H5N1

A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission

Via The Lancet: A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. The summary:

Background 

An ongoing outbreak of pneumonia associated with a novel coronavirus was reported in Wuhan city, Hubei province, China. Affected patients were geographically linked with a local wet market as a potential source. No data on person-to-person or nosocomial transmission have been published to date. 

Methods 

In this study, we report the epidemiological, clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after returning to Shenzhen, Guangdong province, China, after a visit to Wuhan, and an additional family member who did not travel to Wuhan. Phylogenetic analysis of genetic sequences from these patients were done. 

Findings 

From Jan 10, 2020, we enrolled a family of six patients who travelled to Wuhan from Shenzhen between Dec 29, 2019 and Jan 4, 2020. Of six family members who travelled to Wuhan, five were identified as infected with the novel coronavirus. Additionally, one family member, who did not travel to Wuhan, became infected with the virus after several days of contact with four of the family members. None of the family members had contacts with Wuhan markets or animals, although two had visited a Wuhan hospital. 

Five family members (aged 36–66 years) presented with fever, upper or lower respiratory tract symptoms, or diarrhoea, or a combination of these 3–6 days after exposure. They presented to our hospital (The University of Hong Kong-Shenzhen Hospital, Shenzhen) 6–10 days after symptom onset. They and one asymptomatic child (aged 10 years) had radiological ground-glass lung opacities. Older patients (aged >60 years) had more systemic symptoms, extensive radiological ground-glass lung changes, lymphopenia, thrombocytopenia, and increased C-reactive protein and lactate dehydrogenase levels. 

The nasopharyngeal or throat swabs of these six patients were negative for known respiratory microbes by point-of-care multiplex RT-PCR, but five patients (four adults and the child) were RT-PCR positive for genes encoding the internal RNA-dependent RNA polymerase and surface Spike protein of this novel coronavirus, which were confirmed by Sanger sequencing. 

Phylogenetic analysis of these five patients' RT-PCR amplicons and two full genomes by next-generation sequencing showed that this is a novel coronavirus, which is closest to the bat severe acute respiratory syndrome (SARS)-related coronaviruses found in Chinese horseshoe bats. 

Interpretation 

Our findings are consistent with person-to-person transmission of this novel coronavirus in hospital and family settings, and the reports of infected travellers in other geographical regions.

Wuhan Municipal Health Committee: 60 new nCoV2019 cases, 2 deaths

The January 21 update from the Wuhan Municipal Health Committee, Google-translated:

2020 Nian 1 Yue 20 0 Shi - at 4:20 on January 2 days, new cases 60 cases, 2 deaths, no discharge cases.  

The city continued to increase the collection and testing of samples, and immediately collected the collected patient samples from hospitals and sent them to the Provincial Center for Disease Control for new coronavirus detection. The expert group made comprehensive investigations based on clinical manifestations, epidemiological history, and pathogenic test results, and newly confirmed 60 cases of pneumonia confirmed by new coronavirus infection.  

Of the 60 patients, 33 were male and 27 were female; the youngest was 15 years old and the oldest was 88 years old; the onset dates were before January 18, 2020; the first symptoms were mostly fever, cough or chest tightness, and dyspnea. Among the patients, 17 were critically ill and 3 were critically ill. Epidemiological investigations of new cases are underway, and close contacts are being tracked. 

The deceased Li Moumou, male, 66 years old, was admitted to the hospital for "intermittent cough, headache, fatigue and fever for 6 days" on January 16, 2020; dyspnea occurred on January 17, and multiple organs appeared at 10:35 on January 20 Functional failure, rescue ineffective death. The deceased had basic diseases such as COPD, hypertension, type 2 diabetes, and chronic renal insufficiency. 

The deceased Yin Moumou, female, 48 years old, became ill on December 10, 2019, developed dyspnea on December 27, and was transferred to Wuhan Jinyintan Hospital for treatment on December 31. She had severe respiratory distress upon admission, January 20, 2020 At 14:31, multiple organ failure occurred, and the rescue died. The deceased had basic diseases such as diabetes, cerebral infarction and gallstones during her lifetime. 

As of 24:00 on January 20, 258 cases of pneumonia of new coronavirus infection have been reported in our city, 25 cases have been cured and 6 cases have died. Currently, 227 patients are still being treated in the hospital, of which 51 cases are critically ill and 12 cases are critically ill. They are all under isolation treatment at designated medical institutions in Wuhan. A total of 988 close contacts have been tracked, 739 have been released from medical observation, and 249 are still receiving medical observation. 

We will continue to conduct timely sampling and detection of newly discovered suspected cases.

WHO: DRC Ebola update, January 16

WHO has published Ebola virus disease – Democratic Republic of the Congo. Note one error in the last paragraph of the excerpt, which refers to the start of the outbreak on May 8, 2018. That was the beginning of the 9th outbreak, in Equateur province, and it was briskly wrapped up even as the 10th outbreak began in North Kivu; it was declared on August 1, 2018.

Fourteen new confirmed cases were reported from 8 to 14 January in the ongoing Ebola virus disease (EVD) outbreak in the Democratic Republic of the Congo. The confirmed cases were reported from Mabalako (64%, n=9), Beni (29%, n=4) and Musienene (7%, n=1) Health Zones in North Kivu Province. All new confirmed cases (100%, 14/14) reported in the past seven days were registered contacts prior to symptom onset and had epidemiological links to the transmission chain which originated from Aloya Health Area in Mabalako Health Zone. 

In the past 21 days (25 December 2019 to 14 January 2020), 40 confirmed cases were reported from 14 health areas within seven active health zones in North Kivu and Ituri Provinces (Figure 1, Figure 2, Table 1): Mabalako (43%, n=17), Butembo (20%, n=8), Beni (13%, n=5), Mambasa (10%, n=4), Kalunguta (8%, n=3), Katwa (5%, n=2), and Musienene (3%, n=1). Mabalako Health Zone remains the current hotspot of the outbreak, having reported 43% of confirmed cases in the past 21 days. The majority of cases (88%, 35/40) reported from this period are linked to known chains of transmission, which is similar to the period from 4 to 24 December 2019 (89%, 47/53). In the past 21 days, 8% (3/36) of the confirmed EVD deaths were people who died in the community, outside of Ebola treatment centres. From these three community deaths, 15 additional cases occurred, which reinforces the need for continued activities to follow contacts, detect symptomatic patients as early as possible, and engage communities in response efforts.  

As of 14 January, a total of 3406 EVD cases were reported, including 3288 confirmed and 118 probable cases, of which 2236 cases died (overall case fatality ratio 66%) (Table 1). Of the total confirmed and probable cases, 56% (n=1910) were female, 28% (n=960) were children aged less than 18 years, and 169 (5% of all reported cases) were health care workers. 

In the coming week, there will be nine health zones in North Kivu and Ituri Provinces that will have contacts in or entering their high-risk period (seven to 13 days after last exposure to the virus). In Kalunguta Health Zone, North Kivu Province, where five individuals were confirmed with EVD from 24 to 28 December 2019, all 153 contacts have cleared their 21-day follow-up, with no new cases reported. In Mambasa Health Zone, Ituri Province, where four new cases were reported from 4 to 5 January 2020, more than 400 followed contacts are nearing the end of their high-risk period. 

It has been 20 months since the outbreak was first declared on 8 May 2018. The number of cases reported per week is lower than the period from March to September 2019 (Figure 1). However, there are several health areas which are difficult to reach due to insecurity, including Mandima Health Zone, where there are rumours of several community deaths in Lwemba Health Area. Continued response efforts in active health zones, including in insecure areas, and preventing reintroduction of the disease into health zones with dense populations which have previously been cleared are crucial to ending ongoing transmission.

Canada: BC judge orders vaccinations for 2 boys over their mother's objections

Via CBC News Vancouver, some good news: B.C. judge orders vaccinations for 2 boys over their mother's objections. Excerpt:

A B.C. judge has ordered the vaccination of two children over the objections of their mother, who questioned the safety of immunization.  

The case went to provincial court in Salmon Arm, in B.C.'s southern interior, because of the father's concerns about recent measles outbreaks and a warning that education officials might not allow his two sons to attend school during an outbreak unless they were immunized. 

The mother attempted to introduce a report into evidence written by a U.S. doctor who testified in the high-profile case of a Michigan mother who fought for years to keep from vaccinating her young daughter.  

But Judge Stella Frame questioned Dr. Toni Lynn Bark's qualifications to speak about immunology, virology or epidemiology as well as her claims to be an expert in "vaccine adversomics."  

"It is difficult to know whether or not this is junk science or a recognized emerging field," Frame wrote in her eight-page decision. 

"Presented as it is in her report, her theory or opinion sounds like a conspiracy theory."  

'Vaccination is preferable to non-vaccination' 

The ruling highlights the role of the courts in adjudicating splits between parents divided over vaccination.  

Frame's decision refers to an earlier B.C. Supreme Court decision in which a judge rejected attempts to link vaccines to autism. Frame said she had reached the same conclusion.  

"The current best evidence is that vaccination is preferable to non-vaccination, that it is required in order to protect those who cannot be vaccinated as well as to protect ourselves, and that any adverse reaction the person may have from the vaccine is largely outweighed by the risk of contracting the targeted disease," Frame wrote.

Wuhan pneumonia: A timeline

Via the South China Morning Post: Wuhan pneumonia: how the search for the source of the mystery illness unfolded. The report includes a timeline:

December 30 

The health commission in Wuhan issues a directive demanding hospitals trace and report pneumonia cases of unknown cause after several hospitals in the Hubei provincial capital report patients suffering from a mystery illness. 

December 31 

The commission announces there has been a cluster of viral pneumonia cases in the city, some of which had been linked to the seafood market, which also sells live animals. No cases of human-to-human transmission are recorded. 

January 1 

The seafood market closes. Eight people are punished by police for publishing and spreading “untruthful” information about the pneumonia outbreak. The WHO says it is monitoring the situation and is in close contact with national authorities in Beijing. 

January 3 

Wuhan health authority rules out diseases such as bird flu or adenovirus as the cause of the pneumonia outbreak. The number of those affected rises to 44, including 11 who are in a serious condition. The patients are being treated in isolation, and 121 people who were in close contact with them are quarantined. The Centre for Health Protection in Hong Kong starts to check body temperatures of passengers from Wuhan at Hong Kong International Airport and West Kowloon Station. Suspected cases will be referred to public hospitals for isolation and treatment. 

January 4 

Singapore’s health ministry announces that a three-year-old Chinese girl who had visited Wuhan has been taken to hospital and isolated as a precaution after being diagnosed with pneumonia. A day later, it is confirmed she is suffering from a common childhood viral illness. 

January 5 

Wuhan health authority rules out Sars and Mers as the pathogen behind the mystery illness. The number of pneumonia cases in Wuhan rises to 59 – seven of them serious – while 163 people in close contact with the patients are quarantined. It emerges that the first case was reported on December 12. The WHO issues a statement that it has received reports from China’s health authority and advised against any travel or trade restrictions on China. 

January 6 

Li Gang, director of Wuhan Centre for Disease Control and Prevention, says more cases are expected as investigations continue. 

January 7 

Hong Kong announces tougher precautions, laying the groundwork for patients to be quarantined if necessary. New measures include making any “severe respiratory disease associated with a novel infectious agent” a statutory notifiable infectious disease. 

January 8 

Eight of the Wuhan pneumonia patients are discharged from hospital. Meanwhile, in South Korea, a Chinese woman who spent five days in the city in December is being treated in isolation after being diagnosed with pneumonia.

January 9 

China’s health authority says that the outbreak was caused by a new coronavirus from the same family as Sars. The authority says it has obtained the genetic sequencing of the new virus. The WHO says an investigation needs to be carried out to find the source of infection, modes or modes of transmission, extent of infection and countermeasures required. It repeats that it does not see the need for travel or trade restrictions on China. The Centre for Health Protection in Hong Kong contacts China’s National Health Commission for information about the virus, so the city can carry out accurate tests. 

January 10 

Professor Yong-Zhen Zhang, with Shanghai Public Health Clinical Centre and School of Public Health, Fudan University, releases the initial genome sequence of the Wuhan coronavirus.  

January 11 

China reports the first fatality – a 61-year-old man who suffered an abdominal tumour, chronic liver disease and pneumonia who died in hospital two days earlier. It says 41 patients are being treated for the coronavirus. The National Health Commission says it would share the genome sequence with the WHO. 

January 12 

Teams of experts from Hong Kong, Macau and Taiwan are allowed to visit Wuhan to learn more about the pneumonia outbreak. Hong Kong reports 67 suspected cases, while there are none in Macau and Taiwan.

January 13 

Thailand’s health ministry says a 61-year-old Chinese woman from Wuhan has been quarantined since January 8. She becomes the first coronavirus case confirmed outside China. 

January 14 

It is confirmed that the woman in Thailand had not visited the seafood market linked to the Wuhan pneumonia cases. WHO says there has been “limited” human-to-human transmission of the coronavirus, but there is the potential for a wider spread. The organisation later retracts its statement and says there is no evidence of human-to-human transmission. 

January 15 

Chinese health officials say that of the 41 people who had tested positive for the new strain of pneumonia, a small number had not been to the seafood market. They say that human-to-human transmission has yet to be confirmed or ruled out. One case is identified as a woman whose husband worked as a market trader and who had the virus before she did.

At least 78 children died of dengue related illness in Yemen

Via ReliefWeb, a report from Save the Children: At least 78 children died of dengue related illness in Yemen. Excerpt:

Save the Children warns of an epidemic, as 52,000 suspected cases are recorded in the country.  

Seventy-eight children under 16 have already died in the outbreak of Dengue related illness in Yemen[i], with more than 52,000 suspected cases being recorded across the country. Save the Children warned this could signal the start of an epidemic. 

Heavy rainfall, coupled with the ongoing conflict, is disrupting clean water supplies. Because of the disruptions, people use water basins to collect rainwater and these uncovered water sources combined with the rain have contributed to the spread of mosquitoes in the affected areas, resulting in an upsurge in suspected dengue cases. 

If measures are not urgently put in place to strengthen the health care system so that cases can be detected early, the death total which reached 192 people by the end of 2019, could increase sharply. Cases have been recorded in almost all governorates in Yemen with the most affected being Hodeidah and Aden which recorded more than 60% of the deaths in the country.  

Save the Children Hodeidah Field Manager Mariam Aldogani, herself recovering from dengue fever, said: 

“Hodeidah has the second highest death rate in the country with 62 adult and children deaths in 2019. We have never seen anything like this before. More than 40 of our staff including their families have been affected by the fever. We are getting reports of deaths on a daily basis in remote areas of the governorate. Some of our health facilities are working 24 hours a day and last week one of our facilities recorded 30 cases in one day, most of which were children. 

“The economic situation in the country has not made it any better for people. Parents cannot afford to bring their children to the hospital or to buy the medication. Hospitals are full, and some patients are kept in hospitals having to lay on the floor because of a bed shortage. It’s really bad. Children as young as eight months have not been spared by the dengue fever. In some of the hospitals all you can hear are children crying in pain. We are currently supporting 48 health facilities in Hodeidah which recorded more than 6000 dengue fever suspected cases in 2019.”  

Save the Children's health centres have been receiving many cases of children suffering from dengue, and its teams on the ground are diagnosing and treating patients whilst referring the most severe cases.

Wuhan pneumonia: 6 more cases in Hong Kong take total to more than 50

Via the South China Morning Post: Wuhan pneumonia: six more cases in Hong Kong take total to more than 50 but professor says risk of spread during Lunar New Year mass migration unlikely. Excerpt:

Six more people have been admitted to hospitals in Hong Kong after developing respiratory symptoms on their return from the mainland Chinese city of Wuhan, health authorities said on Friday. 

It brought the number of suspected cases in the city to 54. 

A new coronavirus strain was revealed by mainland health authorities on Thursday to be the cause of the mystery pneumonia outbreak in the central Chinese city, where 59 people have been infected since December. 

In Hong Kong, six more people who recently returned from Wuhan showed either symptoms of fever and respiratory infection or pneumonia. The new cases – reported between Thursday noon and midday on Friday – included two three-year-old girls and a four-year-old boy. 

Four were already found to be infected with flu or other known viruses. 

So far, 31 of the 54 suspected cases in the city have already been discharged. 

Hu Ke, a respiratory medicine professor from Hubei General Hospital who had treated patients in Wuhan, told mainland Chinese media on Friday that most patients’ conditions were “mild to moderate”.

“Conditions of patients in general come under control after treatment,” Hu said, adding that most patients who were still in hospital remained stable. 

He said that more than 90 per cent of the patients had a fever at the early stage of the disease, and around 15 per cent had difficulty breathing. 

Infectious diseases expert Professor Yuen Kwok-yung, from the University of Hong Kong, predicted that the risk of the disease spreading from Wuhan – one of mainland China’s largest transport hubs – during the Lunar New Year’s mass movement of people would be small. This year’s migration began on Friday, two weeks ahead of the festival at the end of January. 

Yuen’s prediction was based on information released by the mainland that no evidence had been found of a human to human transmission. 

“Avian flu, 99 per cent of the time, is transmitted to humans from live birds at markets,” Yuen told a radio programme on Friday morning. 

He said if the transmission route of the Wuhan virus was the same as avian flu, the risk of transmission should be “low”.

WHO: Ebola virus disease – Democratic Republic of the Congo

WHO has published Ebola virus disease – Democratic Republic of the Congo. Excerpt:

Twelve new confirmed cases were reported from 1 to 7 January in the ongoing Ebola virus disease (EVD) outbreak in North Kivu and Ituri Provinces. The confirmed cases in this week were reported from nine health areas in four health zones: Butembo (42%, n=5), Mambasa (33%, n=4), Mangina (17%, n=2), and Beni (8%, n=1). The new case reported in Beni is linked to a transmission chain that originated in Aloya Health Area, Mabalako Health Zone. 

In the past 21 days (18 December 2019 to 7 January 2020), 41 confirmed cases were reported from 13 health areas within six active health zones in North Kivu and Ituri Provinces (Figure 2, Table 1): Mabalako (49%, n=20), Butembo (22%, n=9), Kalunguta (12%, n=5), Mambasa (10%, n=4), Katwa (5%, n=2), and Beni (2%, n=1). Mabalako Health Zone remains the main hotspot of the outbreak having reported 49% of confirmed cases in the past 21 days. 

Although the majority of the cases (76%, n=31) are linked to known chains of transmission, there are concerns around the reintroduction of the disease into health zones with dense populations which have previously been cleared, such as Butembo, Katwa, and Beni Health Zones. The sources of exposure for five new cases reported in Kalunguta Health Zone and four new cases reported in Mambasa Health Zone in the past 21 days are currently under investigation. 

As of 7 January, a total of 3392 EVD cases were reported, including 3274 confirmed and 118 probable cases, of which 2235 cases died (overall case fatality ratio 66%) (Table 1). Of the total confirmed and probable cases, 56% (n=1903) were female, 28% (n=956) were children aged less than 18 years, and 169 (5% of all reported cases) were healthcare workers.

Meanwhile, the MoH/WHO AFRO dashboard reports 1 new case on January  9, making the total 3,393 since the outbreak began.

US: Flu season may yet turn ugly, CDC warns

Via The New York Times: The Flu Season May Yet Turn Ugly, C.D.C. Warns - The New York Times.

The United States may be headed into a bad flu season, according to figures recently released by the Centers for Disease Control and Prevention. 

As of the last week of December, “widespread” flu activity was reported by health departments in 46 states. More ominously, a second measure — the percentage of patients with flu symptoms visiting medical clinics — shot up almost to the peak reached at the height of the 2017-18 flu season, which was the most severe in a decade.  

About 61,000 Americans died of flu that season, the C.D.C. said. (The original estimate of 79,000 was revised downward last year; the agency said the number changed as more death certificate information became available.)  

This year’s flu vaccine may not be particularly effective against the strain of the virus now widespread in the United States, experts said. But even so, it’s worth getting the shot: people who are vaccinated fare better if struck by the flu than those who are not.

It is still too early to know how severe this season will be, said Lynnette Brammer, leader of the agency’s domestic influenza surveillance team. 

Although many people are coming down with flu, the two chief indicators of severity — hospitalizations and deaths — are not yet elevated, she noted.  

Deaths from pneumonia and flu are actually lower than normal at this time. But reports of hospitalization and death normally lag other indicators by at least two weeks. 

The current season did begin unusually early. By late November, the flu had hit hard in the Deep South, from Texas to Georgia. The virus then broke out in California and the Rocky Mountain states, but was not widespread in the Northeast until recently. 

That pattern echoes what happened in Australia, where winter runs from June through August. Flu came unusually early to the Southern Hemisphere in 2019. In seasons when Australia has a bad flu season, the Northern Hemisphere sometimes does, too.

In another important way, however, the United States is not following Australia’s lead. The A(H3N2) strain of influenza was dominant there last year, while most American cases this season have been caused by a very different strain, called B Victoria. (B strains are named for the cities where they were first isolated.)  

B strain flus do not normally arrive until late in the season. But when they do, “they often impact children more than adults and older adults,” Ms. Brammer said.  

The C.D.C. tracks the deaths of children individually, rather than making estimates, as is done for adults. Those over 65 are usually the group hardest hit by flu. Thus far this season, 27 children have died of flu — in 2017-18, 187 died — but pediatric deaths don’t normally start peaking until mid-January.

WHO: Deaths from DR Congo measles outbreak top 6000

WHO AFRO has published Deaths from Democratic Republic of the Congo measles outbreak top 6000.

Kinshasa, 7 January 2020 – With the death toll from the world’s worst measles epidemic in the Democratic Republic of the Congo (DRC) surpassing 6000, the World Health Organization (WHO) is calling for more funding to stop the outbreak.  

Under the leadership of the DRC Ministry of Health, WHO, Gavi, the Vaccine Alliance, and other partner aid agencies vaccinated more than 18 million children under five across the country in 2019. However, in some areas, routine vaccination coverage remains low and 25% of the reported measles cases are in children over the age of five, who are the most vulnerable. 

“We are doing our utmost to bring this epidemic under control. Yet to be truly successful we must ensure that no child faces the unnecessary risk of death from a disease that is easily preventable by a vaccine. We urge our donor partners to urgently step up their assistance,” said Dr Matshidiso Moeti, WHO Regional Director for Africa. 

Since the start of 2019, around 310 000 suspected measles cases have been reported. The epidemic has been aggravated by low vaccination coverage among vulnerable communities, malnutrition, weak public health systems, outbreaks of other epidemic-prone diseases, difficult access by vulnerable populations to health care and insecurity that has hampered response in some areas.  

Lack of funding remains a huge impediment to successfully curbing the outbreak. So far, US$ 27.6 million have been mobilized. However, a further US$ 40 million are required for a six-month plan to extend the vaccination to children between six and 14 years and to reinforce elements of the outbreak response beyond vaccination, including improving treatment, health education, community engagement, health system strengthening, epidemiological surveillance and response coordination.  

“We recognize the Government’s engagement in the efforts to end the outbreak and we are grateful for the generosity of our donors. But we still need to do more,” said Dr Amédée Prosper Djiguimdé, Officer in charge of WHO office in the DRC. “Thousands of Congolese families need our help to lift the burden of this prolonged epidemic from their backs. We cannot achieve this without adequate finances.” 

The European Civil Protection and Humanitarian Aid Operations, Gavi, the Vaccine Alliance, Médecins du Monde, Médecins Sans Frontières, United Nations Children’s Fund, WHO and other partners have been supporting the Government to bring the long-running epidemic under control. In December 2019, WHO trained 60 health professionals from the Ministry of Health to conduct a range of services, including community engagement, health education and surveillance. These health professionals are being deployed this week as part of the response.