 66 (20.4%) spent more than eight hours (Table 3).

Of the 323 participants, 42 said they slept for less than six hours a day, 110 said they slept six to eight hours, 133 said they slept 8-10 hours, and only 38 indicated that they sleptfor more than 10 hours a day. In terms of sleep quality among children and adolescents during the pandemic, it was very poor in 1.9% of the total participants, poor in 5.6%, good in 40.9%, excellent in 31.9%, while 19.8% had excellent sleep quality. Parents of 95 children stated that their children experienced unusual nightmares during sleep (Table 4).

In this survey,the vast majority had recently canceled their summer vacation plans. Precautionary measures included washing hands, using hand sanitizer, wearing a mask, avoiding shaking hands, etc. Of the 323 people, nearly allwashed their hands more frequently and most carried a hand sanitizer.Additionally, it was observed that almost every childengaged in increased leisure television (TV)/movie time and increased their social media usage during the COVID-19 lockdown (Table 5).

These results indicate that COVID-19 had an impact on the lifestyle behaviors and attitudes of children and adolescents. The pandemic and the subsequent containment strategies driven by governments around the world have adversely affected the behavioral health of children and adolescents. Further studies are however needed to study the nature of these impacts in a detailed manner.

This study explored the experiences of children and adolescents during the COVID-19 pandemic and its impact onlifestyle attitudes and behaviors in this age group. The study gathered its findings primarily through observations by parents and caregivers. The major alterations that we observed included changes in eating behavior,physical activity, and screen time; we also noted changes in sleep,mental health, and lifestyle attitudes. A Brazilian study on food habits during the pandemic showed continued worsening in dietary patterns, with reduced intake of fruits and vegetables and increased consumption of sweets and fast food [11]. Another study in Italy showed that during the COVID-19 pandemic, 25.6% of people increased their consumption of junk food, while 29.8% reduced their consumption of fried food [12]. This disruption of healthy eating patterns can lead to obesity and malnutrition in children and adolescents. According to an Australian study (n=5,469), a significant proportion of individuals engaged in binge eating, overeating, and using food to cope during the pandemic [13]. In another UK study, more than half (53.7%) of the respondents said that their healthy perception of the food they ate in the last week had not changed compared to pre-COVID-19, while 27.9% said they were eating an unhealthy diet, and 18.4% said they ate more [14].

COVID-19 restrictions appear to have had a greatimpact on physical activity and behavior in children and adolescents. In an Italian study, during COVID-19 isolation, the proportion of low-active individuals increased to 39.62%, while the proportions of moderately active and highly active individuals were 29.75% and 30.63%, respectively [15]. A Canadian study of children and adolescents (n=1,472) found that during the COVID-19 pandemic, only 3.6% of children (aged 5-11 years) and 2.6% of adolescents (aged 12-17 years) carried out the suggested strategies of 60 minutes of moderate-intensity physical activity per day, which is lower than in a 2019 report thatfound that12.7%met the guidelines [16].

A Chinese survey of children and adolescents (n=2,427, aged 6-17 years) reported that leisure screen time significantly increasedcompared to that before the COVID-19 lockdown. The total screen time increased by approximately 30 hours/week, and thetime spent in the long term (2 hours/day) increased by 23.6% [16]. In another Canadian study, those who reduced physical activity had greater changes in screen-related sedentary behavior than those who reported increased physical activity (p=0.005) [17].

Parents reported higher levels of family stress, depression, and anxiety due to social isolation. These findings are relevant to healthy development, as adverse psychological experiences in childhood are associated with an increased risk of anxiety later in life. The public health concern is that these short-term behavioral changes in response to COVID-19 may become entrenched. In a survey conducted in Portugal, Spain, and Italy, more than half of the participants felt bored (52.2%) and a third felt lonely (37.7%), particularly among Portuguese and Italian children [18].Another study in Turkey revealed that 54.8% of participants reported that they were afraid of getting infected by the virus, and 45.6%stated that they were afraid of spreading the virus to others [19]. In a related study in the Netherlands, 19 families with children mentioned having anxiety (25%) and following self-isolation measures in addition to government lockdown measures [20].According to the National Coalition of Mental Illness in New York City, the number of callers seeking help with stress or anxiety increased by 60% and the average call time increased by 15 minutes in the weeks following the implementation of social distancing measures [21].

A Portuguese study showed that most patients (69.6%) reported difficulty sleeping, with waking up frequently being the most common problem during the COVID-19 lockdown [22]. Interestingly, in the Netherlands, a quarter of pre-pandemic (clinical) insomniacs had significantly improved sleep quality, while 20% of pre-pandemic good sleepers experienced poor sleep quality during lockdown measures [23]. Similarly, in a Canadian study of dream changes during the pandemic, 55% of participants (39/71) said that their dreams were more stressful, while 50.7% (36/71) said that their dreams were more stressful and vivid, while 42.2% reported experiencing more nightmares overall, with girls more likely to experience the increase in nightmares during the pandemic [24].

The rapid spread of COVID-19 to almost all regions of the world has brought about enormous health-related, environmental, economic, and social challenges. Social distancing, surgical masks, hand washing, and other precautions are considered the only way to fight the spread of the virus. All these factors can lead to changes in an individual's lifestyle. In a study conducted in Brazil, results showed that only 3.0% of the total participants reported not practicing physical and social distancing during the study period [11]. In another study, 40.9% of 4,975adultUS respondents said that they delayed or avoided any medical care, including urgent or emergency care (12.0%) and usual care (31.5%), due to concerns about COVID-19 [25].

Likewise, in a survey conducted in Hong Kong, 74.2%, 72.7%, and 59.7% of 1,501 respondents said they avoided going out, going to crowded places, and attending social gatherings of more than four people, respectively [26]. In another study conducted in Greece, one-third (28.7%) of participants said that they had canceled plans for their summer vacation, while the majority (44.9%) had not made up their minds. Only a small percentage (17.5%) believed that they will continue with their summer vacation plans with some modifications [27].

In another study conducted in Iran, the overall frequency of use of masks was 45.6% and the proportion of women using masks was significantly higher than that of men [28]. Similarly, a study conducted in Jordan showed that approximately 68.4% of contributors believed that wearing a mask could prevent infection [29] and an Indian study showed that the majority (80%) of the total participants gave an ideal answer that they avoided shaking hands during COVID-19 [30]. A major lifestyle change was the increased use of social media during the lockdown, as a study conducted in India showed an increase in the number of social media users, with 87% of people reporting an increase in their use, and 75% spending more time on social media [31].

Like all observational studies, our study also had somelimitations. Firstly, due to a strict lockdown that was in place, the studyquestionnaire was distributed via online platforms, including social media. The availability and use of the internet vary with different sociodemographic indicators. Therefore, this could be a hindrance to the precision of the results, especially when the ability to judge the changes in the behavior of their children also varies with the different sociodemographic settings. Secondly, our sample size of 323 also presents a challenge in adequately predicting the public perception at large and generalizing the results.

Our study, however,has been successful in addressing the specific concerns that family physicians, pediatricians, and psychiatrists would face in the future in the aftermath of the pandemic. It could also provide a framework through which morestudies can be conducted to devise a strategy to cope with an upcoming "behavioral" pandemic in the future.

The COVID-19 pandemic has had a major effect on the health and lifestyle behaviors of both adolescents and children. Children are less affected by COVID-19 directly but suffer indirect, potentially long-term health consequences due to changes inlifestyle, eating behavior, physical activity, sleep patterns, screen time, and mental well-being. Due to an unbalanced diet, children are at a higher risk of both obesity and malnutrition. Governments around the world have imposed social distancing, leading to adverse short-term and long-term negative mental health issues such as unhappiness, fear, worry, irritability, depressive symptoms, anxiety, and post-traumatic stress disorder (PTSD).

Parents must take care of their mental health and coping strategies and develop positive mental attitudes to support children and adolescents through this pandemic. Interventions should focus on building resilience in children and adolescents, addressing their fears and concerns through better communication, encouraging routine and physical activity, and taking measures to alleviate loneliness. Even with social distancing, social interaction is important; video conferencing, phone calls, or real-time texting may be worth considering, possibly on a daily basis.

We believe our findings on the impact of the COVID-19 pandemic on the lifestyles and behaviors of children and adolescents will encourage parents, healthcare professionals, and policymakers to put appropriate measures in place to counter them. Further studies should be conducted to investigate thenature of these impacts and to draw long-term strategies to cope with their consequences and promote physical and mental health in this age group.

Read this article:

The Impact of COVID-19 on the Behaviors and Attitudes of Children and Adolescents: A Cross-Sectional Study - Cureus

Patient deaths: 1,057,247

Total vaccine doses distributed: 843,692,095

Patients whove received the first dose: 263,812,108

Patients whove received the second dose: 224,980,931

% of population fully vaccinated (both doses, not including boosters): 67.8%

% tied to Omicron variant: 100%

% tied to Other: 0%

See the original post:

Coronavirus Omicron variant, vaccine, and case numbers in the United States: Sept. 28, 2022 - Medical Economics

Monkeypox Shots, Treatments and Tests Are Unavailable in Much of the World  The New York Times

See the original post:

Monkeypox Shots, Treatments and Tests Are Unavailable in Much of the World - The New York Times

The number of cases has been growing but the pace seems to have slowed in recent weeks. The monkeypox virus is still circulating, he said. However, it does not look like it is exponentially increasing like it had before.

The states dashboard shows how monkeypox has spread in Colorado. The first two cases were found in the state in May. The numbers grew from there to six in June, 66 in July, 157 in August and 51 so far in September. That state has recorded a total of 282 to date.

Based on the data being collected both here in Colorado and nationally, we are seeing that the greatest risk at this time is among, gay, bisexual, or other men who have sex with men, said state epidemiologist Dr. Rachel Herlihy last month. That is primarily, here in Colorado, in the Denver metro area, but we have seen cases outside of the metro area as well.

Monkeypox is a virus in the orthopox family of viruses, according to the states website. It is rare, but can be serious.

It can spread from person to person when someone who has monkeypox has close skin-to-skin contact with someone else. Close contact can mean physical contact with sores, bumps, or lesions of someone who has monkeypox. That contact includes sex. The virus can also spread through touching the bed linens or clothing of an infected person and can also live on other surfaces for some time.

Recent cases in the United States have been infected through person-to-person contact. Brief interactions without physical contact are unlikely to result in getting the virus.

Monkeypox has recently been spreading elsewhere, like in Canada, Europe, and Australia. It is endemic in central and west Africa.

Recent data suggest people who have recently traveled to a country where monkeypox has been reported or men who have sex with other men are at heightened risk.

The type of monkeypox spreading in the United States is rarely deadly and has a fatality rate of less than 1 percent, according to the states website.

In fact, in most cases, it will resolve on its own. Symptoms of the virus may begin with flu-like symptoms that can include fever, headache, muscle aches, swollen lymph nodes, and exhaustion. Typically, a rash or skin bumps develop within one to three days after the onset of fever, often beginning on the face then spreading to other parts of the body.

Visit link:

Rare monkeypox-related illness that causes brain inflammation reported in Colorado - Colorado Public Radio

The Pandemic Response Accountability Committee, one of the three oversight bodies created by the CARES Act, launched a new data initiative this week to display information about COVID funding.

These new agency funding profiles enable the public to see the total amount of pandemic relief money that nearly 40 federal agencies received, and the specific programs funded, said a press release. They also include relevant oversight work from federal offices of inspectors general, whose audits and investigations alert the public and policymakers of any fraud, waste, and abuse.

Robert Westbrooks, executive director of the committee, said this new website feature reflects our dual responsibilities of transparency and oversight. Here are some of the other recent headlines you might have missed.

Despite various layers of control from the Small Business Administration, individuals with foreign IP addresses were able to access the application system for the economic injury disaster loan program for COVID relief, the agencys watchdog said in a report this week. SBA received millions of attempts to submit COVID-19 EIDL applications from foreign IP addresses and stopped most of them; however, the agency processed more than 233,000 of these applications from March 20, 2020 to November 12, 2021, our review period, said the report. Although applicants that reside overseas may qualify for this assistance, transnational crime entities in foreign countries have fraudulently obtained funding from this and other U.S. programs in the past.

On Wednesday, the Justice Department announced it established three COVID fraud strike force teams, which will operate out of the U.S. Attorneys Offices in the Southern District of Florida, the District of Maryland, and jointly between the Central and Eastern Districts of California. These strike force teams will build on the departments historic enforcement efforts to deter, detect, and disrupt pandemic fraud wherever it occurs, said Attorney General Merrick Garland, in a statement. Since the start of this pandemic, the Justice Department has seized over $1.2 billion in relief funds that criminals were attempting to steal and charged over 1,500 defendants with crimes in federal districts across the country, but our work is far from over.

Members of the teams include prosecutors and agents from the Labor, SBA, Homeland Security inspector general offices, FBI, Secret Service, Homeland Security Investigations, Internal Revenue Service Criminal Investigations, and the U.S. Postal Inspection Service. The Pandemic Response Accountability Committee and the Special Inspector General for Pandemic Recovery are also helping.

The Centers for Disease Control and Preventions advisory committee on immunization practices will meet next month, during which a voteis planned to make recommendations on the child/adolescent immunization schedule and COVID -19 vaccines, which could mean the updated booster shot, per a notice in the Federal Register. Also, a vote on Vaccines for Children (a federally funded program that provides free vaccines to children who might not otherwise get vaccines) on COVID-19 vaccine is scheduled.

The U.S. Attorneys Office for the Southern District of Texas announced on Tuesday what it believes to be the countrys first False Claims Act settlement with a Paycheck Protection Program lender. The False Claims Act is a Civil War-era law to protect the government from being defrauded.

Help us understand the situation better. Are you a federal employee, contractor or military member with information, concerns, etc. about how your agency is handling the coronavirus? Email us at newstips@govexec.com.

Go here to see the original:

Coronavirus Roundup: New COVID Datasets and Strike Teams Are Targeting Fraud - GovExec.com

Africalagged in genome sequencing during the first two years of the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, with increased funding, over 100,000 genomes have now been sequenced from this continent.

A new study sums up the results of genomic surveillance so far, indicating how the variants of concern of the virus have spread while indicating future directions for response readiness.

Africa appeared to be relatively spared of high cases and deaths during the ongoing pandemic, with approximately 11 million cases out of a global total of over600 million and a quarter of a million deaths out of over 6.4 million deaths worldwide.

However, as the virus continued to change and mutate, new variants emerged that showed, in some cases, higher transmissibility and infectivity or virulence. Immune escape mutations were identified in some variants, making them capable of increased spread even among vaccinated or previously infected populations. These were called variants of concern (VOC), and so far, there have been five of them Alpha, Beta, Gamma, Delta, and Omicron.

Of these, Beta and Omicron were first detected in Africa, though the other two also caused significant cases on this continent. In response to the growing threat posed by the emergence of VOCs, samples were collected from multiple sites for sequencing. However, in April 2020, only 20 African countries had this capability.

As global supply chains petered out, these efforts stopped towards the end of the year. After the first 10,000, an analysis showed some missing areas, in response to which increased funds poured into the building of increased infrastructure and training staff for genomic surveillance.

Both the Africa Centers for Disease Control (Africa CDC) and the regional office of the WHO in Africa (or WHO AFRO) shared the responsibility for this, aided by many other individuals and organizations. The result was that another 90,000 sequences were uploaded from April 2021 to March 2022.

To put this in perspective, less than 4000 sequences of the human immunodeficiency virus (HIV) and 12,000 influenza sequences have been uploaded so far, despite their presence in Africa in alarming numbers for many years.

The current study, published in Science, explores the contribution of genomic sequencing to the scientific understanding of COVID-19 in this continent and alsointroduces global public health measures via the ability to pick up new variants early enough.

The data demonstrates multiple waves of infection, different in scale and period from country to country. After the first two waves, dominated by B.1 and Alpha variants, however, Delta and Omicron swept across Africa in grim succession.

Different strains predominated in various parts of Africa, such as C.36 and C.36.3, which caused 40% of infections in Egypt, vs. B.1.160 lineage in Tunisia. In both cases, these gave way to Delta during the third wave.

In South Africa, Beta dominated the second wave instead of Alpha. Interestingly, though the C.1.2 variant showed signs of immune escape, it failed to make a significant impact against the Delta background.

Other lineages that competed with Alpha included B.1.525 and A.23.1, which were finally outcompeted by later emerging VOCs. The differences in lineage by region could be due to virus genetics, human mobility, competition between co-circulating lineages, and immunity levels.

Delta caused the greatest impact, causing over a third of all infections in Africa, according to many analysts. Beta caused about one in seven, and Alpha only about 4% overall. Omicron, which is still spreading, caused over a fifth of all infections, as judged by genomic sequencing.

Unlike the earlier VOCs, Omicron became prominent against a background of high infection and vaccination rates, with high associated immunity levels. Along with its lower intrinsic virulence, Omicron has led to fewer deaths than other VOCs, corresponding to the lower South African mortality rate during this wave.

The first part of the pandemic was caused by strains belonging to the B.1 clade, or ancestral viruses, which were then replaced by the first cluster of VOCs from late 2020 onwards: Alpha, Beta, and then, in 2021, Delta and Omicron. While Alpha and Beta circulated mostly in distinct regions of Africa, Delta and Omicron dominated infections in Africa beginning soon after their emergence.

The data comes from combining epidemiologic data with genomic sequencing data, along with information on the temporal and size-related characteristics of these waves. However, some countries have tested only one in ten million population, while others have tested over 10,000 per ten million, indicating grossly heterogeneous testing rates.

Interestingly, countries with high testing rates have reported higher case rates as well, but under-reporting continues to be a reality, as in the rest of the world. Increased reporting was achieved largely by the use of relatively inexpensive sequencing technology.

There is an urgent need to increase sequencing capacity, with 16 countries still lacking local sequencing facilities while many others have limited capacity. Three premier sequencing centers, and multiple regional sequencing hubs, have been set up to help consolidate resources in a few countries to maximize sequencing across the whole continent. These centers helped mostly sub-Saharan countries by handling the whole of the local sequencing efforts in some countries like Angola and Namibia, but also cooperating with local sequencing efforts during waves.

Other facilities outside Africa have also been pressed into service to increase surveillance, especially for West and North African countries.

Ultimately, a mix of strategies from local sequencing, collaborative resource sharing among African countries and sequencing with academic collaborators outside the continent helped close surveillance blind spots.

Even with low levels of sequencing, representative sampling over time has helped maintain genomic surveillance and detect variants in time, including Beta and Omicron. Moreover, the turnaround time is being reduced progressively from, for instance, ~180 days to 50 days from October 2020 to one year later.

This is favored by using local sequencing networks compared to regional or external facilities, which indicates the need to invest in the latter. The travel bans that followed the detection and reporting of the Beta and Omicron VOCs show how countries could hesitate to report such data in the future. If sequencing can be performed only outside the country, this will inevitably lead to the absence of surveillance in such situations.

Thus, encouraging local sequencing capacity will help generate timely and regular data for local and regional decision making. This would allow emerging variants to be detected early enough to allow time to interrupt their spread.

For example, Beta was detected three months after its origin, but for Omicron, it was within five weeks. Moreover, the World Health Organization declared the latter a VOC within 72 hours of depositing its sequence in the database.

Sequencing efforts should be built up, not just for SARS-CoV-2 but other new or re-introduced pathogens, including Ebola, measles, and H1N1 influenza. According to Africa CDC, over 200 infectious disease outbreaks occur annually in this continent.

Beyond the current pandemic, continued investment in diagnostic and sequencing capacity for these pathogens could serve the public health of the continent well into the 21st century.

Read more here:

Genomic sequencing reveals the course of COVID-19 in Africa - News-Medical.Net

PARIS Frances national health body warned on Friday of a resurgence of COVID-19 cases in the country, and urged people to continue to get vaccinated to protect themselves against the virus.

The Sante Publique France (SPF) body said that during the week of Sept 5-Sept 11, there had been 186 confirmed COVID cases for every 100,000 people in France a figure up 12% versus the previous week representing an average of around 18,000 new cases per day.

Earlier this week, Emer Cooke the executive director for the European Medicines Agency (EMA) watchdog told a Reuters Next Newsmaker interview that people in Europe should take whatever COVID-19 booster vaccine is available to them, given expectations of an autumn rise in infections.

New infections have been steadily rising since 10 days and the seven-day moving average of daily new cases reached an almost five-weeks high of 24,042 on Thursday.

Read the rest here:

France's health body warns of resurgence of COVID virus in the country - Euronews

Background

False-negative results derived from RT-PCR tests for diagnosing coronavirus disease (COVID-19) have raised questions about whether to consider them the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using an imperfect gold standard to assess other diagnostic tests would never let the other tests show better diagnostic performance. The best strategy in such cases is to do an agreement analysis, and this study aims to estimate the agreement between real-time reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid antigen test (RAT) for COVID-19 detection.

A retrospective study was done using paired data of individuals tested for COVID-19, both by RT-PCR and RAT, obtained from the virology laboratory of Government Bundelkhand Medical College, Sagar, Madhya Pradesh, India. A sample size of 93 was calculated, and the data were abstracted in a data abstraction sheet. Variables included were results of RT-PCR and RAT, age, gender, presence of symptoms, test kit used, and the time duration between sampling for RT-PCR and RAT. Apart from descriptive statistics, keeping in mind the binary outcome of RT-PCR and RAT, Cohens kappa was calculated for agreement analysis. A p-value of <0.05 was considered significant.

The data on 100 participants suspected to be infected with COVID-19 (58 male and 42 female) with a mean age of 39.8 (19.0) years were analysed. The number of discordant pairs was eight. Cohens kappa showed substantial agreement between RT-PCR and RAT, =0.646, (95% CI 0.420 to 0.871), p<0.001.

Considering the ease of conducting RAT with quick results and substantial agreement with RT-PCR, RAT could be a better choice in detecting SARS-CoV-2 and, hence, COVID-19 disease on a large scale.

Rapid and accurate diagnostic tests are crucial for controlling any communicable disease; the same goes for the coronavirus disease (COVID-19) pandemic. Quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) is recommended by the World Health Organization (WHO) as the reference test for the laboratory diagnosis of COVID-19 [1]. Researchers have developed other forms of diagnostic tools, such as antigen-detection diagnostic tests. Generally, the ease-of-use and rapid turnaround time of antigen-detecting rapid diagnostic tests (RDTs) offer to decrease the delays in diagnosis by shifting to decentralised testing of patients with early symptoms [2]. The Indian Council of Medical Research (ICMR) published an advisory regarding the use of the rapid antigen test (RAT) on June 14, 2020, and since then it has been used extensively [3].

No test is expected to produce 100% accurate results. Ideally, a new test is compared with an existing "gold standard" and parameters like sensitivity, specificity, and predictive values of the new test are calculated. There are reports of false-negative RT-PCR results in patients with COVID-19 during the pandemic course [1]. An early study [4] showed that the sensitivity of RT-PCR varies from 68% to 100%, and the specificity is 98.9%, but several authors [5,6] have pointed out the poor performance of this technique, particularly in terms of sensitivity. According to Liu et al., the positivity rate of RT-PCR could be as low as 38% [5] (i.e., not better than chance). The accuracy of the result depends on the site and the quality of sampling as well. Li et al. in a recent study [7] also found a high rate of false-negative RT-PCR results, which were tested on specimens collected from 610 hospitalised patients from Wuhan, China. Thus, using RT-PCR as a reference standard would constitute using an imperfect gold standard. This would never let the other test show a better diagnostic performance. The additional patients identified would be regarded as false positives. With the use of chest computed tomography (CT) scans as a diagnostic method, the same mistake has also been made [8,9].In such a scenario, instead of calculating the sensitivity, specificity, and predictive values of the test (which would require one of the tests to be the gold standard), the best strategy would be to measure the degree of agreement (using the Kappa coefficient) between the two tests [10], i.e., neither of the two tests is considered to be the reference, and therefore, any discrepancies could be linked to either of the tests. Studies determining agreement between these tests are lacking in the literature. This study aims to estimate the agreement between RT-PCR and RAT for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., COVID-19 infection.

We conducted a retrospective record-based study between July 2021 and August 2021 after getting clearance from the Institutional Ethics Committee, Government Bundelkhand Medical College, Sagar, Madhya Pradesh, India (IECBMC/2021/24). Data was collected from the virology laboratory of the Government Bundelkhand Medical College from August 2020 to December 2020. It is prudent to mention here that vaccinations against COVID-19 in India started in January 2021. Hence, subjects in this study were unvaccinated for COVID-19. This tertiary care centre caters to a population from both urban and rural areas, and being a referral centre for COVID-19, it has facilities for both RT-PCR and rapid antigen tests. Patients, during their course of management, undergo both tests as per protocol. The study population consisted of people suspected of being infected by COVID-19 (who had symptoms) or contacts of confirmed cases (who could have been asymptomatic) identified through contact tracing.

We included only those subjects who had undergone both RT-PCR and RAT tests. The maximum acceptable duration between both tests was set to three days. We believe that three days is short enough to not have affected the severity of the condition and hence the diagnosis. The subjects and investigators were blinded to the result of the first test in cases where the second test was RAT. In those instances where RAT was conducted initially, it was not possible to blind the participant. Those subjects with data showing faulty sample collection (from sites other than the prescribed site) were excluded. Standard procedures were followed for conducting RT-PCR and RAT as recommended by the ICMR.

The kit used for RAT was the STANDARD Q COVID-19 Ag detection kit (SD Biosensor Inc., South Korea), and for RT-PCR, VIRALDTECT-II (Genes2Me Pvt. Ltd., India). All RT-PCR samples were oropharyngeal and all RAT samples were nasopharyngeal, as recommended by the manufacturer.

The minimum required sample size was calculated using the formula for determining Cohens kappa, where we took the proportion of positive rating by rater one (i.e., RT-PCR) as 68% (sensitivity) [4], the proportion of positive rating by rater two (i.e., RAT) as 50% (sensitivity) [3], and assumed =85% at 95% CI with 10% precision. It was calculated to be 93. We took 100 subjects. Universal sampling was done, and subjects were included or excluded as per the criteria set above.

Data were abstracted in a data abstraction sheet designed with the help of Epi Info software (version 7.2.4.0, CDC, Atlanta) for Windows. We abstracted data on results of RT-PCR and RAT (positive and negative), age, sex, the test kit used, the time duration between samples taken for RT-PCR and RAT, and the presence of symptoms (cough, fever, sore throat, and generalised body ache) from the records of subjects for further analysis. Participants were classified as "symptomatic" if any of the symptoms were present. We used IBM Statistical Package for Social Sciences (SPSS) software (IBM Corp., released 2019. IBM SPSS Statistics for Windows, Version 26.0. Armonk, NY: IBM Corp.) for data analysis. Qualitative variables were summarised using percentages, and quantitative variables were summarised using mean (SD) and median (IQR). Keeping in mind the binary outcome of RT-PCR and RAT, Cohens Kappa Coefficient () and agreement percentage (accuracy) were calculated. Kappa was classified as <0.00: poor, 0.00-0.20: slight agreement, 0.21-0.40: fair agreement, 0.41-0.60: moderate agreement, 0.61-0.80: substantial agreement, and 0.81-1.00: almost perfect agreement [11]. P-values <0.05 were considered significant throughout. All digital records were password protected, and only the chief investigator had access to them. The reporting was done as per the guidelines for reporting reliability and agreement studies (GRRAS) checklist [12].

We shortlisted 124 subjects, out of which 24 were excluded owing to incomplete information or other lacunae. Data on 100 subjects were finalised for analysis, which met all the inclusion and exclusion criteria. Fifty-eight (58%) were males and 42 (42%) were females, with ages ranging from two to 88 years. The mean age was 39.8 (SD 19.0) years; the median age was 39 years (IQR 25.5-55 years).

Out of 100 subjects, 13 tested positive and 87 tested negative on both RT-PCR and RAT, with eight discordant pairs. Cohens kappa showed substantial agreement, =0.646, (95% CI 0.420 to 0.871), p<0.001 (Table 1).

The Kappa varied with the intervals between taking samples for tests. Figure 1 shows this variation when the sample was collected on the same day and with a one-day difference, with accuracies of 95.1% and 88.9%, respectively. Both were statistically significant, with p-values <0.000 and <0.001 respectively.

When stratified based on the presence or absence of symptoms, 31 participants were symptomatic, having at least one of the symptoms, and 69 were asymptomatic. The corresponding kappa values were =0.59 (95% CI 0.28 to 0.91), p<0.001 and =0.64 (95% CI 0.27 to 1.0), p<0.001, showing moderate and substantial agreement among symptomatic and asymptomatic participants, respectively.

On RT-PCR, out of 13 participants who tested positive and 87 who tested negative, respectively, nine (69.2%) and 22 (25.3%) were symptomatic. Likewise, on the RAT, out of 13 participants who tested positive and 87 who tested negative, the number of symptomatic participants was eight (61.5%) and 23 (26.4%), respectively.

This study investigated the agreement between these two tests for SARS-CoV-2 detection with the help of Cohens Kappa [11]. Since the commencement of RAT testing in India, few reliable kits have been available. At that time, an independent two-site study of the sole available or stand-alone antigen detection assay in India, STANDARD Q COVID-19 Ag detection kit, was performed to assess its sensitivity, specificity, and practicality of application as a point-of-care test for early detection of SARS-CoV-2. However, the agreement between the two tests was not tested or mentioned. There are very few studies that have evaluated the agreement between these two tests. The majority of the papers available in the literature have evaluated diagnostic accuracy mainly using sensitivity and specificity [13-16]. With a Cohens kappa, =0.646, (95% CI 0.420 to 0.871), p<0.001, our study showed a substantial agreement between the two tests.

Jskelinen et al. [17] evaluated the performance of three rapid diagnostic tests (RDTs), viz., Sofia, STANDARD Q and Panbio and found overall agreements of 84.57%, 84.85%, and 86.32%, respectively, with a kappa value of 0.636, 0.633, and 0.660, respectively. This is similar to the results of our study on the STANDARD Q COVID-19 Ag detection kit. The study by Pea M et al. [18] on 854 asymptomatic individuals from the Chilean region calculated an accuracy of 97.04% with a kappa value of 0.78 (95% CI 0.70-0.86), which showed better performance than that of our study. Felipe PrezGarca et al. [19] did a retrospective comparative evaluation between two antigen rapid diagnostic tests (Ag-RDTs), viz., Panbio and SD-Biosensor, for detection of SARS-CoV-2 and found agreement in accuracy and values of 80.9% and 0.596 and 82.6% and 0.646, respectively. The results were similar to our study. They also concluded that RDTs were excellent for the diagnosis of high viral load samples and those early in the disease.

Risti M et al. [20] evaluated the clinical performance of the STANDARD Q COVID-19 Ag Test (SD Biosensor, Gyeonggi-do, South Korea) by analysing prospectively collected data on 120 symptomatic patients and concluded a strong agreement between the STANDARD Q COVID-19 Ag Test and RT-PCR with a kappa of 0.852 and a pooled accuracy of 92%, whereas our study reported a similar agreement percentage and a =0.59 (95% CI 0.28 to 0.91), p<0.001 among symptomatic patients. This difference could be explained by the fact that they included suspects who were in their first five days of illness, whereas our sample included a mix of suspects who had samples taken on various days after symptoms began.

Among the studies done in India, the strength of agreement between these two tests ranged from moderate to almost perfect. A prospective study [21] done among 756 patients from a district hospital in North India shows a substantial agreement like ours with a value of 0.6482 (95% CI: 0.5801 to 0.7163). However, Pandey et al. found moderate agreement between these two tests [22]. The reported value in their retrospective study was 0.57. Whereas, a value of 0.86 was reported by Gupta et al. in their study, which showed almost perfect agreement between RAT and RT-PCR [23].

In contrast, findings by Amer RM et al. in their cross-sectional study [24] on 83 COVID suspects showed much less agreement with a kappa of 0.3 (95% CI 0.16-0.59) and an accuracy of 75.9%, recommending against using RAT alone for COVID-19 diagnosis. With a smaller sample size in the Amer RM study, this sharp contrast between results needs to be interpreted carefully.

Owing to the pandemic, logistical hurdles, and the retrospective nature of the study, we did not have control over the quality of samples for both tests. However, we considered only those participants for whom the sample was taken from the recommended site as mentioned by the kit manufacturer. We also could not consider the order in which the tests were conducted. However, we did take into account the time difference (in days) between collecting samples for the respective tests. The time interval between symptom onset and sample collection could not be recorded, even though the number of subjects included in the analysis is more than the minimum required sample size calculated with the given precision. However, evidence from a larger sample study would have been more conclusive.

Evaluating the ease of conducting tests, the quick results, the lack of requiring a laboratory setup, the affordability, and the substantial agreement (=0.646, 95% CI 0.420 to 0.871, 92% agreement accuracy) with RT-PCR, we conclude that RAT may be a better choice for detecting SARS-CoV-2 and hence COVID-19 disease on a large scale. However, larger prospective studies would be needed to substantiate our findings.

Read more:

The Agreement Between Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) and Rapid Antigen Test (RAT) in Diagnosing COVID-19 - Cureus

Bobby Jackson narrowly survived his COVID-19 infection, but the effects on his body still linger.

SAGINAW, Mich. (WJRT) - For some, COVID-19 almost feels like a distant memory. But many are still struggling with the virus's effect on their lives.

Two years ago, 51-year-old Bobby Jackson of Saginaw survived a months-long battle with severe COVID-19. In 2022, he's still on oxygen and the effects of COVID-19 are still affecting his daily life.

"Some stuff just tastes horrible. Some stuff I can't taste, or even smell. So, it's very difficult," said Jackson.

He realized in early 2021 that he had long COVID.

"They said it usually takes like two months. You should be back to normal after the COVID. And it never, ever, ever came back," Jackson said.

On a daily basis, Jackson deals with aches, fatigue and numbness. But the most visible change is his oxygen pump, which he has to wear 24/7.

"My levels keep dropping. It's at like 88% oxygen levels, which is really low," Jackson said.

For perspective, the average person's blood oxygen level should be at 95%. Without his pump, Jackson gets dizzy and short of breath. He said that limitation has fundamentally changed his daily life.

"There was times I used to walk the block. There was times I could cut the grass or things of that nature. Now I can't," Jackson said.

When he can go outside, his mobile backpack's charge only lasts six hours. It's why he's so thankful for the little things.

"Mainly just walking. Being able to walk now, like being able to get into the kitchen, stand, and cook meals. There was a period I wasn't even able to do that," Jackson said.

But he and his wife, Tracy, say there's at least one upside: it's made their marriage stronger than ever before.

"I mean we, you know, are here for each other. We know, you know, what we have to do to get through it together," said Tracy.

Bobby said he and his doctors are still working on a path towards recovery. And while he doesn't plan on resuming his original career as a nurse assistant, he's taking college classes to get ready for managerial work.

Flint-area Dr. Bobby Mukkamala said the exact cause of Long COVID is still unknown. He said long-term symptoms can seemingly strike anyone whether they were hospitalized like Jackson or just had mild symptoms.

To avoid the risk, Mukkamala encourages people to get the fall booster shot, which he said will provide greater protection as the country enters flu season.

"And so the vaccine, while it has some efficacy- the original vaccine- for this new strain. It's not nearly as effective as this bivalent vaccine, which is specifically made to- one: cover the original. And they added to it coverage for this new variant. So it's much more effective, according to the data," said Mukkamala.

The Genesee County Health Department is already providing bivalent COVID-19 booster shots. A calendar for clinics, as well as information for immunization appointments, can be found here.

Continue reading here:

Saginaw COVID-19 survivor still dealing with long COVID two years later - WJRT

Viruses may be watching you some microbes lie in wait until their hosts unknowingly give them the signal to start multiplying and kill them  Kiowa County Press

View post:

Viruses may be watching you some microbes lie in wait until their hosts unknowingly give them the signal to start multiplying and kill them - Kiowa...