Why New Zealand needs to ramp up genome sequencing to trace the source of its new COVID-19 outbreak

Shutterstock/Syuzann

David Welch

Genetic surveillance — a technology that uses the genetic fingerprint of a virus to track its spread — is part of the public health response to New Zealand’s new COVID-19 community outbreak and could help pinpoint its source.

There are now 17 cases of community transmission, all in Auckland, and health officials are treating the group as a single cluster, with an expectation that case numbers will grow.

Ideally, we should be sequencing all positive test swabs, regardless of whether they are found at the border or in the community. The community cases could then be compared to all other cases to find a close match. This would suggest a likely chain of transmission, help with contact tracing and reveal the sequence of the outbreak.

But not all samples are currently sequenced. In total, New Zealand had 1225 confirmed cases of COVID-19, and about 700 of the positive samples have been sequenced.

I argue the Ministry of Health should now make genetic sequencing mandatory. Here’s why.

Tracking epidemics using genomes

Genetic surveillance of infectious diseases is a maturing technology that has played a major role in the effort to control the Ebola and Zika epidemics, and now the COVID-19 pandemic.

We can now obtain a complete viral genome quickly and cheaply to identify mutations that provide clues about transmission chains.

Cases that are part of the same transmission chain will have genomes that look very similar: they share the same mutations compared to a reference genome. Cases from different transmission chains have genomes with differing patterns of mutations.

SARS-CoV-2, the virus that causes COVID-19, does not have a particularly high mutation rate. It acquires mutations at about half the rate of seasonal influenza, but it mutates fast enough to leave a signal of where it has come from.

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Read more:
‘Genomic fingerprinting’ helps us trace coronavirus outbreaks. What is it and how does it work?

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This brings us to how this is helping in our efforts to control the current community outbreak.

There are four main theories about where the new cases could have come from:

• A failure of managed isolation or quarantine, as we saw in the Australian state of Victoria

• contact via an undetected border-related case, such as an airline or airport worker

• transmission via goods that have arrived from overseas

• or a transmission chain that has persisted undetected in the community for the 102 days since the last confirmed case.

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Read more:
Masking the outbreak: despite New Zealand’s growing COVID-19 cases, there are more ways to get back to elimination faster

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The genomes of the new cases could identify the first scenario of a quarantine leak if we found a match between viral genomes from people in quarantine and in the new cluster. This relies on comprehensive sequencing of all cases in quarantine, but currently, there are still gaps.

Similarly, in the unlikely scenario of a transmission chain that has persisted since New Zealand’s first wave, we’d expect a match with one of the cases sequenced during the first outbreak, although the genomes would have diverged somewhat over that period of time.

The scenarios of transmission through goods or an undetected border case are more difficult to decipher using genomic methods. We would be looking to match the viral genome from the new local cases to one of more than 80,000 publicly available genomes that have been sampled worldwide. This would point to a country of origin but not necessarily distinguish between the scenarios.

Early results from sequencing of the first four cases from the new Auckland cluster suggest no link to a known (sequenced) New Zealand case, and the UK as the closest match. For now, this leaves all possibilities still open.

A global map of cumulative cases of COVID-19.
Johns Hopkins University

Ongoing surveillance

With widespread testing now underway, new cases will be identified in the community over the coming weeks. It is important that they are rapidly sequenced to determine whether they belong to the same transmission chain.

Genomic analysis will tell us whether we are dealing with a single or multiple clusters. Even the best contact tracing cannot be sure of the origin of an infection, and supplementing it with genomic data is crucial.

But genomic analysis is not limited to establishing transmission chains. It can also tell us about the overall size of an outbreak, which is directly related to the genomic diversity of the virus. We can also date events to establish when transmission started within a cluster, provided there is sufficient diversity in the cluster.

The genomes we have so far in New Zealand show a huge diversity of cases, with many introductions from around the globe. Indeed, the diversity of early samples largely reflects the diversity of the virus globally, with most cases that led to further transmission coming from North America and Australia in line with travel patterns to New Zealand.

This graph shows how COVID-19 travelled to New Zealand (see research https://www.medrxiv.org/content/10.1101/2020.08.05.20168930v2)
Author provided

Most introductions did not result in further community transmission. This shows how effective New Zealand’s first lockdown was, when transmission rates declined dramatically soon after level 3 and 4 measures were put in place.

Genomes were also used in real time during the first outbreak to help attribute cases to clusters. Retrospectively, this has shown that contact tracing was effective, with relatively few cases being wrongly attributed.

But genome analysis is neither foolproof nor a panacea. Sometimes positive samples are found that cannot be sequenced because they contain only a small amount of viral material. The rather slow rate of mutation of Sars-COV-2 means many cases are essentially carrying identical copies of the virus, even across different countries.

This greatly reduces our ability to attribute an infection to a particular outbreak. There are also real computational bottlenecks – data is generated faster than we can sensibly analyse it.

Despite these limitations, genomic surveillance gives us near real-time insights into the spread of COVID-19 that were not possible in any previous pandemic. That’s why I argue it’s time for the Ministry of Health to now make immediate genetic sequencing mandatory for all positive test swabs in New Zealand, not just some.

David Welch, Senior lecturer

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Pastor Seriously Wounded by Suspected Hindu Extremists

Assailants leave church leader in Andhra Pradesh bleeding, unconscious on village road.

NEW DELHI, September 28 (CDN) — Suspected Hindu extremists struck a pastor with what appeared to be sharp-edged metal rods on Sept. 20 in Andhra Pradesh state, leaving him unconscious and profusely bleeding on a village road.

At least three unidentified men attacked Pastor Vanamali Parishudham, 35, as he returned from Sunday worship in Yellareddygudam village, five kilometers (nearly three miles) from his home village of Narketpalli, in Nalgonda district. Suspected of being members of the Hindu extremist Rashtriya Swayamsevak Sangh (RSS), the assailants left him for dead in the middle of a road in Yellareddygudam.

Pastor Parishudham told Compass that he was walking alone toward the main road to return home when he was attacked from behind.

“I can recollect three major strikes on the back of my head,” he said. “I felt excruciating pain in my head, and I fell unconscious immediately after the strikes.”

He described the weapons used as “like an iron rod” with a sharp edge. The pastor said he did not see their faces and could not identify them.

Nirmala Desai, deputy nursing superintendent at the Kamineni Institute of Medical Sciences in Narketpalli village, told Compass that Pastor Parishudham sustained “a lot of blood loss” from the head injury. She said someone from the village called an emergency number for an ambulance.

“He was brought to the hospital in time, saving him from excessive blood loss, or else it could have led to becoming fatal,” she said. “The wound was deep, and Parishudham received six stitches on his head. He is still undergoing head scans to trace for internal injuries, if any.”

While Pastor Parishudham said he believed there were only three men who attacked him, police have yet to verify if there were more, Sub-Inspector Jagannath Reddy told Compass.

Desai of the Kamineni Institute, where the pastor was hospitalized, said that the hospital informed police of the attack. A First Information Report has been filed, and Sub-Inspector Reddy told Compass that a case has been registered of causing hurt by dangerous weapons or means.

The sub-inspector added that after police receive a medical certificate from the hospital on the extent of injuries, more serious charges could be added such as attempted murder or causing “grievous” hurt by dangerous weapons or means.

Villagers who visited Pastor Parishudham in the hospital told him that the attackers were members of the Hindu extremist RSS who oppose his preaching and the new prayer house he recently opened in Narketpalli, the pastor told Compass.

Police have yet to make any arrests.

Coincidentally, Pastor Parishudham has worked as a trauma-center technician for the past seven years at the same Kamineni Institute where he was treated. A convert from Hinduism, he became a Christian six years ago and has faced fierce opposition from staunch Hindus, including his parents. His wife Prassana, 32, and their three children ages 13, 8 and 6, worship at the small fellowship he pastors in Narketpalli, with 10 other families.

With 14 incidents of anti-Christian violence recorded from January through August of this year, Andhra Pradesh was second only to Karnataka state in assaults on Christians and Christian institutions, according to advocacy organizations.

Pastor Parishudham spoke of a similar attack on another pastor three years ago in which Hindu extremists threatened to harm the leader if he did not stop preaching; the pastor left the village and never returned.

“I am scared and fear facing more attacks in the future,” Pastor Parishudham said, “but I will continue to preach and go to the prayer house.”

Report from Compass Direct News 

BANGLADESH: SUSPECTS CHARGED IN RAPE OF PASTOR’S DAUGHTER

Investigation, DNA test point toward two alleged rapists; one remains at large.

DHAKA, Bangladesh, October 1 (Compass Direct News) – Police have submitted a charge sheet to a district court accusing two persons of raping a pastor’s daughter in the village of Laksmipur, said a state prosecutor.

Sayed Tariqul Islam told Compass that police submitted the charge sheet on Sept. 7 based on an extensive investigation following a DNA test that turned out positive. Pastor Motilal Das, who has long received threats from villagers upset with his success as an evangelist, said that local residents gang-raped his 13-year-old daughter in an attempt to drive him from the area.

State prosecutor Islam said Shakil Ahmed Shebul and Dulal Miah are charged with raping Elina Das at 3 a.m. on May 2. If convicted, they will receive life terms in prison, he said.

“The DNA report is everything to prove them guilty, and I expect that they will be punished with life-term imprisonment,” said Islam.

Previously a medical college had submitted a false forensic test report indicating no evidence of sexual assault. Villagers in Laksmipur, in Fulbaria sub-district 120 kilometers (75 miles) north of Dhaka, believe relatives of the accused men paid off the Mymensingh Medical College Hospital Forensic Department to fabricate the false test results.

Pastor Das has said relatives of the alleged rapists have offered him a large sum of money to withdraw the case or settle out of court – while continuing to threaten him. He had found his daughter lying unconscious in front of his house early in the morning of May 2, he said, after five men from Mymensingh district raped her.

The charge sheet submitted by police and the positive DNA report state that the girl’s clothes were torn and marked with the semen of Shebul. A close neighbor of Pastor Das, Shebul applied for bail on Tuesday (Sept. 29), but the court refused to grant it, said Islam.

Miah remains at large. Local police inspector Tarapod Shikder told Compass that assiduous efforts were underway to arrest him.

Pastor Das told Compass that he was dismayed that the charge sheet did not require Shebul to be taken on remand by police for interrogation.

“If the arrested person was held on remand for interrogation, police would get more information regarding other rapists,” Pastor Das.

Inspector Shikder told him that police had already taken Shebul on remand for interrogation and obtained little information, Pastor Das said.

“Nonetheless,” Pastor Das said, “the charge sheet will help to heal the scars of my grief-stricken daughter if proper justice is done.”

 

Upset Neighbors

Defending the initial false DNA report, Forensic Department head Akhteruzzaman Talukder of Mymensingh Medical College Hospital had told Compass that he did not find any gang-rape injury or trace of forced sexual activity.

Pastor Das’s daughter “might have had a love affair with someone in the village,” Talukder said. “Her lover might have been guarded there by his several friends. When the family members came to know the incident, they cooked it up as gang rape.”

Pastor Das and Muslim villagers were extremely upset by the initial forensic report. He subsequently had his daughter’s clothes tested for DNA profiling at the National Forensic DNA Profiling Laboratory of Dhaka Medical College Hospital.

His Muslim neighbors, he said, consider the positive DNA test a ray of hope for proper judgment. Pastor Das acknowledged his gratitude to some of the village neighbors who gave him moral support during that time.

“I cannot express my gratitude in words to some of my Muslim neighbors in the village who gave me courage and moral support to go forward when I got the false forensic report from Mymensingh Medical College,” he said.

When Pastor Das initially went to police to file charges, he said, police were reluctant to register the case.

“Police told me that it was a false case,” he said. “They also said that it was a fabricated drama. Police spoke with my daughter in filthy language and showed prurient interest in the details of the incident in front of us rather than filing the case quickly.”

The U.S. Department of State’s 2008 International Religious Freedom Report, released in Sept. 19, notes that Bangladeshi government officials, “including the police, were often ineffective in upholding law and order and were sometimes slow to assist religious minority victims of harassment and violence.”

The day of the alleged rape, the U.S. Commission on International Religious Freedom announced annual recommendations for countries to be designated “Countries of Particular Concern,” but it did not include Bangladesh.

Rather, the commission put Bangladesh on its “Watch List” due to the nature and extent of violations of religious freedom engaged in or tolerated by the government. Other countries on the Watch List are Afghanistan, Belarus, Cuba, Egypt, Indonesia and Nigeria.

According to USCIRF, Islamist radicalism and violence, the threat of serious violence and continued discrimination against members of religious minority communities remain significant concerns in Bangladesh.

Story from Compass Direct News